1209 Citations
Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus ZikV and the four serotypes of Dengue virus DenV - must elicit broadly neutralizing antibodies bnAbs to prevent the risk of enhancement of infection by non-neutralizing antibodies We recently discovered new orthoflavivirus-directed bnAbs including F S which neutralizes DenV - and ZikV with comparable or superior potency to the previously characterized E dimer epitope EDE bnAbs Here we used cryoEM and X-ray crystallography to understand the basis of cross-neutralization of F S at the molecular level We obtained a cryoEM structure of F S Fab bound to a ... More
Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus (ZikV) and the four serotypes of Dengue virus (DenV1-4) must elicit broadly neutralizing antibodies (bnAbs) to prevent the risk of enhancement of infection by non-neutralizing antibodies. We recently discovered new orthoflavivirus-directed bnAbs, including F25.S02, which neutralizes DenV1-4 and ZikV with comparable or superior potency to the previously characterized E dimer epitope (EDE) bnAbs. Here, we used cryoEM and X-ray crystallography to understand the basis of cross-neutralization of F25.S02 at the molecular level. We obtained a ~ 4.2 Å cryoEM structure of F25.S02 Fab bound to a stabilized DenV3 soluble E protein dimer and a 2.3 Å crystal structure of F25.S02 Fab bound to ZikV soluble E protein dimer. Like previously described EDE1 bnAbs, the structural epitope of F25.S02 is at the E dimer interface, encompassing predominantly conserved regions in domain II, including the fusion loop. However, unlike EDE1 bnAbs, F25.S02 binding is almost entirely dependent on the heavy chain and is shifted slightly away from the dimer symmetry axis. Our findings emphasize the importance of this cross-neutralizing site of vulnerability for DenV and ZikV that can facilitate rational design of vaccines and therapeutics. Less
-Hemolysin Ahly is a major Staphylococcus aureus virulence determinant implicated in tissue injury and immune dysregulation antibody inhibitors have reached clinical trials but alternatives with improved ease of manufacture and tissue penetration are desirable Here we demonstrate that phage-derived bicyclic peptides can serve as compact chemically tractable Ahly neutralisers Using TATB-scaffolded M phage libraries we identified WNP-motif containing bicyclic binders with a lead hit of Peptide KD nM and progressed the lead by iterative affinity maturation to Peptide KD nM and by incorporation of strategically chosen non-canonical amino acids to yield Peptide KD nM A co-crystal structure with AhlyH A ... More
α-Hemolysin (Ahly) is a major Staphylococcus aureus virulence determinant implicated in tissue injury and immune dysregulation; antibody inhibitors have reached clinical trials but alternatives with improved ease of manufacture and tissue penetration are desirable. Here we demonstrate that phage-derived bicyclic peptides can serve as compact, chemically tractable Ahly neutralisers. Using TATB-scaffolded M13 phage libraries we identified WNP-motif containing bicyclic binders, with a lead hit of Peptide 14 (KD = 1792nM) and progressed the lead by iterative affinity maturation to Peptide 20 (KD = 609 nM) and by incorporation of strategically chosen non-canonical amino acids to yield Peptide 88 (KD = 96 nM). A 2.2 Å co-crystal structure with AhlyH35A locates the binding footprint on the rim domain and explains the critical role of the WNP motif in target engagement. Functional assays show that the Peptide 88 blocks Ahly mediated hemolysis, inhibits Ahly driven ADAM10 activation, and elucidate its inhibitory mechanism of preventing Ahly binding to human A549 epithelial cells. Peptide 88 protects A549 cells from recombinant toxin and attenuates cytotoxicity in S. aureus co-culture experiments, whilst showing no toxicity to A549 cells. Bicyclic peptides thus represent a new and promising anti-virulence modality: small, synthetically accessible molecules that mimic antibody recognition, with therapeutic potential against S. aureus infections. Less
Imidazolium LipidBrick cationic lipid nanoparticles LNPs provide a pH-independent alternative to conventional ionizable systems for nucleic acid delivery Through a high-throughput screen of formulations spanning eight imidazolium cores three helper lipids and varying PEG densities we found that more than half of the library outperformed the clinical ionizable benchmark ALC- in multiple representative mammalian cell types Top-performing candidates showed robust cellular uptake efficient endosomal escape and strong transgene expression both in vitro and following intramuscular administration A lead formulation C LNP incorporating an imidazolium lipid core bearing a hydroxyethyl substituent with mol DOPE achieved comparable intramuscular luciferase expression and antibody ... More
Imidazolium LipidBrick® cationic lipid nanoparticles (LNPs) provide a pH-independent alternative to conventional ionizable systems for nucleic acid delivery. Through a high-throughput screen of 1,944 formulations spanning eight imidazolium cores, three helper lipids, and varying PEG densities, we found that more than half of the library outperformed the clinical ionizable benchmark ALC-0315 in multiple representative mammalian cell types. Top-performing candidates showed robust cellular uptake, efficient endosomal escape, and strong transgene expression both in vitro and following intramuscular administration. A lead formulation (C3 LNP), incorporating an imidazolium lipid core bearing a hydroxyethyl substituent, with 30 mol% DOPE, achieved comparable intramuscular luciferase expression and antibody titers to ALC-0315, while eliciting ∼ 3-fold stronger ovalbumin-specific IFN-γ+ T-cell responses and maintaining low cytotoxicity. Machine-learning analysis of the dataset further distilled transferable design rules to inform future formulation strategies. Collectively, these findings establish cationic LipidBrick® LNPs as a versatile platform for mRNA delivery, offering a generalizable framework for the high-throughput discovery of ionization-independent systems that effectively prime adaptive immune responses. Less
Tankyrases are poly-ADP-ribosyltransferases that orchestrate numerous biological processes involved in disease Their established regulatory roles particularly within the WNT -catenin pathway have driven notable drug discovery efforts aimed at inhibiting their catalytic activity Targeting tankyrases interaction with proteins through their ARC domains represents an alternative strategy to be explored as a therapeutic approach against specific protein-protein interactions In this article we employed a pre-established FRET-based assay to screen the EU-OPENSCREEN libraries for identification of ARC inhibitors We discovered a series of pyrrolone-based compounds and we synthesized compound S ARCher- which binds selectively to ARC with a potency of M NMR ... More
Tankyrases are poly-ADP-ribosyltransferases that orchestrate numerous biological processes involved in disease. Their established regulatory roles, particularly within the WNT/β-catenin pathway, have driven notable drug discovery efforts aimed at inhibiting their catalytic activity. Targeting tankyrases’ interaction with proteins through their ARC domains represents an alternative strategy to be explored as a therapeutic approach against specific protein-protein interactions. In this article, we employed a pre-established FRET-based assay to screen the EU-OPENSCREEN libraries for identification of ARC4 inhibitors. We discovered a series of pyrrolone-based compounds, and we synthesized compound S8 (ARCher-142), which binds selectively to ARC4 with a potency of 8 μM. NMR analysis and X-ray crystallography allowed us to identify the binding site and to rationalize the observed selectivity. Despite binding exclusively to ARC4, the inhibitor can attenuate the WNT/β-catenin signaling pathway in cells. Our work demonstrates that targeting single ARC domains is possible, offering an inhibition approach tailored to tankyrase ARC4. Less
