1191 Citations
A series of nondeuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally constrained cyclohexane moiety was synthesized and found to potently inhibit severe acute respiratory syndrome coronavirus- CL protease in biochemical and cell-based assays Several of the inhibitors were also found to be nanomolar inhibitors of Middle East respiratory syndrome coronavirus CL protease The corresponding latent aldehyde bisulfite adducts were found to be equipotent to the precursor aldehydes High-resolution cocrystal structures confirmed the mechanism of action and illuminated the structural determinants involved in binding The spatial disposition of the compounds disclosed herein provides ... More
A series of nondeuterated and deuterated dipeptidyl aldehyde and masked aldehyde inhibitors that incorporate in their structure a conformationally constrained cyclohexane moiety was synthesized and found to potently inhibit severe acute respiratory syndrome coronavirus-2 3CL protease in biochemical and cell-based assays. Several of the inhibitors were also found to be nanomolar inhibitors of Middle East respiratory syndrome coronavirus 3CL protease. The corresponding latent aldehyde bisulfite adducts were found to be equipotent to the precursor aldehydes. High-resolution cocrystal structures confirmed the mechanism of action and illuminated the structural determinants involved in binding. The spatial disposition of the compounds disclosed herein provides an effective means of accessing new chemical space and optimizing pharmacological activity. The cellular permeability of the identified inhibitors and lack of cytotoxicity warrant their advancement as potential therapeutics for COVID-19. Less
Severe acute respiratory syndrome coronavirus SARS-CoV- infection continues to be a serious global public health threat The C-like protease CLpro is a virus protease encoded by SARS-CoV- which is essential for virus replication We have previously reported a series of small-molecule CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV- in cell culture and in animal models Here we generated a series of deuterated variants of a CLpro inhibitor GC and evaluated the antiviral effect against SARS-CoV- The deuterated GC displayed potent inhibitory activity against SARS-CoV- in the enzyme- and the cell-based assays The K -hACE mice develop ... More
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease (3CLpro) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small-molecule 3CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme- and the cell-based assays. The K18-hACE2 mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and were proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18-hACE2 mice at 24 h postinfection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2–treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro of SARS-CoV-2 and SARS-CoV with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2. Less
Rhodopsins most of which are proton pumps generating transmembrane electrochemical proton gradients span all three domains of life are abundant in the biosphere and could play a crucial role in the early evolution of life on earth Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins rhodopsins from unicellular eukaryotes have not been well characterized To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach we performed a structural and functional analysis of the light-driven proton pump LR Mac from the ... More
Rhodopsins, most of which are proton pumps generating transmembrane electrochemical proton gradients, span all three domains of life, are abundant in the biosphere, and could play a crucial role in the early evolution of life on earth. Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins, rhodopsins from unicellular eukaryotes have not been well characterized. To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach, we performed a structural and functional analysis of the light-driven proton pump LR (Mac) from the pathogenic fungus Leptosphaeria maculans. The first high-resolution structure of fungi rhodopsin and its functional properties reveal the striking similarity of its membrane part to archaeal but not to bacterial rhodopsins. We show that an unusually long N-terminal region stabilizes the protein through direct interaction with its extracellular loop (ECL2). We compare to our knowledge all available structures and sequences of outward light-driven proton pumps and show that eukaryotic and archaeal proton pumps, most likely, share a common ancestor. Less
Selective agonism of the estrogen receptor ER subtypes ER and ER has historically been difficult to achieve due to the high degree of ligand-binding domain structural similarity Multiple efforts have focused on the use of classical organic scaffolds to model -estradiol geometry in the design of ER selective agonists with several proceeding to various stages of clinical development Carborane scaffolds offer many unique advantages including the potential for novel ligand receptor interactions but remain relatively unexplored We synthesized a series of para-carborane estrogen receptor agonists revealing an ER selective structure activity relationship We report ER agonists with low nanomolar potency ... More
Selective agonism of the estrogen receptor (ER) subtypes, ERα and ERβ, has historically been difficult to achieve due to the high degree of ligand-binding domain structural similarity. Multiple efforts have focused on the use of classical organic scaffolds to model 17β-estradiol geometry in the design of ERβ selective agonists, with several proceeding to various stages of clinical development. Carborane scaffolds offer many unique advantages including the potential for novel ligand/receptor interactions but remain relatively unexplored. We synthesized a series of para-carborane estrogen receptor agonists revealing an ERβ selective structure–activity relationship. We report ERβ agonists with low nanomolar potency, greater than 200-fold selectivity for ERβ over ERα, limited off-target activity against other nuclear receptors, and only sparse CYP450 inhibition at very high micromolar concentrations. The pharmacological properties of our para-carborane ERβ selective agonists measure favorably against clinically developed ERβ agonists and support further evaluation of carborane-based selective estrogen receptor modulators. Less
Odorant-binding proteins OBPs as they occur in insects form a distinct class of proteins that apparently has no closely related representatives in other animals However ticks mites spiders and millipedes contain genes encoding proteins with sequence similarity to insect OBPs In this work we have explored the structure and function of such non-insect OBPs in the mite Varroa destructor a major pest of honey bee Varroa OBPs present six cysteines paired into three disulphide bridges but with positions in the sequence and connections different from those of their insect counterparts VdesOBP structure was determined in two closely related crystal forms ... More
Odorant-binding proteins (OBPs), as they occur in insects, form a distinct class of proteins that apparently has no closely related representatives in other animals. However, ticks, mites, spiders and millipedes contain genes encoding proteins with sequence similarity to insect OBPs. In this work, we have explored the structure and function of such non-insect OBPs in the mite Varroa destructor, a major pest of honey bee. Varroa OBPs present six cysteines paired into three disulphide bridges, but with positions in the sequence and connections different from those of their insect counterparts. VdesOBP1 structure was determined in two closely related crystal forms and appears to be a monomer. Its structure assembles five α-helices linked by three disulphide bridges, one of them exhibiting a different connection as compared to their insect counterparts. Comparison with classical OBPs reveals that the second of the six α-helices is lacking in VdesOBP1. Ligand-binding experiments revealed molecules able to bind only specific OBPs with a moderate affinity, suggesting that either optimal ligands have still to be identified, or post-translational modifications present in the native proteins may be essential for modulating binding activity, or else these OBPs might represent a failed attempt in evolution and are not used by the mites. Less
Aerogels are ultralight porous materials whose matrix structure can be formed by interlinking nm long M phage particles In theory changing the phage properties would alter the aerogel matrix but attempting this using the current production system leads to heterogeneous lengths A phagemid system that yields a narrow length distribution that can be tuned in nm increments from to nm is designed and independently the persistence length varies from to nm by mutating the coat protein A robotic workflow that automates each step from DNA construction to aerogel synthesis is used to build aerogels This is applied to compare Ni ... More
Aerogels are ultralight porous materials whose matrix structure can be formed by interlinking 880 nm long M13 phage particles. In theory, changing the phage properties would alter the aerogel matrix, but attempting this using the current production system leads to heterogeneous lengths. A phagemid system that yields a narrow length distribution that can be tuned in 0.3 nm increments from 50 to 2500 nm is designed and, independently, the persistence length varies from 14 to 68 nm by mutating the coat protein. A robotic workflow that automates each step from DNA construction to aerogel synthesis is used to build 1200 aerogels. This is applied to compare Ni–MnOx cathodes built using different matrixes, revealing a pareto-optimal relationship between performance metrics. This work demonstrates the application of genetic engineering to create “tuning knobs” to sweep through material parameter space; in this case, toward creating a physically strong and high-capacity battery. Less
SARS-CoV- is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades The development of a universal human coronavirus vaccine could prevent future pandemics We characterize antibodies isolated from four COVID- subjects and identify SARS-CoV- neutralizing antibodies One targets the N-terminal domain NTD one recognizes an epitope in S and bind the receptor-binding domain RBD Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV- by effectively blocking binding of both the SARS-CoV- and SARS-CoV- RBDs to the ACE receptor Using the K -hACE transgenic mouse model we demonstrate that the neutralization potency and antibody ... More
SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies. Less
Human cannabinoid receptor CB plays an important role in the immune system and is an attractive therapeutic target for pain and for inflammatory and neurodegenerative diseases However the structural basis of CB agonist selectivity is still elusive Here we describe a detailed protocol for the determination of the crystal structure of antagonist AM -bound CB This methodology could be applied to the structural studies of CB with diverse antagonists and agonists or to other class A G-protein-coupled receptors
Blossom-end rot BER is a devastating physiological disorder that affects tomato and other vegetables resulting in significant crop losses To date most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit however the genetic basis of this disorder remains unknown To investigate the genetic basis of BER two F and F populations along with a BC population that segregated for BER occurrence were evaluated in the greenhouse Using the QTL-seq approach quantitative trait loci QTL associated with BER Incidence were identified at the bottom of chromosome ch and ch Additionally linkage-based QTL mapping ... More
Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to the fruit; however, the genetic basis of this disorder remains unknown. To investigate the genetic basis of BER, two F2 and F3:4 populations along with a BC1 population that segregated for BER occurrence were evaluated in the greenhouse. Using the QTL-seq approach, quantitative trait loci (QTL) associated with BER Incidence were identified at the bottom of chromosome (ch) 3 and ch11. Additionally, linkage-based QTL mapping detected another QTL, BER3.1, on ch3 and BER4.1 on ch4. To fine map the QTLs identified by QTL-seq, recombinant screening was performed. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 to 1.58 Mbp with a 1.5-LOD support interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Further, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval comprising of 141 candidate genes. Taken together, our results identified and fine mapped the first loci for BER resistance in tomato that will facilitate marker-assistant breeding not only in tomato but also in many other vegetables suffering for BER. Less