Complement and pathogenic antibodies act independently and together to mediate the pathology of many autoimmune diseases To address these drivers of disease we generated a monoclonal antibody mAb CSL that binds and inhibits both complement and the neonatal Fc fragment crystallizable receptor FcRn The fragment antigen binding Fab portion of CSL was engineered to bind both human C huC zymogen and the active fragment huC b to inhibit the classical and lectin complement pathways in vitro and C b deposition on primary lung endothelial cells using a -dimensional microvascular model system Engineering of a triple amino acid mutation YPY motif ... More
Complement and pathogenic antibodies act independently and together to mediate the pathology of many autoimmune diseases. To address these drivers of disease, we generated a monoclonal antibody (mAb), CSL305, that binds and inhibits both complement and the neonatal Fc (fragment crystallizable) receptor FcRn. The fragment antigen binding (Fab) portion of CSL305 was engineered to bind both human C2 (huC2) zymogen and the active fragment huC2b to inhibit the classical and lectin complement pathways in vitro, and C3b deposition on primary lung endothelial cells using a 3-dimensional microvascular model system. Engineering of a triple amino acid mutation (“YPY” motif) into the Fc region of CSL305 increased its affinity to FcRn at both acidic and neutral pH, allowing it to also act as a potent FcRn antagonist. Intracellular trafficking experiments demonstrated that CSL305, but not the wild-type (WT) mAb lacking the YPY motif, was able to block immunoglobulin G (IgG) recycling in vitro. The generation of a high resolution 2.6Å crystal structure of CSL305 Fab region bound to huC2b showed that the epitope lies directly over the huC2b catalytic triad, providing evidence of its complement mechanism of action as a neutralising mAb. Early pharmacokinetic (PK)/pharmacodynamic (PD) studies using CSL305 in cynomolgus monkeys demonstrated both complement inhibition and FcRn antagonism in vivo, with reductions in complement classical pathway activity and endogenous IgG observed following single intravenous (IV) administration. CSL305 thus represents a dual-functional mAb as a potential therapeutic candidate. Less
Improving health and quality of life in our society is a key focus of drug development Methods for drug discovery are being optimized in multiple ways to reduce costs and timelines Crystallographic fragment screening CFS is increasingly being employed as an early screening method in drug discovery projects Here we demonstrate that selecting the optimal protein crystal form can significantly impact hit rates Two CFS campaigns are carried out against the two crystal forms of the SARS-CoV- main protease using the same fragment library and an almost identical experimental setup Although both crystal forms exhibit similar diffraction properties the observed ... More
Improving health and quality of life in our society is a key focus of drug development. Methods for drug discovery are being optimized in multiple ways to reduce costs and timelines. Crystallographic fragment screening (CFS) is increasingly being employed as an early screening method in drug discovery projects. Here, we demonstrate that selecting the optimal protein crystal form can significantly impact hit rates. Two CFS campaigns are carried out against the two crystal forms of the SARS-CoV-2 main protease, using the same fragment library and an almost identical experimental setup. Although both crystal forms exhibit similar diffraction properties, the observed hit rates in the two campaigns differ significantly. A hit rate of 3% is determined for the monoclinic crystals, while a hit rate of 16% is observed for the orthorhombic crystals. These findings are consistent with the more open molecular packing in the orthorhombic crystals, where the solvent channels leading to the active sites are approximately twice the size of those in the monoclinic crystal form. Our results highlight the critical importance of the crystal form in a crystallographic screening, identifying it as one of the most important parameters to optimize when preparing a CFS campaign. Less
Light Oxygen Voltage LOV domains are important widespread receptors of blue light that also found applications in optogenetics and imaging While LOV domains from mesophiles are relatively well characterized their counterparts from thermophilic microorganisms remain understudied Here we express two constructs of a LOV domain belonging to a histidine kinase from Meiothermus ruber MrLOV and MrLOVe and show that they are photoactive with recovery time values of and min respectively and thermostable Crystal structures reveal that MrLOV which lacks helices A and J forms a parallel dimer whereas MrLOVe is a tetramer organized as an antiparallel dimer of two parallel ... More
Light Oxygen Voltage (LOV) domains are important widespread receptors of blue light that also found applications in optogenetics and imaging. While LOV domains from mesophiles are relatively well characterized, their counterparts from thermophilic microorganisms remain understudied. Here, we express two constructs of a LOV domain belonging to a histidine kinase from Meiothermus ruber, MrLOV and MrLOVe, and show that they are photoactive, with recovery time values of 21 and 27 min, respectively, and thermostable. Crystal structures reveal that MrLOV, which lacks helices A’α and Jα, forms a parallel dimer, whereas MrLOVe is a tetramer organized as an antiparallel dimer of two parallel dimers interacting via helices Jα. One MrLOVe dimer is symmetric, and the other is asymmetric, with conformational differences mirroring activation-related changes in other LOV domains. Our data provide the structural basis for understanding and engineering of thermophilic LOVs and pave the way for development of thermostable and photostable LOV-derived optogenetic tools and flavin-based fluorescent proteins. Less
Abstract Background LABL-Fc-MOGR is a bifunctional peptide inhibitor designed to modulate immune responses in multiple sclerosis including primary progressive multiple sclerosis Although therapeutically promising its development has been hindered by poor physical stability particularly rapid precipitation under standard formulation conditions Methods A high-throughput multi-phase formulation strategy was implemented to improve conformational and colloidal stability An initial Phase evaluation used intrinsic fluorescence differential scanning fluorometry and polyethylene glycol PEG solubility assays to screen formulations spanning a range of pH values buffer systems and excipients Then a Phase study applied a definitive screening design to evaluate key formulation variables including buffer type ... More
Abstract
Background
LABL-Fc-MOGR5 is a bifunctional peptide inhibitor designed to modulate immune responses in multiple sclerosis, including primary progressive multiple sclerosis. Although therapeutically promising, its development has been hindered by poor physical stability, particularly rapid precipitation under standard formulation conditions.
Methods
A high-throughput, multi-phase formulation strategy was implemented to improve conformational and colloidal stability. An initial Phase 1 evaluation used intrinsic fluorescence differential scanning fluorometry and polyethylene glycol (PEG) solubility assays to screen 96 formulations spanning a range of pH values, buffer systems, and excipients. Then, a Phase 2 study applied a definitive screening design to evaluate key formulation variables—including buffer type, excipients, and surfactant concentration—at reduced protein concentration in 96-well plates. A final Phase 3 study compared the lead formulation from Phase 2 with the control formulation at higher protein concentration in glass vials.
Results
The Phase 1 study revealed pronounced sensitivity of LABL-Fc-MOGR5 to pH and ionic strength. Divalent anionic buffers (e.g. citrate, succinate) and excipients such as sucrose and hydroxypropyl-β-cyclodextrin substantially reduced aggregation propensity. In the Phase 2 study, an optimized formulation was identified—10 mM sodium acetate, pH 5.3, 125 mM sucrose, 150 mM HBP-LB-βCD, and 0.025% polysorbate 80—based on statistical modeling. This formulation demonstrated markedly improved resistance to aggregation, fragmentation, and subvisible particle formation under accelerated stress relative to the control.
Conclusions
This work underscores the value of excipient selection and rational design of experiments in stabilizing complex fusion proteins. The optimized formulation provides a significantly enhanced stability profile and supports further development of LABL-Fc-MOGR5 toward clinical evaluation for primary progressive multiple sclerosis. Less
Background
LABL-Fc-MOGR5 is a bifunctional peptide inhibitor designed to modulate immune responses in multiple sclerosis, including primary progressive multiple sclerosis. Although therapeutically promising, its development has been hindered by poor physical stability, particularly rapid precipitation under standard formulation conditions.
Methods
A high-throughput, multi-phase formulation strategy was implemented to improve conformational and colloidal stability. An initial Phase 1 evaluation used intrinsic fluorescence differential scanning fluorometry and polyethylene glycol (PEG) solubility assays to screen 96 formulations spanning a range of pH values, buffer systems, and excipients. Then, a Phase 2 study applied a definitive screening design to evaluate key formulation variables—including buffer type, excipients, and surfactant concentration—at reduced protein concentration in 96-well plates. A final Phase 3 study compared the lead formulation from Phase 2 with the control formulation at higher protein concentration in glass vials.
Results
The Phase 1 study revealed pronounced sensitivity of LABL-Fc-MOGR5 to pH and ionic strength. Divalent anionic buffers (e.g. citrate, succinate) and excipients such as sucrose and hydroxypropyl-β-cyclodextrin substantially reduced aggregation propensity. In the Phase 2 study, an optimized formulation was identified—10 mM sodium acetate, pH 5.3, 125 mM sucrose, 150 mM HBP-LB-βCD, and 0.025% polysorbate 80—based on statistical modeling. This formulation demonstrated markedly improved resistance to aggregation, fragmentation, and subvisible particle formation under accelerated stress relative to the control.
Conclusions
This work underscores the value of excipient selection and rational design of experiments in stabilizing complex fusion proteins. The optimized formulation provides a significantly enhanced stability profile and supports further development of LABL-Fc-MOGR5 toward clinical evaluation for primary progressive multiple sclerosis. Less
Gene expression is governed by dynamic switches between repressive and activating transcriptional states Among the molecules mediating these transitions chromatin readers and transcription factors play pivotal roles However how they assemble with regulatory machineries to enable crosstalk between gene repression and activation remains unknown Here we use an integrative structural dynamics approach combining cryo-EM crosslinking mass spectrometry fragment-resolved protein interactome mapping and crystallography to show how the dual-role chromatin reader Cti and transcription factors Ash and Ume engage the Sin deacetylase complex a major regulatory hub in eukaryotes We find that Cti competes with Ash to drive its dynamic recruitment ... More
Gene expression is governed by dynamic switches between repressive and activating transcriptional states1,2. Among the molecules mediating these transitions, chromatin readers and transcription factors play pivotal roles3,4. However, how they assemble with regulatory machineries to enable crosstalk between gene repression and activation remains unknown. Here, we use an integrative structural dynamics approach – combining cryo-EM, crosslinking mass spectrometry, fragment-resolved protein interactome mapping and crystallography – to show how the dual-role chromatin reader Cti6 and transcription factors Ash1 and Ume6 engage the Sin3 deacetylase complex, a major regulatory hub in eukaryotes5. We find that Cti6 competes with Ash1 to drive its dynamic recruitment to a shared peripheral module, while Ume6 engages the Sin3 scaffold through a defined, minimal interface. Using high-throughput mutational scanning, we reveal deleterious and gain-of-function mutations in Sin3, identifying evolutionarily conserved residues essential for anchoring transcription factors. Together, these results provide structural and functional insights into how dual-role regulators engage the central Sin3 complex, revealing subtle assembly principles that may facilitate crosstalk between gene repression and activation. They also establish an integrative multidisciplinary framework to dissect the dynamics of macromolecular assemblies across biological systems. Less
Filament-forming proteins such as TasA Bacillus subtilis and camelysins CalY CalY Bacillus cereus pose a particular challenge for structural analysis due to their strong tendency to self-association and their polydispersity which severely limits their ability to crystallize or to be a target for NMR-spectroscopy To address this it is necessary to modify the amino acid sequence to prevent filamentation Engineering a series of N- and C-terminal truncated variants by removing flexible parts is often key to success N-terminal extensions are also a powerful tool for obtaining crystals of fiber-forming proteins
Epstein-Barr virus EBV causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies particularly in immune-compromised hosts Transplant patients face high risk of post-transplant lymphoproliferative disease a life-threatening EBV-driven lymphoma There are no EBV-specific vaccines or treatments however neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents EBV entry into B cells involves gp which binds complement receptors and gp which engages HLA class II to trigger fusion Most existing monoclonal antibodies mAbs against these antigens are non-human limiting clinical use Using a transgenic mouse model we generate two gp and eight gp genetically human neutralizing mAbs that ... More