Sphingosine- -phosphate S P regulates numerous important physiological functions including immune response and vascular integrity via its cognate receptors S PR to S PR however it remains unclear how S P activates S PRs upon binding Here we determined the crystal structure of the active human S PR in complex with its natural agonist S P at - resolution S P exhibits an unbent conformation in the long tunnel which penetrates through the receptor obliquely Compared with the inactive S PR structure four residues surrounding the alkyl tail of S P the quartet core exhibit orchestrating rotamer changes that accommodate ... More
Sphingosine-1-phosphate (S1P) regulates numerous important physiological functions, including immune response and vascular integrity, via its cognate receptors (S1PR1 to S1PR5); however, it remains unclear how S1P activates S1PRs upon binding. Here, we determined the crystal structure of the active human S1PR3 in complex with its natural agonist S1P at 3.2-Å resolution. S1P exhibits an unbent conformation in the long tunnel, which penetrates through the receptor obliquely. Compared with the inactive S1PR1 structure, four residues surrounding the alkyl tail of S1P (the “quartet core”) exhibit orchestrating rotamer changes that accommodate the moiety, thereby inducing an active conformation. In addition, we reveal that the quartet core determines G protein selectivity of S1PR3. These results offer insight into the structural basis of activation and biased signaling in G protein–coupled receptors and will help the design of biased ligands for optimized therapeutics. Less
EMBL Grenoble operates the High Throughput Crystallization Laboratory HTX Lab a large-scale user facility offering high throughput crystallography services to users worldwide The HTX lab has a strong focus in the development of new methods in macromolecular crystallography Through the combination of a high throughput crystallization platform the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet These include a protein-to-structure pipeline for the determination of new structures a pipeline for the rapid characterization of protein-ligand complexes in support ... More
EMBL Grenoble operates the High Throughput Crystallization Laboratory (HTX Lab), a large-scale user facility offering high throughput crystallography services to users worldwide. The HTX lab has a strong focus in the development of new methods in macromolecular crystallography. Through the combination of a high throughput crystallization platform, the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet. These include a protein-to-structure pipeline for the determination of new structures, a pipeline for the rapid characterization of protein-ligand complexes in support of medicinal chemistry, and a large-scale, automated fragment screening pipeline enabling evaluation of libraries of over 1000 fragments. Here we describe how to access and use these resources. Less
Mammalian medial and lateral hippocampal networks preferentially process spatial- and object-related information respectively However the mechanisms underlying the assembly of such parallel networks during development remain largely unknown Our study shows that in mice complementary expression of cell surface molecules teneurin- Ten and latrophilin- Lphn in the medial and lateral hippocampal networks respectively guides the precise assembly of CA -to-subiculum connections in both networks In the medial network Ten -expressing Ten CA axons are repelled by target-derived Lphn revealing that Lphn - and Ten -mediated heterophilic repulsion and Ten -mediated homophilic attraction cooperate to control precise target selection of CA ... More
Mammalian medial and lateral hippocampal networks preferentially process spatial- and object-related information, respectively. However, the mechanisms underlying the assembly of such parallel networks during development remain largely unknown. Our study shows that, in mice, complementary expression of cell surface molecules teneurin-3 (Ten3) and latrophilin-2 (Lphn2) in the medial and lateral hippocampal networks, respectively, guides the precise assembly of CA1-to-subiculum connections in both networks. In the medial network, Ten3-expressing (Ten3+) CA1 axons are repelled by target-derived Lphn2, revealing that Lphn2- and Ten3-mediated heterophilic repulsion and Ten3-mediated homophilic attraction cooperate to control precise target selection of CA1 axons. In the lateral network, Lphn2-expressing (Lphn2+) CA1 axons are confined to Lphn2+ targets via repulsion from Ten3+ targets. Our findings demonstrate that assembly of parallel hippocampal networks follows a "Ten3→Ten3, Lphn2→Lphn2" rule instructed by reciprocal repulsions. Less
Background Psoriasis is an inflammatory IL- driven skin disease in which autoantigen-induced CD T cells have been identified as pathogenic drivers Objective Our study focused on comprehensively characterizing the phenotypic variation of CD T cells in psoriatic lesions Methods We used single-cell RNA sequencing to compare CD T-cell transcriptomic heterogeneity between psoriatic and healthy skin Results We identified transcriptionally diverse CD T-cell subsets in psoriatic and healthy skin Among several inflammatory subsets enriched in psoriatic skin we observed Tc cell subsets that were metabolically divergent were developmentally related and expressed CXCL which we found to be a biomarker of psoriasis ... More
Background Psoriasis is an inflammatory, IL-17–driven skin disease in which autoantigen-induced CD8+ T cells have been identified as pathogenic drivers. Objective Our study focused on comprehensively characterizing the phenotypic variation of CD8+ T cells in psoriatic lesions. Methods We used single-cell RNA sequencing to compare CD8+ T-cell transcriptomic heterogeneity between psoriatic and healthy skin. Results We identified 11 transcriptionally diverse CD8+ T-cell subsets in psoriatic and healthy skin. Among several inflammatory subsets enriched in psoriatic skin, we observed 2 Tc17 cell subsets that were metabolically divergent, were developmentally related, and expressed CXCL13, which we found to be a biomarker of psoriasis severity and which achieved comparable or greater accuracy than IL17A in a support vector machine classifier of psoriasis and healthy transcriptomes. Despite high coinhibitory receptor expression in the Tc17 cell clusters, a comparison of these cells with melanoma-infiltrating CD8+ T cells revealed upregulated cytokine, cytolytic, and metabolic transcriptional activity in the psoriatic cells that differed from an exhaustion program. Conclusion Using high-resolution single-cell profiling in tissue, we have uncovered the diverse landscape of CD8+ T cells in psoriatic and healthy skin, including 2 nonexhausted Tc17 cell subsets associated with disease severity. Less
The Parkin co-regulated gene protein PACRG binds at the inner junction between doublet microtubules of the axoneme a structure found in flagella and cilia PACRG binds to the adaptor protein meiosis expressed gene MEIG but how they bind to microtubules is unknown Here we report the crystal structure of human PACRG in complex with MEIG PACRG adopts a helical repeat fold with a loop that interacts with MEIG Using the structure of the axonemal doublet microtubule from the protozoan Chlamydomonas reinhardtii and single-molecule fluorescence microscopy we propose that PACRG binds to microtubules while simultaneously recruiting free tubulin to catalyze formation ... More
The Parkin co-regulated gene protein (PACRG) binds at the inner junction between doublet microtubules of the axoneme, a structure found in flagella and cilia. PACRG binds to the adaptor protein meiosis expressed gene 1 (MEIG1), but how they bind to microtubules is unknown. Here, we report the crystal structure of human PACRG in complex with MEIG1. PACRG adopts a helical repeat fold with a loop that interacts with MEIG1. Using the structure of the axonemal doublet microtubule from the protozoan Chlamydomonas reinhardtii and single-molecule fluorescence microscopy, we propose that PACRG binds to microtubules while simultaneously recruiting free tubulin to catalyze formation of the inner junction. We show that the homologous PACRG-like protein also mediates dual tubulin interactions but does not bind MEIG1. Our findings establish a framework to assess the function of the PACRG family of proteins and MEIG1 in regulating axoneme assembly. Less
Plant pathogens cause disease through secreted effector proteins which act to modulate host physiology and promote infection Typically the sequences of effectors provide little functional information and further targeted experimentation is required Here we utilised a structure function approach to study SnTox an effector from the necrotrophic fungal pathogen Parastagonospora nodorum which causes cell death in wheat-lines carrying the sensitivity gene Snn We developed a workflow for the production of SnTox in a heterologous host that enabled crystal structure determination We show this approach can be successfully applied to effectors from other pathogenic fungi Complementing this an in-silico study uncovered ... More
Plant pathogens cause disease through secreted effector proteins, which act to modulate host physiology and promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilised a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination. We show this approach can be successfully applied to effectors from other pathogenic fungi. Complementing this, an in-silico study uncovered the prevalence of an expanded subclass of effectors from fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. We demonstrate that SnTox3 is a pre-pro-protein and that the protease Kex2 removes the pro-domain. Our in-silico studies suggest that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi, and we demonstrate this experimentally for effectors from Fusarium oxysporum f sp. lycopersici. We propose that K2PP effectors are highly prevalent among fungal effectors. The identification and classification of K2PP effectors has broad implications for the approaches used to study their function in fungal virulence. Less
The zinc-finger transcription factor Helios is critical for maintaining the identity anergic phenotype and suppressive activity of regulatory T Treg cells While it is an attractive target to enhance the efficacy of currently approved immunotherapies no existing approaches can directly modulate Helios activity or abundance Here we report the structure-guided development of small molecules that recruit the E ubiquitin ligase substrate receptor cereblon to Helios thereby promoting its degradation Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of Treg cells establishing a route towards Helios-targeting therapeutics More generally this study provides a framework for the development ... More
The zinc-finger transcription factor Helios is critical for maintaining the identity, anergic phenotype and suppressive activity of regulatory T (Treg) cells. While it is an attractive target to enhance the efficacy of currently approved immunotherapies, no existing approaches can directly modulate Helios activity or abundance. Here, we report the structure-guided development of small molecules that recruit the E3 ubiquitin ligase substrate receptor cereblon to Helios, thereby promoting its degradation. Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of Treg cells, establishing a route towards Helios-targeting therapeutics. More generally, this study provides a framework for the development of small-molecule degraders for previously unligandable targets by reprogramming E3 ligase substrate specificity. Less
Biological macromolecules such as proteins and nucleic acids are composed of linked monomers and play an important role in biological functions based on their three-dimensional D structures Proteins are composed of one or more polypeptide chains of different amino acid residues These polypeptide chains fold into a D structure to constitute a functional protein The D structure information of proteins can be applied to analyze protein-ligand processes and interactions Furthermore the D structure information of proteins can serve as the basis for structure-based target selection for drug discovery research As it is not possible for protein D structures to be ... More
Biological macromolecules, such as proteins and nucleic acids, are composed of linked monomers and play an important role in biological functions based on their three-dimensional (3D) structures. Proteins are composed of one or more polypeptide chains of different amino acid residues. These polypeptide chains fold into a 3D structure to constitute a functional protein. The 3D structure information of proteins can be applied to analyze protein-ligand processes and interactions. Furthermore, the 3D structure information of proteins can serve as the basis for structure-based target selection for drug discovery research. As it is not possible for protein 3D structures to be seen even under the most advanced light microscope, other methods are employed to determine their 3D structures. Since proteins can form crystals, X-ray crystallography can be used to solve the 3D structures of these proteins. In the deposited protein data bank (PDB), nearly 90% of protein structures are solved through X-ray crystallography. As a result, X-ray crystallography is the fundamental method for characterizing the atomic structure of proteins.
Notably, the primary and oldest method of X-ray crystallography is single-crystal X-ray diffraction. The major challenge of using this method is obtaining well-ordered crystals with a suitable size for crystallographic data collection. The demand for larger and well-ordered protein crystals has introduced difficulties for those proteins which cannot grow to larger dimensions.
With the development of synchrotron radiation, the brilliant beams achieved through synchrotron radiation have decreased the necessary protein crystal size for conventional X-ray diffraction crystallography. A free-electron laser (FEL) uses a much brighter beam, which decreases the dimensions of protein crystals that are required for diffraction data collection. Consequently, today micro-sized and nano-sized protein crystals are preferred. This preference for small crystals creates a strong demand to develop and establish new methods and instrumentation to identify, detect and analyze protein nano- and micro-crystals.
Current methods to detect micro-sized and nano-sized protein crystals mainly include bright-field imaging, ultraviolet fluorescence (UV) imaging, second harmonic generation (SHG) imaging and X-ray powder diffraction. However, each of these imaging methods has its own limitations. Because of this, a reliable and advanced imaging method is required.
The present work describes an in-house developed multi-modalities multiphoton instrument that is composed of three imaging methods, which are third-harmonic generation (THG), second-harmonic generation (SHG) and three-photon excited ultraviolet fluorescence (3PEUVF). To analyze the feasibility and detection sensitivity of the multimodal MPM system, different protein crystals and salt crystals were prepared with different symmetries. The combined effect of THG, SHG and 3PEUVF imaging is precise, as the system is able to identify nano- or micro-sized protein crystals and can distinguish between protein crystals, salt crystals and amorphous aggregates.
During the testing process, a detailed study of the angular-dependent SHG polarization response was conducted. The results demonstrated that the SHG polarization response of the crystal is highly sensitive to the lattice orientation of crystals. As a result, SHG polarization can extend its potential for protein crystal detection and characterization.
To better compare the differences between commercial imaging instruments and MPM system instruments, the in vitro nanocrystal samples were simultaneously tested with dynamic light scattering (DLS), depolarized dynamic light scattering (DDLS), transmission electron microscopy (TEM) and X-ray powder diffraction. For second-order nonlinear optical imaging of chiral crystals (SONICC) and MPM imaging instrument, the experimental results illustrate that the MPM imaging instrument processes a non-invasive detection method and high detection sensitivity to detect in vitro and in vivo protein nanocrystals. Notably, the nano-sized or sub-micro-sized protein crystals can be detected efficiently through the MPM system. For in vitro protein crystals, the MPM system reduces the risk of obtaining false-negative and false-positive results in crystal detection through providing a higher signal sensitivity. Moreover, the MPM imaging system offers the possibility for in vivo crystals to be detected. Furthermore, weak SHG signals from centrosymmetric crystals are also observed with the MPM system. Less
Notably, the primary and oldest method of X-ray crystallography is single-crystal X-ray diffraction. The major challenge of using this method is obtaining well-ordered crystals with a suitable size for crystallographic data collection. The demand for larger and well-ordered protein crystals has introduced difficulties for those proteins which cannot grow to larger dimensions.
With the development of synchrotron radiation, the brilliant beams achieved through synchrotron radiation have decreased the necessary protein crystal size for conventional X-ray diffraction crystallography. A free-electron laser (FEL) uses a much brighter beam, which decreases the dimensions of protein crystals that are required for diffraction data collection. Consequently, today micro-sized and nano-sized protein crystals are preferred. This preference for small crystals creates a strong demand to develop and establish new methods and instrumentation to identify, detect and analyze protein nano- and micro-crystals.
Current methods to detect micro-sized and nano-sized protein crystals mainly include bright-field imaging, ultraviolet fluorescence (UV) imaging, second harmonic generation (SHG) imaging and X-ray powder diffraction. However, each of these imaging methods has its own limitations. Because of this, a reliable and advanced imaging method is required.
The present work describes an in-house developed multi-modalities multiphoton instrument that is composed of three imaging methods, which are third-harmonic generation (THG), second-harmonic generation (SHG) and three-photon excited ultraviolet fluorescence (3PEUVF). To analyze the feasibility and detection sensitivity of the multimodal MPM system, different protein crystals and salt crystals were prepared with different symmetries. The combined effect of THG, SHG and 3PEUVF imaging is precise, as the system is able to identify nano- or micro-sized protein crystals and can distinguish between protein crystals, salt crystals and amorphous aggregates.
During the testing process, a detailed study of the angular-dependent SHG polarization response was conducted. The results demonstrated that the SHG polarization response of the crystal is highly sensitive to the lattice orientation of crystals. As a result, SHG polarization can extend its potential for protein crystal detection and characterization.
To better compare the differences between commercial imaging instruments and MPM system instruments, the in vitro nanocrystal samples were simultaneously tested with dynamic light scattering (DLS), depolarized dynamic light scattering (DDLS), transmission electron microscopy (TEM) and X-ray powder diffraction. For second-order nonlinear optical imaging of chiral crystals (SONICC) and MPM imaging instrument, the experimental results illustrate that the MPM imaging instrument processes a non-invasive detection method and high detection sensitivity to detect in vitro and in vivo protein nanocrystals. Notably, the nano-sized or sub-micro-sized protein crystals can be detected efficiently through the MPM system. For in vitro protein crystals, the MPM system reduces the risk of obtaining false-negative and false-positive results in crystal detection through providing a higher signal sensitivity. Moreover, the MPM imaging system offers the possibility for in vivo crystals to be detected. Furthermore, weak SHG signals from centrosymmetric crystals are also observed with the MPM system. Less
The leukotriene B receptor BLT regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious allergic metabolic and tumorigenic human diseases Here we present a crystal structure of human BLT hBLT in complex with a selective antagonist MK-D- developed for the treatment of type diabetes and other inflammatory conditions Comprehensive analysis of the structure and structure-activity relationship data reinforced by site-directed mutagenesis and docking studies reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species The structure helps to identify a putative membrane-buried ligand access channel ... More
The leukotriene B4 receptor 1 (BLT1) regulates the recruitment and chemotaxis of different cell types and plays a role in the pathophysiology of infectious, allergic, metabolic, and tumorigenic human diseases. Here we present a crystal structure of human BLT1 (hBLT1) in complex with a selective antagonist MK-D-046, developed for the treatment of type 2 diabetes and other inflammatory conditions. Comprehensive analysis of the structure and structure-activity relationship data, reinforced by site-directed mutagenesis and docking studies, reveals molecular determinants of ligand binding and selectivity toward different BLT receptor subtypes and across species. The structure helps to identify a putative membrane-buried ligand access channel as well as potential receptor binding modes of endogenous agonists. These structural insights of hBLT1 enrich our understanding of its ligand recognition and open up future avenues in structure-based drug design. Less
The transcription factor Rora has been shown to be important for the development of ILC and the regulation of ILC macrophages and Treg cells Here we investigate the role of Rora across CD T cells in general but with an emphasis on Th cells both in vitro as well as in the context of several in vivo type infection models We dissect the function of Rora using overexpression and a CD -conditional Rora-knockout mouse as well as a RORA-reporter mouse We establish the importance of Rora in CD T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection and ... More
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an emphasis on Th2 cells, both in vitro as well as in the context of several in vivo type 2 infection models. We dissect the function of Rora using overexpression and a CD4-conditional Rora-knockout mouse, as well as a RORA-reporter mouse. We establish the importance of Rora in CD4+ T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection, and have measured the effect on downstream genes using RNA-seq. Using a systematic stimulation screen of CD4+ T cells, coupled with RNA-seq, we identify upstream regulators of Rora, most importantly IL-33 and CCL7. Our data suggest that Rora is a negative regulator of the immune system, possibly through several downstream pathways, and is under control of the local microenvironment. Less
Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle Despite their significant biogeochemical roles the microbial communities especially in the oxygen depleted compartments are poorly known Here we present a comprehensive dataset including shotgun metagenomes from stratified lakes and ponds mainly located in the boreal and subarctic regions but also including one tropical reservoir and one temperate lake For most lakes and ponds the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer The majority of the samples were collected during ... More
Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open water period, but also a total of 29 samples were collected from under the ice. In addition to the metagenomic sequences, the dataset includes environmental variables for the samples, such as oxygen, nutrient and organic carbon concentrations. The dataset is ideal for further exploring the microbial taxonomic and functional diversity in freshwater environments and potential climate change impacts on the functioning of these ecosystems. Less
Existing protocols for full-length single-cell RNA sequencing produce libraries of high complexity thousands of distinct genes with outstanding sensitivity and specificity of transcript quantification These full-length libraries have the advantage of allowing probing of transcript isoforms are informative regarding single-nucleotide polymorphisms and allow assembly of the VDJ region of the T- and B-cell-receptor sequences Since full-length protocols are mostly plate-based at present they are also suited to profiling cell types where cell numbers are limiting such as rare cell types during development A disadvantage of these methods has been the scalability and cost of the experiments which has limited their ... More