Epstein-Barr virus (EBV) causes infectious mononucleosis and contributes to neurodegenerative disorders and malignancies, particularly in immune-compromised hosts. Transplant patients face high risk of post-transplant lymphoproliferative disease, a life-threatening EBV-driven lymphoma. There are no EBV-specific vaccines or treatments; however, neutralizing antibodies against EBV glycoproteins may offer utility as therapeutic agents. EBV entry into B cells involves gp350, which binds complement receptors, and gp42, which engages HLA class II to trigger fusion. Most existing monoclonal antibodies (mAbs) against these antigens are non-human, limiting clinical use. Using a transgenic mouse model, we generate two gp350 and eight gp42 genetically human neutralizing mAbs that block receptor binding. Structural analyses reveal extended sites of vulnerability relevant to vaccine development. Delivery of a gp42 mAb protects humanized mice from EBV challenge, while a gp350 mAb provides partial protection. These mAbs highlight the utility of transgenic mice to produce therapeutic mAbs for preventing EBV-driven disease. Less
HECT E ligases regulate many cellular processes yet how they recognise their substrates and synthesise specific types of poly-ubiquitin chains is still incompletely understood HECTD a member of the other HECT family is implicated in the regulation of inflammation apoptosis and infection and highly expressed in several cancers These functions are largely attributed to its ligase activity and modification of diverse substrates with different types of ubiquitin chains We present a detailed analysis of the ligase activity of HECTD including its ubiquitin linkage preferences oligomeric state and substrate ubiquitination Using cryo-EM we provide the full-length structures of HECTD in both ... More
HECT E3 ligases regulate many cellular processes, yet how they recognise their substrates and synthesise specific types of poly-ubiquitin chains is still incompletely understood. HECTD3, a member of the “other HECT” family, is implicated in the regulation of inflammation, apoptosis, and infection and highly expressed in several cancers. These functions are largely attributed to its ligase activity and modification of diverse substrates with different types of ubiquitin chains. We present a detailed analysis of the ligase activity of HECTD3, including its ubiquitin linkage preferences, oligomeric state and substrate ubiquitination. Using cryo-EM, we provide the full-length structures of HECTD3 in both apo and ubiquitin-loaded forms, revealing key insights into its domain organisation, including discovery of a distinct fold of the N-terminal region, and mechanistic features. Some of these are shared with other HECT ligases, while others are unique to HECTD3 and contribute to differences in its catalytic mechanisms and functional diversity. Less
Autosomal recessive congenital ichthyosis ARCI refers to a group of rare highly debilitating skin disorders that significantly impair patients quality of life and lack any effective treatment options Here we report clinically relevant in situ correction of the most common ARCI-causing mutation TGM c - A G a splice-site aberration in human disease models Targeted skin barrier modulation followed by topical application of the cytosine base editor eTd packaged into lipid nanoparticles yielded functional restoration of of wild-type transglutaminase activity in skin tissue Toxicity studies and comprehensive off-target analysis demonstrated an excellent safety profile even after repeated application without systemic ... More
Autosomal recessive congenital ichthyosis (ARCI) refers to a group of rare, highly debilitating skin disorders that significantly impair patients’ quality of life and lack any effective treatment options. Here, we report clinically relevant in situ correction of the most common ARCI-causing mutation, TGM1 c.877-2A>G, a splice-site aberration, in human disease models. Targeted skin barrier modulation followed by topical application of the cytosine base editor eTd packaged into lipid nanoparticles yielded functional restoration of ∼30% of wild-type transglutaminase 1 activity in skin tissue. Toxicity studies and comprehensive off-target analysis demonstrated an excellent safety profile even after repeated application, without systemic distribution of the lipid nanoparticles or the genetic cargo as determined via highly sensitive methods, including desorption electrospray ionization (DESI) metabolic imaging. This study presents comprehensive preclinical data on the feasibility of in situ gene correction of genodermatoses-causing mutations, showcasing its therapeutic potential and paving the way for curative next-generation treatments for severe genetic skin diseases. Less
Doxorubicin a widely used chemotherapy drug is produced by Streptomyces peucetius ATCC The biosynthesis relies on the cytochrome P monooxygenase DoxA which catalyzes three consecutive late-stage oxidation steps However conversion from daunorubicin to doxorubicin is inefficient necessitating semi-synthetic industrial manufacturing Here we address key limitations in DoxA catalysis We identify the natural redox partners ferredoxin Fdx and ferredoxin reductase FdR by transcriptomic analysis We discovered the vicinal oxygen chelate family protein DnrV to prevent product inhibition by binding doxorubicin Structural analysis of DoxA and density functional theory DFT calculations reveal that inefficient C hydroxylation results from the unfavorable anti-conformation of ... More
Doxorubicin, a widely used chemotherapy drug, is produced by Streptomyces peucetius ATCC27952. The biosynthesis relies on the cytochrome P450 monooxygenase DoxA, which catalyzes three consecutive late-stage oxidation steps. However, conversion from daunorubicin to doxorubicin is inefficient, necessitating semi-synthetic industrial manufacturing. Here, we address key limitations in DoxA catalysis. We identify the natural redox partners ferredoxin Fdx4 and ferredoxin reductase FdR3 by transcriptomic analysis. We discovered the vicinal oxygen chelate family protein DnrV to prevent product inhibition by binding doxorubicin. Structural analysis of DoxA and density functional theory (DFT) calculations reveal that inefficient C14 hydroxylation results from the unfavorable anti-conformation of the methyl ketone side chain of daunorubicin. We harness these advances for rational strain engineering, leading to an 180% increase in doxorubicin yields and an improved production profile. This study provides singular insights into enzymatic constraints in anthracycline biosynthesis and facilitates cost-effective manufacturing to meet the growing global demand for doxorubicin. Less
Transformation of agro-industrial products into value-added products such as prebiotic oligosaccharides is a key element of the emerging bioeconomy Here we characterized a new GH glucuronoxylanase from Bacillus pumilus BpXyn A for its potential in producing xylooligosaccharides XOS BpXyn A showed tolerance to ethanol and NaCl and released both linear and branched XOS containing MeGlcA at the penultimate nonreducing end residue Its X-ray structure determined at resolution revealed high similarity to other glucuronoxylanases Furthermore BpXyn A achieved higher xylan conversion yields from corn cob and Eucalyptus sawdust than Ruminococcus champanellensisRcXyn A Finally fermentation assays showed that Bifidobacterium adolescentis metabolized neutral ... More