Existing protocols for full-length single-cell RNA sequencing produce libraries of high complexity (thousands of distinct genes) with outstanding sensitivity and specificity of transcript quantification. These full-length libraries have the advantage of allowing probing of transcript isoforms, are informative regarding single-nucleotide polymorphisms and allow assembly of the VDJ region of the T- and B-cell-receptor sequences. Since full-length protocols are mostly plate-based at present, they are also suited to profiling cell types where cell numbers are limiting, such as rare cell types during development. A disadvantage of these methods has been the scalability and cost of the experiments, which has limited their popularity as compared with droplet-based and nanowell approaches. Here, we describe an automated protocol for full-length single-cell RNA sequencing, including both an in-house automated Smart-seq2 protocol and a commercial kit–based workflow. The protocols take 3–5 d to complete, depending on the number of plates processed in a batch. We discuss these two protocols in terms of ease of use, equipment requirements, running time, cost per sample and sequencing quality. By benchmarking the lysis buffers, reverse transcription enzymes and their combinations, we have optimized the in-house automated protocol to dramatically reduce its cost. An automated setup can be adopted easily by a competent researcher with basic laboratory skills and no prior automation experience. These pipelines have been employed successfully for several research projects allied with the Human Cell Atlas initiative (www.humancellatlas.org). Less
The adhesion G protein coupled receptor CD and its ligand complement decay-accelerating factor CD are important binding partners in the human immune system Dysfunction in this binding has been linked to immune disorders such as multiple sclerosis and rheumatoid arthritis as well as various cancers Previous literatures have indicated that the CD includes to epidermal growth factor EGF domains at its N terminus and these EGF domains can bind to the N-terminal short consensus repeat SCR domains of CD However the details of this interaction remain elusive especially why the CD binds with the highest affinity to the shortest isoform ... More
The adhesion G protein–coupled receptor CD97 and its ligand complement decay-accelerating factor CD55 are important binding partners in the human immune system. Dysfunction in this binding has been linked to immune disorders such as multiple sclerosis and rheumatoid arthritis, as well as various cancers. Previous literatures have indicated that the CD97 includes 3 to 5 epidermal growth factor (EGF) domains at its N terminus and these EGF domains can bind to the N-terminal short consensus repeat (SCR) domains of CD55. However, the details of this interaction remain elusive, especially why the CD55 binds with the highest affinity to the shortest isoform of CD97 (EGF1,2,5). Herein, we designed a chimeric expression construct with the EGF1,2,5 domains of CD97 and the SCR1–4 domains of CD55 connected by a flexible linker and determined the complex structure by crystallography. Our data reveal that the two proteins adopt an overall antiparallel binding mode involving the SCR1–3 domains of CD55 and all three EGF domains of CD97. Mutagenesis data confirmed the importance of EGF5 in the interaction and explained the binding specificity between CD55 and CD97. The architecture of CD55–CD97 binding mode together with kinetics suggests a force-resisting shearing stretch geometry when forces applied to the C termini of both proteins in the circulating environment. The potential of the CD55–CD97 complex to withstand tensile force may provide a basis for the mechanosensing mechanism for activation of adhesion G protein–coupled receptors. Less
Artemisinin-based combination therapies ACTs the World Health Organization-recommended first-line therapy for uncomplicated falciparum malaria has led to significant decreases in malaria-associated morbidity and mortality in the past two decades Decreased therapeutic efficacy of artemisinins the cornerstone of ACTs is threatening the gains made against this disease As such novel therapeutics with uncompromised mechanisms of action are needed to combat parasite-mediated antimalarial resistance We have previously reported the antimalarial activity of Plasmodium falciparum-specific proteasome inhibitors in conjunction with a variety of antimalarials in clinical use or in preclinical investigations and of proteasome mutants generated in response to these inhibitors Here we ... More
Artemisinin-based combination therapies (ACTs), the World Health Organization-recommended first-line therapy for uncomplicated falciparum malaria, has led to significant decreases in malaria-associated morbidity and mortality in the past two decades. Decreased therapeutic efficacy of artemisinins, the cornerstone of ACTs, is threatening the gains made against this disease. As such, novel therapeutics with uncompromised mechanisms of action are needed to combat parasite-mediated antimalarial resistance. We have previously reported the antimalarial activity of Plasmodium falciparum-specific proteasome inhibitors in conjunction with a variety of antimalarials in clinical use or in preclinical investigations and of proteasome mutants generated in response to these inhibitors. Here, we discover that despite harboring K13C580Y, which has conventionally mediated artemisinin resistance in vitro as measured by increased survival in ring-stage survival assays (RSA), the Cam3.II strain parasites of Cambodian origin that have acquired an additional mutation in the proteasome display increased susceptibility to DHA and OZ439. This discovery implicates the proteasome in peroxide susceptibilities and has favorable implications on the use of peroxide and proteasome inhibitor combination therapy for the treatment of artemisinin-resistant malaria Less
The design of peptides that assemble in membranes to form functional ion channels is challenging Specifically hydrophobic interactions must be designed between the peptides and at the peptide lipid interfaces simultaneously Here we take a multi-step approach towards this problem First we use rational de novo design to generate water-soluble -helical barrels with polar interiors and confirm their structures using high-resolution X-ray crystallography These -helical barrels have water-filled lumens like those of transmembrane channels Next we modify the sequences to facilitate their insertion into lipid bilayers Single-channel electrical recordings and fluorescent imaging of the peptides in membranes show monodisperse cation-selective ... More
The design of peptides that assemble in membranes to form functional ion channels is challenging. Specifically, hydrophobic interactions must be designed between the peptides and at the peptide–lipid interfaces simultaneously. Here, we take a multi-step approach towards this problem. First, we use rational de novo design to generate water-soluble α-helical barrels with polar interiors, and confirm their structures using high-resolution X-ray crystallography. These α-helical barrels have water-filled lumens like those of transmembrane channels. Next, we modify the sequences to facilitate their insertion into lipid bilayers. Single-channel electrical recordings and fluorescent imaging of the peptides in membranes show monodisperse, cation-selective channels of unitary conductance. Surprisingly, however, an X-ray structure solved from the lipidic cubic phase for one peptide reveals an alternative state with tightly packed helices and a constricted channel. To reconcile these observations, we perform computational analyses to compare the properties of possible different states of the peptide. Less
The SpinVessel system provides a methodology using pulsed radial flow to gently mix and uniformly suspend particulates cells magnetic beads silica beads and microcarrier beads for automated assays SpinVessels are well suited for aliquoting on robotic liquid handlers and with robotic reagent dispensers as well as manually The SpinVessel system combines two critical features special internal side fins and projections in the bottom of the vessels and an instrument that quickly spins the vessels and repeatedly reverses the spin direction This rapid reversing motion sends multiple pulses of fluid up the side walls of the SpinVessel creating a circular radial ... More
The SpinVessel system provides a methodology using pulsed radial flow to gently mix and uniformly suspend particulates (cells, magnetic beads, silica beads, and microcarrier beads) for automated assays. SpinVessels are well suited for aliquoting on robotic liquid handlers and with robotic reagent dispensers, as well as manually. The SpinVessel system combines two critical features: (1) special internal side fins and projections in the bottom of the vessels and (2) an instrument that quickly spins the vessels and repeatedly reverses the spin direction. This rapid reversing motion sends multiple pulses of fluid up the side walls of the SpinVessel, creating a circular radial flow pattern. We tested five different particulates and six different SpinVessels with volume capacities varying from 50 mL to 1200 mL. SpinVessels are compatible with either single-, 8-, 12-, 96-, or 384-channel pipettors or with siphon tubing on robotic reagent dispensers. Experiments have demonstrated high viability of cells and undamaged morphology of microcarrier beads even after hours of constant agitation. The uniformity of aliquots collected at various vertical depths and horizontally across the SpinVessels demonstrated that cells, magnetic beads, and silica beads were uniformly suspended throughout the height and breadth of the SpinVessels, and uniformity of samples was consistent from the beginning to the end of the aliquoting procedure. Only 5 min of mixing is required to resuspend settled particulates. This novel mixing methodology has many applications in laboratory automation where particulate aliquot uniformity and/or particulate integrity are important to automating assays. Less
An effective HIV- vaccine will likely need to elicit broadly neutralizing antibodies bNAbs Broad and potent VRC -class bNAbs have been isolated from multiple infected individuals suggesting that they could be reproducibly elicited by vaccination Several HIV- envelope-derived germline-targeting immunogens have been designed to engage naive VRC -class precursor B cells However they also present off-target epitopes that could hinder development of VRC -class bNAbs We characterize a panel of anti-idiotypic monoclonal antibodies ai-mAbs raised against inferred-germline iGL VRC -class antibodies By leveraging binding structural and B cell sorting data we engineered a bispecific molecule derived from two ai-mAbs one ... More
An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two ai-mAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo. Less
Branching pattern formation is common in many microbes Extensive studies have focused on addressing how such patterns emerge from local cell cell and cell environment interactions However little is known about whether and to what extent these patterns play a physiological role Here we consider the colonization of bacteria as an optimization problem to find the colony patterns that maximize colony growth efficiency under different environmental conditions We demonstrate that Pseudomonas aeruginosa colonies develop branching patterns with characteristics comparable to the prediction of modeling for example colonies form thin branches in a nutrient-poor environment Hence the formation of branching patterns ... More
Branching pattern formation is common in many microbes. Extensive studies have focused on addressing how such patterns emerge from local cell–cell and cell–environment interactions. However, little is known about whether and to what extent these patterns play a physiological role. Here, we consider the colonization of bacteria as an optimization problem to find the colony patterns that maximize colony growth efficiency under different environmental conditions. We demonstrate that Pseudomonas aeruginosa colonies develop branching patterns with characteristics comparable to the prediction of modeling; for example, colonies form thin branches in a nutrient-poor environment. Hence, the formation of branching patterns represents an optimal strategy for the growth of Pseudomonas aeruginosa colonies. The quantitative relationship between colony patterns and growth conditions enables us to develop a coarse-grained model to predict diverse colony patterns under more complex conditions, which we validated experimentally. Our results offer new insights into branching pattern formation as a problem-solving social behavior in microbes and enable fast and accurate predictions of complex spatial patterns in branching colonies. Less
Human parainfluenza virus type III HPIV is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations including the immunocompromised There are currently no effective vaccines or therapeutics available resulting in tens of thousands of hospitalizations per year In an effort to discover a protective antibody against HPIV we screened the B cell repertoires from peripheral blood tonsils and spleen from healthy children and adults These analyses yielded five monoclonal antibodies that potently neutralized HPIV in vitro These HPIV -neutralizing antibodies targeted two non-overlapping epitopes of the HPIV F protein with most targeting the apex Prophylactic ... More
Human parainfluenza virus type III (HPIV3) is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations, including the immunocompromised. There are currently no effective vaccines or therapeutics available, resulting in tens of thousands of hospitalizations per year. In an effort to discover a protective antibody against HPIV3, we screened the B cell repertoires from peripheral blood, tonsils, and spleen from healthy children and adults. These analyses yielded five monoclonal antibodies that potently neutralized HPIV3 in vitro. These HPIV3-neutralizing antibodies targeted two non-overlapping epitopes of the HPIV3 F protein, with most targeting the apex. Prophylactic administration of one of these antibodies, PI3-E12, resulted in potent protection against HPIV3 infection in cotton rats. Additionally, PI3-E12 could also be used therapeutically to suppress HPIV3 in immunocompromised animals. These results demonstrate the potential clinical utility of PI3-E12 for the prevention or treatment of HPIV3 in both immunocompetent and immunocompromised individuals. Less
Antibodies are crucial to immune protection against SARS-CoV- with some in emergency use as therapeutics Here we identify human monoclonal antibodies mAbs recognizing the virus spike and focus mainly on that bind the receptor binding domain RBD We devise a competition data-driven method to map RBD binding sites We find that although antibody binding sites are widely dispersed neutralizing antibody binding is focused with nearly all highly inhibitory mAbs IC mg mL blocking receptor interaction except for one that binds a unique epitope in the N-terminal domain Many of these neutralizing mAbs use public Vgenes and are close to germline ... More
Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC50 < 0.1 mg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public Vgenes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models. Less
Rationale Clinical interest in combining targeted radionuclide therapies TRT with immunotherapies is growing External beam radiation therapy EBRT activates a type interferon IFN response mediated via stimulator of interferon genes STING and this is critical to its therapeutic interaction with immune checkpoint blockade However little is known about the time course of IFN activation after EBRT or whether this may be induced by decay of a TRT source Methods We examined the IFN response and expression of immune susceptibility markers in B and B melanomas and MOC head and neck cancer murine models using qPCR and western blot For TRT ... More
Rationale: Clinical interest in combining targeted radionuclide therapies (TRT) with immunotherapies is growing. External beam radiation therapy (EBRT) activates a type 1 interferon (IFN1) response mediated via stimulator of interferon genes (STING), and this is critical to its therapeutic interaction with immune checkpoint blockade. However, little is known about the time course of IFN1 activation after EBRT or whether this may be induced by decay of a TRT source. Methods: We examined the IFN1 response and expression of immune susceptibility markers in B78 and B16 melanomas and MOC2 head and neck cancer murine models using qPCR and western blot. For TRT, we used 90Y chelated to NM600, an alkylphosphocholine analog that exhibits selective uptake and retention in tumor cells including B78 and MOC2. Results: We observed significant IFN1 activation in all cell lines, with peak activation in B78, B16, and MOC2 cell lines occurring 7, 7, and 1 days, respectively, following RT for all doses. This effect was STING-dependent. Select IFN response genes remained upregulated at 14 days following RT. IFN1 activation following STING agonist treatment in vitro was identical to RT suggesting time course differences between cell lines were mediated by STING pathway kinetics and not DNA damage susceptibility. In vivo delivery of EBRT and TRT to B78 and MOC2 tumors resulted in a comparable time course and magnitude of IFN1 activation. In the MOC2 model, the combination of 90Y-NM600 and dual checkpoint blockade therapy reduced tumor growth and prolonged survival compared to single agent therapy and cumulative dose equivalent combination EBRT and dual checkpoint blockade therapy. Conclusions: We report the time course of the STING-dependent IFN1 response following radiation in multiple murine tumor models. We show the potential of TRT to stimulate IFN1 activation that is comparable to that observed with EBRT and this may be critical to the therapeutic integration of TRT with immunotherapies. Less
Stem cell dysfunction drives many age-related disorders Identifying mechanisms that initially compromise stem cell behavior represent early targets to promote tissue function later in life Here we pinpoint multiple factors that disrupt neural stem cell NSC behavior in the adult hippocampus Clonal tracing showed that NSCs exhibit asynchronous depletion by identifying short-term NSCs ST-NSCs and long-term NSCs LT-NSCs ST-NSCs divide rapidly to generate neurons and deplete in the young brain Meanwhile multipotent LT-NSCs are maintained for months but are pushed out of homeostasis by lengthening quiescence Single-cell transcriptome analysis of deep NSC quiescence revealed several hallmarks of molecular aging in ... More
Stem cell dysfunction drives many age-related disorders. Identifying mechanisms that initially compromise stem cell behavior represent early targets to promote tissue function later in life. Here, we pinpoint multiple factors that disrupt neural stem cell (NSC) behavior in the adult hippocampus. Clonal tracing showed that NSCs exhibit asynchronous depletion by identifying short-term NSCs (ST-NSCs) and long-term NSCs (LT-NSCs). ST-NSCs divide rapidly to generate neurons and deplete in the young brain. Meanwhile, multipotent LT-NSCs are maintained for months but are pushed out of homeostasis by lengthening quiescence. Single-cell transcriptome analysis of deep NSC quiescence revealed several hallmarks of molecular aging in the mature brain and identified tyrosine-protein kinase Abl1 as an NSC aging factor. Treatment with the Abl inhibitor imatinib increased NSC activation without impairing NSC maintenance in the middle-aged brain. Our study indicates that hippocampal NSCs are particularly vulnerable and adaptable to cellular aging. Less
Brain metastases develop in over of advanced melanoma patients and negatively impact quality of life and prognosis In a murine melanoma model we previously showed that an in situ vaccination ISV regimen combining radiation treatment and intratumoral IT injection of immunocytokine IC anti-GD antibody fused to IL along with the immune checkpoint inhibitor anti-CTLA- robustly eliminates peripheral flank tumors but only has modest effects on co-occurring intracranial tumors In this study we investigated the ability of low-dose radiation to the brain to potentiate anti-tumor immunity against a brain tumor when combined with ISV anti-CTLA- B GD immunologically cold melanoma tumor ... More
Brain metastases develop in over 60% of advanced melanoma patients and negatively impact quality of life and prognosis. In a murine melanoma model, we previously showed that an in situ vaccination (ISV) regimen, combining radiation treatment and intratumoral (IT) injection of immunocytokine (IC: anti-GD2 antibody fused to IL2), along with the immune checkpoint inhibitor anti-CTLA-4, robustly eliminates peripheral flank tumors but only has modest effects on co-occurring intracranial tumors. In this study, we investigated the ability of low-dose radiation to the brain to potentiate anti-tumor immunity against a brain tumor when combined with ISV + anti-CTLA-4. B78 (GD2+, immunologically “cold”) melanoma tumor cells were implanted into the flank and the right striatum of the brain in C57BL/6 mice. Flank tumors (50–150 mm3) were treated following a previously optimized ISV regimen [radiation (12 Gy × 1, treatment day 1), IT-IC (50 µg daily, treatment days 6–10), and anti-CTLA-4 (100 µg, treatment days 3, 6, 9)]. Mice that additionally received whole-brain radiation treatment (WBRT, 4 Gy × 1) on day 15 demonstrated significantly increased survival compared to animals that received ISV + anti-CTLA-4 alone, WBRT alone or no treatment (control) (P < 0.001, log-rank test). Timing of WBRT was critical, as WBRT administration on day 1 did not significantly enhance survival compared to ISV + anti-CTLA-4, suggesting that the effect of WBRT on survival might be mediated through immune modulation and not just direct tumor cell cytotoxicity. Modest increases in T cells (CD8+ and CD4+) and monocytes/macrophages (F4/80+) but no changes in FOXP3+ regulatory T cells (Tregs), were observed in brain melanoma tumors with addition of WBRT (on day 15) to ISV + anti-CTLA-4. Cytokine multiplex immunoassay revealed distinct changes in both intracranial melanoma and contralateral normal brain with addition of WBRT (day 15) to ISV + anti-CTLA-4, with notable significant changes in pro-inflammatory (e.g., IFNγ, TNFα and LIX/CXCL5) and suppressive (e.g., IL10, IL13) cytokines as well as chemokines (e.g., IP-10/CXCL10 and MIG/CXCL9). We tested the ability of the alkylphosphocholine analog, NM600, to deliver immunomodulatory radiation to melanoma brain tumors as a targeted radionuclide therapy (TRT). Yttrium-86 (86Y) chelated to NM600 was delivered intravenously by tail vein to mice harboring flank and brain melanoma tumors, and PET imaging demonstrated specific accumulation up to 72 h at each tumor site (∼12:1 brain tumor/brain and ∼8:1 flank tumor/muscle). When NM600 was chelated to therapeutic β-particle-emitting 90Y and administered on treatment day 13, T-cell infiltration and cytokine profiles were altered in melanoma brain tumor, like that observed for WBRT. Overall, our results demonstrate that addition of low-dose radiation, timed appropriately with ISV administration to tumors outside the brain, significantly increases survival in animals co-harboring melanoma brain tumors. This observation has potentially important translational implications as a treatment strategy for increasing the response of tumors in the brain to systemically administered immunotherapies. Less
To enhance the bioavailability of poorly soluble therapeutics enabling formulations that generate supersaturation are currently of great interest There is limited knowledge of how the gastrointestinal environment can influence the complex phase behavior of these systems in particular crystallization Simulated media are generally used to mimic physiologically relevant fluids although their predictability remains unknown for crystallizing systems since they are simplified models of the gastrointestinal fluids The purpose of this study was to evaluate and compare how different simulated media as well as aspirated intestinal fluid impact the phase behavior of supersaturated solutions of two poorly soluble compounds atazanavir and ... More