Transformation of agro-industrial products into value-added products, such as prebiotic oligosaccharides, is a key element of the emerging bioeconomy. Here, we characterized a new GH30_8 glucuronoxylanase from Bacillus pumilus (BpXyn30_8A) for its potential in producing xylooligosaccharides (XOS). BpXyn30_8A showed tolerance to ethanol and NaCl and released both linear and branched XOS containing MeGlcA at the penultimate nonreducing end residue. Its X-ray structure, determined at 2.16 Å resolution, revealed high similarity to other glucuronoxylanases. Furthermore, BpXyn30_8A achieved higher xylan conversion yields from corn cob and Eucalyptus sawdust than Ruminococcus champanellensisRcXyn30A. Finally, fermentation assays showed that Bifidobacterium adolescentis metabolized neutral XOS to acetate and lactate, whereas acidic XOS were poorly utilized. These results highlight the potential of BpXyn30_8A as a valuable enzyme for the green transformation of plant biomass into prebiotic oligosaccharides with promising applications in human and animal nutrition, health, and biotechnology. Less
Stable carbon and nitrogen isotope ratios are widely used in the life sciences to investigate diet trophic interactions and metabolic fluxes but conventional isotope ratio mass spectrometry requires milligram-scale samples limiting its applicability to small or rare biological specimens Fourier Transform Isotopic Ratio Mass Spectrometry FT IsoR MS enables amino acid resolved isotope analysis in a proteomics-compatible workflow and has previously been demonstrated at the microgram scale Here we assess the lower sample limit of FT IsoR MS by integrating it with single-cell proteomics style sample preparation Using human HeLa cells cultured in C-glucose enriched and control media we show ... More
Stable carbon and nitrogen isotope ratios are widely used in the life sciences to investigate diet, trophic interactions, and metabolic fluxes, but conventional isotope ratio mass spectrometry requires milligram-scale samples, limiting its applicability to small or rare biological specimens. Fourier Transform Isotopic Ratio Mass Spectrometry (FT IsoR MS) enables amino acid–resolved isotope analysis in a proteomics-compatible workflow and has previously been demonstrated at the microgram scale. Here, we assess the lower sample limit of FT IsoR MS by integrating it with single-cell proteomics–style sample preparation. Using human HeLa cells cultured in 13C-glucose–enriched and control media, we show that reliable relative δ13C measurements can be obtained from as few as 50 cells, corresponding to <10 ng of total protein, with a precision of approximately ±9‰. The observed amino acid–specific labeling patterns are metabolically coherent and consistent with bulk measurements, while smaller cell numbers (≤10 cells) do not yield statistically robust results. These findings establish the practical sensitivity threshold of FT IsoR MS at the low-nanogram level and demonstrate its suitability for isotope-resolved analyses of small cell populations, micro-organoids, and other low-input biological samples, thereby extending stable isotope analysis toward single-cell–scale applications. Less
Mitochondrial crista junctions CJs operate as regulated gateways into the cristae microenvironment whose protein metabolite and ion compositions are finely tuned for mitochondrial function The Mic -Mic complex of the mitochondrial contact site and cristae organizing system MICOS complex was suggested to span across CJs and act as a diffusion barrier but little is known of how its dynamic architecture facilitates this task To address this open question we determined the crystal structure of an amino-terminal dimeric helical bundle of human Mic These and previous structural and biochemical data were harnessed in molecular dynamic MD simulations to develop a dynamic ... More
Mitochondrial crista junctions (CJs) operate as regulated gateways into the cristae microenvironment, whose protein, metabolite, and ion compositions are finely tuned for mitochondrial function. The Mic60-Mic19 complex of the mitochondrial contact site and cristae organizing system (MICOS) complex was suggested to span across CJs and act as a diffusion barrier, but little is known of how its dynamic architecture facilitates this task. To address this open question, we determined the crystal structure of an amino-terminal dimeric helical bundle of human Mic60. These and previous structural and biochemical data were harnessed in molecular dynamic (MD) simulations to develop a dynamic model of the human tetrameric Mic60-Mic19 subcomplex in the CJ environment, to validate its architecture using in organello cross-linking data and to computationally characterize its function as a diffusion barrier. Our integrative structural biology approach enables the functional investigation of flexible, multidomain protein complexes which escape conventional structural biology methods. Less
Natural resistance-associated macrophage proteins Nramps are divalent transition metal transporters found in most organisms typically coupling metal uptake to proton co-transport How this coupling evolved however remains unclear We present structural functional and evolutionary analyses of a clade B Nramp from the gut bacterium Bacteroides fragilis BfraNramp Phylogenetic reconstruction positions clade B as the most basal group of canonical Nramps retaining conserved metal-binding motifs while lacking most residues that form the canonical proton pathway We show that BfraNramp efficiently transports Mn and Cd with high apparent affinity but without proton co-transport or dependence on membrane potential or pH Structures of ... More
Natural resistance-associated macrophage proteins (Nramps) are divalent transition metal transporters found in most organisms, typically coupling metal uptake to proton co-transport. How this coupling evolved, however, remains unclear. We present structural, functional, and evolutionary analyses of a clade B Nramp from the gut bacterium Bacteroides fragilis (BfraNramp). Phylogenetic reconstruction positions clade B as the most basal group of canonical Nramps, retaining conserved metal-binding motifs while lacking most residues that form the canonical proton pathway. We show that BfraNramp efficiently transports Mn²⁺ and Cd²⁺ with high apparent affinity but without proton co-transport or dependence on membrane potential or pH. Structures of metal-free and Mn²⁺-bound BfraNramp reveal an inward-open conformation and a distinct metal coordination geometry involving a conserved glutamate on transmembrane helix 3. Together, these results identify clade B Nramps as proton-independent transition metal uniporters and suggest that proton coupling emerged later in Nramp evolution, following establishment of the metal-binding site. Less
The recent discovery of the isonitrile biosynthetic enzyme ScoE expanded the catalytic repertoire of the Fe II KG-dependent dioxygenase enzyme family ScoE synthesizes an isonitrile functional group from a glycyl-fatty acid adduct with both the isonitrile nitrogen and carbon atoms coming from the glycyl moiety This challenging chemistry cannot be performed in a single step Instead the mechanism appears to require two half reactions each involving KG cleavage to generate a highly reactive iron-oxygen species Here we report sixteen crystal structures that provide snapshots along the reaction trajectory of Rv a ScoE homolog from Mycobacterium tuberculosis These structures which are ... More