To enhance the bioavailability of poorly soluble therapeutics, enabling formulations that generate supersaturation are currently of great interest. There is limited knowledge of how the gastrointestinal environment can influence the complex phase behavior of these systems, in particular, crystallization. Simulated media are generally used to mimic physiologically relevant fluids, although their predictability remains unknown for crystallizing systems since they are simplified models of the gastrointestinal fluids. The purpose of this study was to evaluate and compare how different simulated media, as well as aspirated intestinal fluid, impact the phase behavior of supersaturated solutions of two poorly soluble compounds, atazanavir and posaconazole, in fasted-state conditions. The onset of nucleation and progression of crystallization were found to be highly medium dependent. In the aspirated fluid, the crystallization kinetics for both compounds was significantly reduced compared to commercial simulated media. The use of simple buffers or current simulated fluids as surrogates for intestinal fluids appears to require further verification when attempting to predict crystallization kinetics of supersaturated solutions, based on the observed lack of correlation between commercial media and human fluids. The findings highlight the importance of carefully considering the composition of in vitro testing media for assessing crystallization kinetics, particularly in the context of supersaturating formulations. Less
A bispecific antibody BsAb targeting the epidermal growth factor receptor EGFR and mesenchymal epithelial transition factor MET pathways represents a novel approach to overcome resistance to targeted therapies in patients with non small cell lung cancer In this study we sequentially screened a panel of BsAbs in a combinatorial approach to select the optimal bispecific molecule The BsAbs were derived from different EGFR and MET parental monoclonal antibodies Initially molecules were screened for EGFR and MET binding on tumor cell lines and lack of agonistic activity toward MET Hits were identified and further screened based on their potential to induce ... More
A bispecific antibody (BsAb) targeting the epidermal growth factor receptor (EGFR) and mesenchymal–epithelial transition factor (MET) pathways represents a novel approach to overcome resistance to targeted therapies in patients with non–small cell lung cancer. In this study, we sequentially screened a panel of BsAbs in a combinatorial approach to select the optimal bispecific molecule. The BsAbs were derived from different EGFR and MET parental monoclonal antibodies. Initially, molecules were screened for EGFR and MET binding on tumor cell lines and lack of agonistic activity toward MET. Hits were identified and further screened based on their potential to induce untoward cell proliferation and cross-phosphorylation of EGFR by MET via receptor colocalization in the absence of ligand. After the final step, we selected the EGFR and MET arms for the lead BsAb and added low fucose Fc engineering to generate amivantamab (JNJ-61186372). The crystal structure of the anti-MET Fab of amivantamab bound to MET was solved, and the interaction between the two molecules in atomic details was elucidated. Amivantamab antagonized the hepatocyte growth factor (HGF)-induced signaling by binding to MET Sema domain and thereby blocking HGF β-chain—Sema engagement. The amivantamab EGFR epitope was mapped to EGFR domain III and residues K443, K465, I467, and S468. Furthermore, amivantamab showed superior antitumor activity over small molecule EGFR and MET inhibitors in the HCC827-HGF in vivo model. Based on its unique mode of action, amivantamab may provide benefit to patients with malignancies associated with aberrant EGFR and MET signaling. Less
Alginate is the structural polysaccharide of the cell wall of brown algae which is an important carbon source for marine life The depolymerization of alginate is dependent on alginate lyases Recent studies showed that the alginate utilization ability had been obtained by human gut microbes In contrast to the great number of studies on alginate lyases from marine soil organisms studies on alginate lyases from gut microbes are still limited Here the structure of a polysaccharide lyase family PL alginate lyase from human gut microbe Bacteroides clarus was solved by X-ray crystallography which represents the cluster of two-domain PL alginate ... More
Alginate is the structural polysaccharide of the cell wall of brown algae, which is an important carbon source for marine life. The depolymerization of alginate is dependent on alginate lyases. Recent studies showed that the alginate utilization ability had been obtained by human gut microbes. In contrast to the great number of studies on alginate lyases from marine/soil organisms, studies on alginate lyases from gut microbes are still limited. Here, the structure of a polysaccharide lyase family 6 (PL6) alginate lyase from human gut microbe Bacteroides clarus was solved by X-ray crystallography, which represents the cluster of two-domain PL6 alginate lyases from Bacteroidetes. Similar with the two-domain alginate lyase AlyGC originated from marine bacterium, both the N terminal domain (NTD) and C terminal domain (CTD) of BcAlyPL6 show right-handed parallel β-helix fold. However, unlike AlyGC, which forms a homodimer, BcAlyPL6 functions as a monomer. Biochemical analysis indicates that the substrate binding affinity is mainly contributed by the NTD while the CTD of BcAlyPL6 is involved in the formation of −1 subsite, which is essential for substrate turnover rate. Furthermore, CTD is involved in shaping a closed catalytic pocket, and deletion of it leads to increased activity towards highly polymerized substrate. Structure comparison of PL6 family alginate lyases implies that the linkers of two-domain alginate lyases might have evolutionary relationship with the N/C terminal extension of single-domain lyases. Less
Catalysis of human phosphoglycerate mutase is dependent on a -bisphosphoglycerate cofactor dPGM whereas the nonhomologous isozyme in many parasitic species is cofactor independent iPGM This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms We previously discovered ipglycermide a potent inhibitor of iPGM from a large combinatorial cyclic peptide library To fully delineate the ipglycermide pharmacophore herein we construct a detailed structure activity relationship using substituted ipglycermide analogs Binding affinities of these analogs to immobilized Caenorhabditis elegans iPGM measured as fold enrichment relative to the index residue by deep sequencing of an mRNA ... More
Catalysis of human phosphoglycerate mutase is dependent on a 2,3-bisphosphoglycerate cofactor (dPGM), whereas the nonhomologous isozyme in many parasitic species is cofactor independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure–activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized Caenorhabditis elegans iPGM, measured as fold enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using cocrystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from Brugia malayi, Onchocerca volvulus, Dirofilaria immitis, and Escherichia coli, is achieved by a codependence between (1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ in the iPGM phosphatase domain and (2) shape complementarity surrounding the macrocyclic core at the phosphotransferase–phosphatase domain interface. Our results show that the high-affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex. Less
Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute HWI to efficiently inspect their crystallization experiments Polo aims to increase efficiency reducing time spent manually reviewing crystallization images and to improve the potential of identifying positive crystallization conditions Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes MARCO convolutional neural network for automated image classification as well as powerful tools to view and score crystallization images to ... More
Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo's basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0. Less
Light-oxygen-voltage LOV domains are widespread photosensory modules that can be used in fluorescence microscopy optogenetics and controlled production of reactive oxygen species All of the currently known LOV domains have absorption maxima in the range of to nm and it is not clear whether they can be shifted significantly using mutations Here we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP Gln to asparagine aspartate glutamate histidine lysine and arginine Absorption spectra of all of the mutants are blue-shifted with the maximal shift of nm ... More
Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins. Less
DNA enzymes also known as deoxyribozymes are synthetic single-stranded DNA molecules able to catalyze chemical reactions There are two main reasons for studying deoxyribozymes their practical value in various applications and the understanding of basic properties - such as folding and catalysis - of a biopolymer that is of central importance for life Compared to ribozymes the DNA enzymes have a potential value as tools for industrial or therapeutic applications owing to more cost-effective synthesis and higher stability The first crystal structure of a deoxyribozyme demonstrated that DNA possesses the intrinsic ability to adopt complex tertiary folds that support catalysis ... More
DNA enzymes, also known as deoxyribozymes, are synthetic single-stranded DNA molecules able
to catalyze chemical reactions. There are two main reasons for studying deoxyribozymes: their
practical value in various applications, and the understanding of basic properties - such as folding
and catalysis - of a biopolymer that is of central importance for life. Compared to ribozymes, the
DNA enzymes have a potential value as tools for industrial or therapeutic applications, owing to
more cost-effective synthesis and higher stability. The first crystal structure of a deoxyribozyme
demonstrated that DNA possesses the intrinsic ability to adopt complex tertiary folds that support
catalysis and unveiled the active site of a DNA enzyme in the post-catalytic state (Ponce-Salvatierra,
Wawrzyniak-Turek et al. 2016). The second reported crystal structure of the RNA-cleaving
deoxyribozyme complements observations about the folds and catalysis of DNA enzymes although
the structure was derived with DNA as a substrate mimic of RNA (Liu, Yu et al. 2017). These
crystal structures represent a breakthrough in the field, but they are still insufficient to derive a clear
mechanistic picture of the specific features of different RNA ligating and RNA cleaving
deoxyribozymes. Therefore, ongoing efforts are devoted to structurally investigating additional
deoxyribozymes. The new DNA enzymes were evolved to discriminate modified and unmodified
RNA substrates and provide attractive tools for studying the natural epitranscriptomic RNA
modification N6-methyladenosine (Sednev, Mykhailiuk et al. 2018). In the present study, the goal
is to elucidate the structural basis for recognition of the methylated nucleobase by solving the
crystal structure of the m6A sensitive RNA-cleaving deoxyribozyme in complex with an
uncleavable analog of the RNA substrate, containing either methylated and unmethylated
adenosine. Surprisingly, the RNA substrate dissociated from the deoxyribozyme during the
crystallization process. Two structures for unmethylated and one of the methylated RNA substrate
analog were solved. The next goal is to elucidate the crystal structure of the RNA-ligating
deoxyribozyme in the pre-catalytic state of reaction. The previously reported crystal structure of
the 9DB1 in the post-catalytic state of reaction could not explain the role of magnesium cations as
cofactors for accelerating RNA ligation and properly describe the ligation mechanism. The
structural investigation of the 9DB1 in the pre-catalytic state resulted in the ligation of the two
RNA substrates during the crystallization process. In the future, other strategies are necessary to
solve the questions on substrate recognition and catalytic mechanism of the RNA-cleaving and
RNA-ligating deoxyribozymes investigated in this study.
The second project deals with synthetic RNA aptamers that were identified by in vitro selection to
mimic fluorescent proteins for RNA imaging and the development of biosensors. Several examples
2
of fluorogen-activating RNA aptamers are known, and for some, the crystal structures have
recently been solved e.g. of the Spinach, Mango, and Corn aptamers, that bind synthetic analogs
of the GFP chromophore (Neubacher and Hennig 2019). The Chili is a new fluorogenic-RNA
aptamer that mimics large Stokes shift (LSS) fluorescent proteins (FPs) by inducing highly Stokesshifted
emission from several new green and red HBI (4-hydroxybenzylidene imidazolinone)
derivatives that are non‐fluorescent when free in solution (Steinmetzger, Palanisamy et al. 2019).
The new fluorophores are the first variants of fluorogenic aptamer ligands with permanently
cationic sidechains that are bound by the RNA in their protonated phenol form, while emission
occurs from the phenolate intermediate after excited-state proton transfer. The Chili–DMHBO+
complex is the longest wavelength-emitting (592 nm) and tightest binding (KD=12 nM) RNA
fluorophore currently known in the growing family of HBI-binding aptamers. By employing X-ray
crystallography, I have elucidated the three-dimensional structure of the Chili fluorophore binding
site and revealed the structural basis for the large apparent Stokes shift and the promiscuity of the
Chili aptamer to activate red and green-emitting chromophores. Less
to catalyze chemical reactions. There are two main reasons for studying deoxyribozymes: their
practical value in various applications, and the understanding of basic properties - such as folding
and catalysis - of a biopolymer that is of central importance for life. Compared to ribozymes, the
DNA enzymes have a potential value as tools for industrial or therapeutic applications, owing to
more cost-effective synthesis and higher stability. The first crystal structure of a deoxyribozyme
demonstrated that DNA possesses the intrinsic ability to adopt complex tertiary folds that support
catalysis and unveiled the active site of a DNA enzyme in the post-catalytic state (Ponce-Salvatierra,
Wawrzyniak-Turek et al. 2016). The second reported crystal structure of the RNA-cleaving
deoxyribozyme complements observations about the folds and catalysis of DNA enzymes although
the structure was derived with DNA as a substrate mimic of RNA (Liu, Yu et al. 2017). These
crystal structures represent a breakthrough in the field, but they are still insufficient to derive a clear
mechanistic picture of the specific features of different RNA ligating and RNA cleaving
deoxyribozymes. Therefore, ongoing efforts are devoted to structurally investigating additional
deoxyribozymes. The new DNA enzymes were evolved to discriminate modified and unmodified
RNA substrates and provide attractive tools for studying the natural epitranscriptomic RNA
modification N6-methyladenosine (Sednev, Mykhailiuk et al. 2018). In the present study, the goal
is to elucidate the structural basis for recognition of the methylated nucleobase by solving the
crystal structure of the m6A sensitive RNA-cleaving deoxyribozyme in complex with an
uncleavable analog of the RNA substrate, containing either methylated and unmethylated
adenosine. Surprisingly, the RNA substrate dissociated from the deoxyribozyme during the
crystallization process. Two structures for unmethylated and one of the methylated RNA substrate
analog were solved. The next goal is to elucidate the crystal structure of the RNA-ligating
deoxyribozyme in the pre-catalytic state of reaction. The previously reported crystal structure of
the 9DB1 in the post-catalytic state of reaction could not explain the role of magnesium cations as
cofactors for accelerating RNA ligation and properly describe the ligation mechanism. The
structural investigation of the 9DB1 in the pre-catalytic state resulted in the ligation of the two
RNA substrates during the crystallization process. In the future, other strategies are necessary to
solve the questions on substrate recognition and catalytic mechanism of the RNA-cleaving and
RNA-ligating deoxyribozymes investigated in this study.
The second project deals with synthetic RNA aptamers that were identified by in vitro selection to
mimic fluorescent proteins for RNA imaging and the development of biosensors. Several examples
2
of fluorogen-activating RNA aptamers are known, and for some, the crystal structures have
recently been solved e.g. of the Spinach, Mango, and Corn aptamers, that bind synthetic analogs
of the GFP chromophore (Neubacher and Hennig 2019). The Chili is a new fluorogenic-RNA
aptamer that mimics large Stokes shift (LSS) fluorescent proteins (FPs) by inducing highly Stokesshifted
emission from several new green and red HBI (4-hydroxybenzylidene imidazolinone)
derivatives that are non‐fluorescent when free in solution (Steinmetzger, Palanisamy et al. 2019).
The new fluorophores are the first variants of fluorogenic aptamer ligands with permanently
cationic sidechains that are bound by the RNA in their protonated phenol form, while emission
occurs from the phenolate intermediate after excited-state proton transfer. The Chili–DMHBO+
complex is the longest wavelength-emitting (592 nm) and tightest binding (KD=12 nM) RNA
fluorophore currently known in the growing family of HBI-binding aptamers. By employing X-ray
crystallography, I have elucidated the three-dimensional structure of the Chili fluorophore binding
site and revealed the structural basis for the large apparent Stokes shift and the promiscuity of the
Chili aptamer to activate red and green-emitting chromophores. Less
Unique challenges in formulating the next generation of active pharmaceutical ingredients APIs into stable formulations demand analytical tools not currently available using common benchtop methods Herein we review approaches to address some of these challenges through leveraging nonlinear optical NLO interactions between light and matter Applications in dissolution testing polymorphism and accelerated stability testing highlight the breadth of these methods The specificity of second harmonic generation SHG to chiral crystals supports rapid polymorphism analysis at the limit of individual crystals and informs formulations designs to address solubility challenges common in emerging drug candidates Coherent anti-Stokes Raman spectroscopy CARS and stimulated ... More
Unique challenges in formulating the next generation of active pharmaceutical ingredients (APIs) into stable formulations demand analytical tools not currently available using common benchtop methods. Herein, we review approaches to address some of these challenges through leveraging nonlinear optical (NLO) interactions between light and matter. Applications in dissolution testing, polymorphism, and accelerated stability testing highlight the breadth of these methods. The specificity of second harmonic generation (SHG) to chiral crystals supports rapid polymorphism analysis at the limit of individual crystals and informs formulations designs to address solubility challenges common in emerging drug candidates. Coherent anti-Stokes Raman spectroscopy (CARS) and stimulated Raman spectroscopy (SRS) provide vibration-specific microscopy of final dosage forms to inform composition at video-rate acquisition speeds and ~1 μm spatial resolution. Recent results are reviewed to illustrate challenges in designing formulations for emerging drug candidates and opportunities for the development of NLO tools tailored to meet them. Less
Nicotinamide adenine dinucleotide NAD is a key molecule in cellular bioenergetics and signalling Various bacterial pathogens release NADase enzymes into the host cell that deplete the host s NAD pool thereby causing rapid cell death Here we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa The enzymes harbour a tuberculosis necrotizing toxin TNT domain and are predominately present in pathogenic species The X-ray structure of the homodimeric A fumigatus protein reveals unique properties including N-linked glycosylation and a Ca -binding site whose occupancy regulates activity The structure ... More
Nicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca2+-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms. Less
Understanding antibody responses to SARS-CoV- is indispensable for the development of containment measures to overcome the current COVID- pandemic Recent studies showed that serum from convalescent patients can display variable neutralization capacities Still it remains unclear whether there are specific signatures that can be used to predict neutralization Here we performed a detailed analysis of sera from a cohort of recovered healthcare workers and we addressed their SARS-CoV- antibody response by ELISA against SARS-CoV- Spike receptor binding domain and nucleoprotein Both ELISA methods detected sustained levels of serum IgG against both antigens Yet the majority of individuals from our cohort ... More
Understanding antibody responses to SARS-CoV-2 is indispensable for the development of containment measures to overcome the current COVID-19 pandemic. Recent studies showed that serum from convalescent patients can display variable neutralization capacities. Still, it remains unclear whether there are specific signatures that can be used to predict neutralization. Here, we performed a detailed analysis of sera from a cohort of 101 recovered healthcare workers and we addressed their SARS-CoV-2 antibody response by ELISA against SARS-CoV-2 Spike receptor binding domain and nucleoprotein. Both ELISA methods detected sustained levels of serum IgG against both antigens. Yet, the majority of individuals from our cohort generated antibodies with low neutralization capacity and only 6% showed high neutralizing titers against both authentic SARS-CoV-2 virus and the Spike pseudotyped virus. Interestingly, higher neutralizing sera correlate with detection of -IgG, IgM and IgA antibodies against both antigens, while individuals with positive IgG alone showed poor neutralization response. These results suggest that having a broader repertoire of antibodies may contribute to more potent SARS-CoV-2 neutralization. Altogether, our work provides a cross sectional snapshot of the SARS-CoV-2 neutralizing antibody response in recovered healthcare workers and provides preliminary evidence that possessing multiple antibody isotypes can play an important role in predicting SARS-CoV-2 neutralization. Less
Multimeric immunoglobulin-like molecules arose early in vertebrate evolution yet the unique contributions of multimeric IgM antibodies to infection control are not well understood This is partially due to the difficulty of distinguishing low-affinity IgM secreted rapidly by plasmablasts from high-affinity antibodies derived from later-arising memory cells We developed a pipeline to express B cell receptors BCRs from Plasmodium falciparum specific IgM and IgG human memory B cells MBCs as both IgM and IgG molecules BCRs from both subsets were somatically hypermutated and exhibited comparable monomeric affinity Crystallization of one IgM MBC-derived antibody complexed with antigen defined a linear epitope within ... More
Multimeric immunoglobulin-like molecules arose early in vertebrate evolution, yet the unique contributions of multimeric IgM antibodies to infection control are not well understood. This is partially due to the difficulty of distinguishing low-affinity IgM, secreted rapidly by plasmablasts, from high-affinity antibodies derived from later-arising memory cells. We developed a pipeline to express B cell receptors (BCRs) from Plasmodium falciparum–specific IgM+ and IgG+ human memory B cells (MBCs) as both IgM and IgG molecules. BCRs from both subsets were somatically hypermutated and exhibited comparable monomeric affinity. Crystallization of one IgM+ MBC-derived antibody complexed with antigen defined a linear epitope within a conserved Plasmodium protein. In its physiological multimeric state, this antibody displayed exponentially higher antigen binding than a clonally identical IgG monomer, and more effectively inhibited P. falciparum invasion. Forced multimerization of this IgG significantly improved both antigen binding and parasite restriction, underscoring how avidity can alter antibody function. This work demonstrates the potential of high-avidity IgM in both therapeutics and vaccines. Less
We previously developed a panel of one-step real-time quantitative reverse transcription PCR one-step qRT-PCR hereafter referred to as qRT-PCR assays to assess compound efficacy However these high-cost conventional qRT-PCR manual assays are not amenable to high-throughput screen HTS analysis in a time-sensitive and complex drug discovery process Here we report the establishment of an automated gene expression platform using in-house lysis conditions that allows the study of various cell lines including primary T cells This process innovation provides the opportunity to perform genotypic profiling in both immunology and oncology therapeutic areas with quantitative studies as part of routine drug discovery ... More