The recent discovery of the isonitrile biosynthetic enzyme ScoE expanded the catalytic repertoire of the Fe(II)/αKG-dependent dioxygenase enzyme family. ScoE synthesizes an isonitrile functional group from a glycyl-fatty acid adduct, with both the isonitrile nitrogen and carbon atoms coming from the glycyl moiety. This challenging chemistry cannot be performed in a single step. Instead, the mechanism appears to require two half reactions, each involving αKG cleavage to generate a highly reactive iron-oxygen species. Here, we report sixteen crystal structures that provide snapshots along the reaction trajectory of Rv0097, a ScoE homolog from Mycobacterium tuberculosis. These structures, which are both of wild-type and Rv0097 variants, include a substrate 3-((carboxymethyl)amino)decanoic acid (CADA)-bound structure, an αKG-bound structure, and a structure with both CADA and αKG bound. These structural data reveal how Rv0097 employs conformational rearrangements to protect the unstable CADA-reaction intermediate that is formed in the first half reaction while swapping out αKG cleavage products for a second molecule of αKG. Additionally, these structures, together with data from site-directed mutagenesis, provide insight into Rv0097’s preference for substrates with long alkyl chains, potentially facilitating efforts to re-engineer ScoE/Rv0097 to synthesize isonitrile functional groups on a wider range of small molecules. Less
Functional testing of cytotoxic lymphocytes is essential for research and quality control QC but most assays require freshly prepared target cells and extensive handling A ready-to-thaw no-wash flow cytometry based cytotoxicity assay was developed using pre-labeled K targets cryopreserved in STEM-CELLBANKER EX SCB as suitably sized aliquots SCB tolerability was evaluated in K NK- and primary natural killer NK cells post-cryopreservation label stability of CellTrace Violet CTV and carboxyfluorescein succinimidyl ester CFSE was assessed freezing and thawing conditions were optimized and wash versus no-wash workflows were compared using viability-based and absolute-count readouts across effector-to-target E T ratios with NK donors ... More
Functional testing of cytotoxic lymphocytes is essential for research and quality control (QC), but most assays require freshly prepared target cells and extensive handling. A ready-to-thaw, no-wash, flow cytometry–based cytotoxicity assay was developed using pre-labeled K562 targets cryopreserved in STEM-CELLBANKER® EX (SCB) as suitably sized aliquots. SCB tolerability was evaluated in K562, NK-92, and primary natural killer (NK) cells; post-cryopreservation label stability of CellTrace™ Violet (CTV) and carboxyfluorescein succinimidyl ester (CFSE) was assessed; freezing and thawing conditions were optimized; and wash versus no-wash workflows were compared using viability-based and absolute-count readouts, across effector-to-target (E:T) ratios with NK donors and NK-92 cells. Effector viability remained high at SCB concentrations up to 10%, and 5% SCB was selected for assay design. After cryopreservation, CTV labeling remained stable over the tested storage period, whereas CFSE showed substantial signal loss. Warm-medium thawing performed comparably to water-bath thawing, and the consolidated protocol (SCB plus fetal calf serum and thermal buffering) maintained high post-thaw target viability and recovery. In killing assays, lysis increased with increasing E:T ratios; omission of the post-thaw wash had minimal impact, and 5% SCB did not impair cytotoxic function. This ready-to-thaw workflow reduces hands-on time and sample manipulation, while improving standardization for reproducible results and enabling high-throughput functional testing and QC. Less
TIR Toll interleukin- receptor domains are found in proteins involved in immunity pathways in organisms ranging from humans and plant to bacteria Bacterial TIR domain-containing proteins have been shown to contribute to pathogenicity and anti-viral activity of bacteria During bacterial infection some TIR domain-containing proteins act as virulence factors to inhibit immune responses by interfering with Toll-like receptor signalling Other bacterial TIR domain-containing proteins are involved in bacterial anti-viral defence Many of TIR domain-containing proteins have been shown to have NAD cleavage activity and relevant to host cell death and bacterial anti-phage defence system In addition some TIR domain-containing proteins ... More
TIR (Toll/interleukin-1 receptor) domains are found in proteins involved in immunity pathways in organisms ranging from humans and plant to bacteria. Bacterial TIR domain-containing proteins have been shown to contribute to pathogenicity and anti-viral activity of bacteria. During bacterial infection, some TIR domain-containing proteins act as virulence factors to inhibit immune responses by interfering with Toll-like receptor signalling. Other bacterial TIR domain-containing proteins are involved in bacterial anti-viral defence. Many of TIR domain-containing proteins have been shown to have NAD+ cleavage activity and relevant to host cell death and bacterial anti-phage defence system. In addition, some TIR domain-containing proteins have been reported that has DNA binding activity. Here, we report our studies on two bacterial TIR domain-containing proteins: AbTir and PumA. AbTir (Acinetobacter baumannii TIR domain-containing) is one of the few bacterial proteins that has been reported to produce a variant of cyclic ADPR (ADP ribose) after NAD+ cleavage. Previous study in our lab determined the crystal structure of AbTir TIR domain in its monomeric form and the chemical structure of the cyclic ADPR it produces (termed 2’cADPR). However, we could not find the significant NAD+ binding pocked in the AbTirTIR crystal structure. PumA is a TIR domain-containing protein from the multi-drug resistant pathogen Pseudomonas aeruginosa PA7 is essential for its virulence. Study shows that PumA can block host’s immune signalling pathway
In Chapter 2, we demonstrated that PumA, like AbTir, has NAD⁺ cleavage activity and forms filaments upon 3AD binding. We used nanobodies to stabilize PumA and successfully obtained several PumA:nanobody complex crystals. NADase assays showed that some nanobodies significantly inhibit its enzymatic activity, offering potential inhibitory tools.
In Chapter 3, we extended the structural analysis of PumA. We solved the crystal structure of a PumA mutant and characterized several nanobody-bound complexes. Cryo-EM and MicroED efforts revealed filament formation in the presence of 3AD, but bundling limited resolution. Nanobodies again showed inhibitory effects on NADase activity.
In Chapter 4, we investigated DNA binding by bacterial TIR proteins. We found that AbTir lacks DNA-binding activity, while PumA and its homologs from other pathogens bind DNA and form filaments upon DNA interaction. Cryo-EM confirmed DNA-induced filament formation by PumA, suggesting a role in nucleic acid sensing.
Overall, my project shows bacterial TIR domain-containing proteins assemblies in bacterial virulence and antiviral defense, and to identify potential small-molecule inhibitors targeting these mechanisms. Less
In Chapter 2, we demonstrated that PumA, like AbTir, has NAD⁺ cleavage activity and forms filaments upon 3AD binding. We used nanobodies to stabilize PumA and successfully obtained several PumA:nanobody complex crystals. NADase assays showed that some nanobodies significantly inhibit its enzymatic activity, offering potential inhibitory tools.
In Chapter 3, we extended the structural analysis of PumA. We solved the crystal structure of a PumA mutant and characterized several nanobody-bound complexes. Cryo-EM and MicroED efforts revealed filament formation in the presence of 3AD, but bundling limited resolution. Nanobodies again showed inhibitory effects on NADase activity.
In Chapter 4, we investigated DNA binding by bacterial TIR proteins. We found that AbTir lacks DNA-binding activity, while PumA and its homologs from other pathogens bind DNA and form filaments upon DNA interaction. Cryo-EM confirmed DNA-induced filament formation by PumA, suggesting a role in nucleic acid sensing.