We previously developed a panel of one-step real-time quantitative reverse transcription PCR (one-step qRT-PCR; hereafter referred to as qRT-PCR) assays to assess compound efficacy. However, these high-cost, conventional qRT-PCR manual assays are not amenable to high-throughput screen (HTS) analysis in a time-sensitive and complex drug discovery process. Here, we report the establishment of an automated gene expression platform using in-house lysis conditions that allows the study of various cell lines, including primary T cells. This process innovation provides the opportunity to perform genotypic profiling in both immunology and oncology therapeutic areas with quantitative studies as part of routine drug discovery program support. This newly instituted platform also enables a panel screening strategy to efficiently connect HTS, lead identification, and lead optimization in parallel. Less
We report the development automation and validation of a D microfluidic liver-on-a-chip for high throughput hepatotoxicity screening the OrganoPlate LiverTox The model is comprised of aggregates of induced pluripotent stem cell iPSC -derived hepatocytes iHep seeded in an extracellular matrix in the organ channel and co-cultured with endothelial cells and THP- monoblasts differentiated to macrophages seeded in the vascular channel of the well Mimetas OrganoPlate -lane A key component of high throughput screening is automation and we report a protocol to seed dose collect and replenish media and add assay reagents in the OrganoPlate -lane using a standard laboratory liquid ... More
We report the development, automation and validation of a 3D, microfluidic liver-on-a-chip for high throughput hepatotoxicity screening, the OrganoPlate LiverTox™. The model is comprised of aggregates of induced pluripotent stem cell (iPSC)-derived hepatocytes (iHep) seeded in an extracellular matrix in the organ channel and co-cultured with endothelial cells and THP-1 monoblasts differentiated to macrophages seeded in the vascular channel of the 96 well Mimetas OrganoPlate 2-lane. A key component of high throughput screening is automation and we report a protocol to seed, dose, collect and replenish media and add assay reagents in the OrganoPlate 2-lane using a standard laboratory liquid handling robot. A combination of secretome measurements and image-based analysis was used to demonstrate stable 15 day cell viability, albumin and urea secretion. Over the same time-period, CYP3A4 activity increased and alpha-fetoprotein secretion decreased suggesting further maturation of the iHeps. Troglitazone, a clinical hepatotoxin, was chosen as a control compound for validation studies. Albumin, urea, hepatocyte nuclear size and viability staining provided Robust Z’factors > 0.2 in plates treated 72 h with 180 μM troglitazone compared with a vehicle control. The viability assay provided the most robust statistic for a Robust Z’ factor = 0.6. A small library of 159 compounds with known liver effects was added to the OrganoPlate LiverTox model for 72 h at 50 μM and the Toxicological Prioritization scores were calculated. A follow up dose-response evaluation of select hits revealed the albumin assay to be the most sensitive in calculating TC50 values. This platform provides a robust, novel model which can be used for high throughput hepatotoxicity screening. Less
Aiming at streamlining GPCR production from E coli inclusion bodies for structural analysis we present a generic approach to assess and optimize refolding yield through thermostability analysis Since commonly used hydrophobic dyes cannot be applied as probes for membrane protein unfolding we adapted a technique based on reacting cysteins exposed upon thermal denaturation with fluorescent -Diethylamino- - -maleimidophenyl - -methylcoumarin CPM Successful expression purification and refolding is shown for two G protein-coupled receptors GPCR the sphingosine- -phosphate receptor S P and the orphan receptor GPR Refolded receptors were subjected to lipidic cubic phase crystallization screening
Here a protocol is presented to facilitate the creation of large volumes L of micro-crystalline slurries suitable for serial crystallography experiments at both synchrotrons and XFELs The method is based upon an understanding of the protein crystal phase diagram and how that knowledge can be utilized The method is divided into three stages optimizing crystal morphology transitioning to batch and scaling Stage involves finding well diffracting single crystals hopefully but not necessarily presenting in a cube-like morphology In Stage the Stage condition is optimized by crystal growth time This strategy can transform crystals grown by vapor diffusion to batch Once ... More
Here, a protocol is presented to facilitate the creation of large volumes (> 100 µL) of micro-crystalline slurries suitable for serial crystallography experiments at both synchrotrons and XFELs. The method is based upon an understanding of the protein crystal phase diagram, and how that knowledge can be utilized. The method is divided into three stages: (1) optimizing crystal morphology, (2) transitioning to batch, and (3) scaling. Stage 1 involves finding well diffracting, single crystals, hopefully but not necessarily, presenting in a cube-like morphology. In Stage 2, the Stage 1 condition is optimized by crystal growth time. This strategy can transform crystals grown by vapor diffusion to batch. Once crystal growth can occur within approximately 24 h, a morphogram of the protein and precipitant mixture can be plotted and used as the basis for a scaling strategy (Stage 3). When crystals can be grown in batch, scaling can be attempted, and the crystal size and concentration optimized as the volume is increased. Endothiapepsin has been used as a demonstration protein for this protocol. Some of the decisions presented are specific to endothiapepsin. However, it is hoped that the way they have been applied will inspire a way of thinking about this procedure that others can adapt to their own projects. Less
The human neuropeptide Y NPY Y receptor Y R plays essential roles in food intake bone formation and mood regulation and has been considered an important drug target for obesity and anxiety However development of drugs targeting Y R remains challenging with no success in clinical application yet Here we report the crystal structure of Y R bound to a selective antagonist JNJ- at resolution The structure reveals molecular details of the ligand-binding mode of Y R Combined with mutagenesis studies the Y R structure provides insights into key factors that define antagonistic activity of diverse antagonists Comparison with the ... More
The human neuropeptide Y (NPY) Y2 receptor (Y2R) plays essential roles in food intake, bone formation and mood regulation, and has been considered an important drug target for obesity and anxiety. However, development of drugs targeting Y2R remains challenging with no success in clinical application yet. Here, we report the crystal structure of Y2R bound to a selective antagonist JNJ-31020028 at 2.8 Å resolution. The structure reveals molecular details of the ligand-binding mode of Y2R. Combined with mutagenesis studies, the Y2R structure provides insights into key factors that define antagonistic activity of diverse antagonists. Comparison with the previously determined antagonist-bound Y1R structures identified receptor-ligand interactions that play different roles in modulating receptor activation and mediating ligand selectivity. These findings deepen our understanding about molecular mechanisms of ligand recognition and subtype specificity of NPY receptors, and would enable structure-based drug design. Less
The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects Fully automated data collection is now possible at several synchrotrons which means that the number of samples tested at the synchrotron is currently increasing rapidly Therefore the protein crystallography research communities at the University of Oulu Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron In ... More
The web-based IceBear software is a versatile tool to monitor the results of crystallization experiments and is designed to facilitate supervisor and student communications. It also records and tracks all relevant information from crystallization setup to PDB deposition in protein crystallography projects. Fully automated data collection is now possible at several synchrotrons, which means that the number of samples tested at the synchrotron is currently increasing rapidly. Therefore, the protein crystallography research communities at the University of Oulu, Weizmann Institute of Science and Diamond Light Source have joined forces to automate the uploading of sample metadata to the synchrotron. In IceBear, each crystal selected for data collection is given a unique sample name and a crystal page is generated. Subsequently, the metadata required for data collection are uploaded directly to the ISPyB synchrotron database by a shipment module, and for each sample a link to the relevant ISPyB page is stored. IceBear allows notes to be made for each sample during cryocooling treatment and during data collection, as well as in later steps of the structure determination. Protocols are also available to aid the recycling of pins, pucks and dewars when the dewar returns from the synchrotron. The IceBear database is organized around projects, and project members can easily access the crystallization and diffraction metadata for each sample, as well as any additional information that has been provided via the notes. The crystal page for each sample connects the crystallization, diffraction and structural information by providing links to the IceBear drop-viewer page and to the ISPyB data-collection page, as well as to the structure deposited in the Protein Data Bank. Less
Mutations in two different domains of the ubiquitously expressed TRIM protein give rise to two clinically separate diseases one of which is Limb-girdle muscular dystrophy type H LGMD H Uncovering the muscle-specific role of TRIM in LGMD H pathogenesis has proven difficult as neurogenic phenotypes independent of LGMD H pathology are present in TRIM KO mice We previously established a platform to study LGMD H pathogenesis using Drosophila melanogaster as a model Here we show that LGMD H disease-causing mutations in the NHL domain are molecularly and structurally conserved between fly and human TRIM Furthermore transgenic expression of a subset ... More
Mutations in two different domains of the ubiquitously expressed TRIM32 protein give rise to two clinically separate diseases, one of which is Limb-girdle muscular dystrophy type 2H (LGMD2H). Uncovering the muscle-specific role of TRIM32 in LGMD2H pathogenesis has proven difficult, as neurogenic phenotypes, independent of LGMD2H pathology, are present in TRIM32 KO mice. We previously established a platform to study LGMD2H pathogenesis using Drosophila melanogaster as a model. Here we show that LGMD2H disease-causing mutations in the NHL domain are molecularly and structurally conserved between fly and human TRIM32. Furthermore, transgenic expression of a subset of myopathic alleles (R394H, D487N, and 520fs) induce myofibril abnormalities, altered nuclear morphology, and reduced TRIM32 protein levels, mimicking phenotypes in patients afflicted with LGMD2H. Intriguingly, we also report for the first time that the protein levels of βPS integrin and sarcoglycan δ, both core components of costameres, are elevated in TRIM32 disease-causing alleles. Similarly, murine myoblasts overexpressing a catalytically inactive TRIM32 mutant aberrantly accumulate α- and β-dystroglycan and α-sarcoglycan. We speculate that the stoichiometric loss of costamere components disrupts costamere complexes to promote muscle degeneration. Less