Overall, my project shows bacterial TIR domain-containing proteins assemblies in bacterial virulence and antiviral defense, and to identify potential small-molecule inhibitors targeting these mechanisms. Less
Insulin resistance drives cardiometabolic disease yet its molecular signatures and tissue origins remain incompletely characterized and scalable assessment methods are lacking Here we apply Multi-Workflow Proteomics on plasma from individuals spanning the metabolic spectrum defined by hyperinsulinemic euglycemic clamp derived insulin sensitivity We identify proteins associated with insulin sensitivity revealing contributions from liver adipose tissue and immune cells alongside underappreciated roles for brain and heart An exercise intervention demonstrated these signatures are modifiable We developed a model combining proteins including IGFBP LEP GDF PON and LDLR with clinical variables sex HbA c TG HDL ratio that estimates hyperinsulinemic euglycemic clamp-derived ... More
Insulin resistance drives cardiometabolic disease, yet its molecular signatures and tissue origins remain incompletely characterized, and scalable assessment methods are lacking. Here, we apply Multi-Workflow Proteomics on plasma from 161 individuals spanning the metabolic spectrum defined by hyperinsulinemic–euglycemic clamp–derived insulin sensitivity. We identify 488 proteins associated with insulin sensitivity, revealing contributions from liver, adipose tissue, and immune cells alongside underappreciated roles for brain and heart. An exercise intervention demonstrated these signatures are modifiable. We developed a model combining 13 proteins, including IGFBP1, LEP, GDF15, PON3, and LDLR, with clinical variables (sex, HbA1c, TG/HDL ratio) that estimates hyperinsulinemic–euglycemic clamp-derived insulin sensitivity (R² = 0.73). Applied to ~20,000 UK Biobank participants, estimated insulin sensitivity outperformed TG/HDL in predicting type 2 diabetes (c-index 0.86 vs. 0.71) and other cardiometabolic outcomes, including obesity, cardiovascular disease, and chronic kidney disease. This proteomic atlas enables scalable insulin resistance assessment and precision risk stratification. Less
Liver-enriched antimicrobial peptide LEAP can act as a natural antagonist or inverse agonist of the growth hormone secretagogue receptor also known as the ghrelin receptor In our previous studies palm-LEAP a truncated palmitoylated analogue of LEAP proved highly stable and exerted an acute anorexigenic effect Ghrelin the endogenous agonist of the ghrelin receptor and the anorexigenic hormone leptin have opposing effects on appetite We hypothesized that leptin supplementation combined with long-term antagonism of the ghrelin receptor using palm-LEAP might have a beneficial and potentially additive effect on obesity-related metabolic stress in leptin-deficient ob ob mice influencing diabetes liver steatosis impaired ... More
Liver-enriched antimicrobial peptide 2 (LEAP2) can act as a natural antagonist or inverse agonist of the growth hormone secretagogue receptor, also known as the ghrelin receptor. In our previous studies, palm-LEAP2(1–14), a truncated palmitoylated analogue of LEAP2, proved highly stable and exerted an acute anorexigenic effect. Ghrelin, the endogenous agonist of the ghrelin receptor, and the anorexigenic hormone leptin have opposing effects on appetite. We hypothesized that leptin supplementation combined with long-term antagonism of the ghrelin receptor using palm-LEAP2(1–14) might have a beneficial and potentially additive effect on obesity-related metabolic stress in leptin-deficient ob/ob mice, influencing diabetes, liver steatosis, impaired locomotor activity, and hypothermia.
Here, we demonstrated a clear additive effect of combined leptin and palm-LEAP2(1–14) treatment, which increased locomotor activity, reduced plasma cholesterol, liver steatosis, and mRNA expression of the metabolic stress marker Fgf21, and upregulated hypothalamic Pomc gene expression – outcomes not achieved by either treatment alone. Additionally, leptin, palm-LEAP2(1–14), and both treatments combined each reduced cumulative food intake and circulating FGF21 levels. Only leptin reduced body weight, elevated rectal temperature, increased Ucp1 and Pgc1 mRNA expression in brown adipose tissue, and attenuated hyperinsulinemia, indicating that the weight-reducing and antidiabetic effects were attributable to leptin – not palm-LEAP2(1–14). Liver metabolic stress was further alleviated by decreases in plasma FGF21 and hepatic expression of the lipogenic enzymes.
Our study demonstrated the beneficial effects of palm-LEAP2(1–14) on obesity-induced metabolic stress, which were further attenuated when palm-LEAP2(1–14) was coadministered with leptin in ob/ob mice. Less
Here, we demonstrated a clear additive effect of combined leptin and palm-LEAP2(1–14) treatment, which increased locomotor activity, reduced plasma cholesterol, liver steatosis, and mRNA expression of the metabolic stress marker Fgf21, and upregulated hypothalamic Pomc gene expression – outcomes not achieved by either treatment alone. Additionally, leptin, palm-LEAP2(1–14), and both treatments combined each reduced cumulative food intake and circulating FGF21 levels. Only leptin reduced body weight, elevated rectal temperature, increased Ucp1 and Pgc1 mRNA expression in brown adipose tissue, and attenuated hyperinsulinemia, indicating that the weight-reducing and antidiabetic effects were attributable to leptin – not palm-LEAP2(1–14). Liver metabolic stress was further alleviated by decreases in plasma FGF21 and hepatic expression of the lipogenic enzymes.
Our study demonstrated the beneficial effects of palm-LEAP2(1–14) on obesity-induced metabolic stress, which were further attenuated when palm-LEAP2(1–14) was coadministered with leptin in ob/ob mice. Less
Quantitative proteomics relies on accurate selection of fragment ions for quantification yet most current algorithms apply simple strategies such as median intensity or single quality filters Modern data-independent acquisition DIA searches generate rich features such as fragment ion correlations retention time and many others that could be leveraged to assess fragment quality We introduce QuantSelect a novel strategy to select optimal fragments by systematically integrating these features via self-supervised deep learning QuantSelect uses a regularized weighted-variance loss on intensity traces normalized via our directLFQ algorithm This allows learning a fragment quality score without ground truth labels enabling on-the-fly training on ... More
Quantitative proteomics relies on accurate selection of fragment ions for quantification, yet most current algorithms apply simple strategies such as median intensity or single quality filters. Modern data-independent acquisition (DIA) searches generate rich features such as fragment ion correlations, retention time and many others that could be leveraged to assess fragment quality. We introduce QuantSelect, a novel strategy to select optimal fragments by systematically integrating these features via self-supervised deep learning. QuantSelect uses a regularized, weighted-variance loss on intensity traces normalized via our directLFQ algorithm. This allows learning a fragment quality score without ground truth labels, enabling on-the-fly training on label-free DIA datasets. Integrated within our alphaDIA pipeline, QuantSelect significantly improves quantitative accuracy and in some cases substantially corrects protein intensity estimation. Sensitivity in differential expression improved by 68% in a mixed-species benchmarking dataset and by 18% in single-cell data. QuantSelect provides a practical framework for data-driven fragment selection that improves accuracy, precision and downstream inference in DIA proteomics. Less
The ToxRS system is a member of a two-protein transmembrane transcriptional regulator family of proteins that act as critical environmental stress sensors and regulate virulence gene expression in some bacterial pathogens These systems are thought to operate by sensing environmental stimuli and transmitting signals through periplasmic domains to activate DNA-binding transcription factors In Vibrio parahaemolyticus and Vibrio cholerae the ToxRS system regulates virulence factors responsible for severe gastrointestinal symptoms in humans ToxS has been shown to modulate the activity of its binding partner ToxR by binding bile salts antimicrobial cholesterol metabolites secreted into the human gut However the molecular mechanism ... More
The ToxRS system is a member of a two-protein transmembrane transcriptional regulator family of proteins that act as critical environmental stress sensors and regulate virulence gene expression in some bacterial pathogens. These systems are thought to operate by sensing environmental stimuli and transmitting signals through periplasmic domains to activate DNA-binding transcription factors. In Vibrio parahaemolyticus and Vibrio cholerae, the ToxRS system regulates virulence factors responsible for severe gastrointestinal symptoms in humans. ToxS has been shown to modulate the activity of its binding partner ToxR by binding bile salts, antimicrobial cholesterol metabolites secreted into the human gut. However, the molecular mechanism underlying this regulation is unclear. Here, we present the crystal structures of the V. parahaemolyticus ToxS periplasmic domain (ToxSp) with and without the bile salt glycocholate. ToxSp forms an 8-stranded broken β-barrel with a central α-helix and is structurally homologous to a group of chaperone proteins. Notably, the glycocholate-bound ToxSp structure forms a strand-swapped homodimer containing three bound glycocholate molecules. Modeling two ToxR periplasmic domains in complex with the glycocholate-bound ToxSp dimer provides a structure-based model for bile salt activation of the ToxRS system and suggests that ToxRS homologs may be regulated in a similar manner across diverse bacterial species. Less
Iron homeostasis in various pathogenic bacteria is regulated by bacterioferritins Bfr which function to store Fe and release Fe as needed for metabolic processes The Bfr structure consists of kDa subunits in which dimer pairs bind a heme molecule and are assembled into a highly symmetrical -meric spherical structure with an internal core diameter of approximately Release of iron is facilitated by the binding of a kDa Fe- S ferredoxin Bfd to specific sites on the surface of Bfr which transfers electrons to the core thereby reducing the stored Fe to Fe for mobilization The crystal structures of Bfr from ... More
Iron homeostasis in various pathogenic bacteria is regulated by bacterioferritins (Bfr) which function to store Fe3+ and release Fe2+ as needed for metabolic processes. The Bfr structure consists of 18 kDa subunits in which dimer pairs bind a heme molecule and are assembled into a highly symmetrical 24-meric spherical structure with an internal core diameter of approximately 80 Å. Release of iron is facilitated by the binding of a 7 kDa [2Fe-2S] ferredoxin (Bfd) to specific sites on the surface of Bfr which transfers electrons to the core thereby reducing the stored Fe3+ to Fe2+ for mobilization. The crystal structures of Bfr from Brucella abortus (Ba) in the apo and iron bound forms are presented and compared with those from Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa). Additionally, models of the Bfr:Bfd complexes for Ba and Ab are provided and compared with the Pa complex. Finally, compounds known to target the Bfr:Bfd interaction in Pa were docked to the Ba and Ab structures which provided insight regarding the potential binding mode and inhibitory mechanism. Less
Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing chromatography and MS acquisition Here we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients and samples per day along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer We found that tissue type was as important as gradient length and sample amount in determining proteome coverage Moreover the benefit of increased tissue sampling was gradient- and dynamic range-dependent Analyzing mouse liver a high dynamic range tissue over tenfold more tissue sampling led to only ... More
Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ~30% gain in protein identification for short gradients (120 SPD and 80 SPD). However, even the lowest tested tissue amount (0.04 nL, 40,000 µm3) yielded 3,200 reproducibly quantified proteins for the 120 SPD method. Longer gradients (40 SPD and 20 SPD) instead significantly benefited from more tissue sampling, quantifying over 7,500 proteins from 0.5 nL of tonsil T-cell niches. Finally, we applied our workflow to a rare squamous cell carcinoma of the oral cavity, uncovering disease-associated pathways and region-specific protein level changes. Our study demonstrates that more than 100 high-quality spatial tissue proteomes can be prepared and acquired daily, laying a strong foundation for cohort-size spatial tissue proteomics in translational research. Less
Obtaining high-quality single crystals containing charged molecules from aqueous solutions can sometimes be challenging In this publication we studied the crystallization of polycationic porphyrins Crystals of three polycationic porphyrins -tetrakis -methylpyridin- -ium- -yl porphyrin - -cyanophenyl - -tris -methylpyridin- -ium- -yl porphyrin and - -carboxy phenyl - -tris -methylpyridin- -ium- -yl porphyrin were obtained with different anions We started initially with nano-crystallization' screening in order to identify promising combinations of the cations with suitable anions followed by optimizing the ratio of anions to cations Both steps yielded crystals leading to the determination of one porphyrin-containing crystal structure from each step ... More
Obtaining high-quality single crystals containing charged molecules from aqueous solutions can sometimes be challenging. In this publication, we studied the crystallization of polycationic porphyrins. Crystals of three polycationic porphyrins, [5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)porphyrin, 5-(4-cyanophenyl)-10,15,20-tris(1-methylpyridin-1-ium-4-yl)porphyrin and 5-(4-carboxyphenyl)-10,15,20-tris(1-methylpyridin-1-ium-4-yl)porphyrin], were obtained with different anions. We started initially with `nano-crystallization' screening in order to identify promising combinations of the cations with suitable anions, followed by optimizing the ratio of anions to cations. Both steps yielded crystals, leading to the determination of one porphyrin-containing crystal structure from each step. In the next step, five different organic solvents were trialled as additives in an aqueous hanging-drop crystallization setup, which led to the determination of three more crystal structures. It was shown that it was possible to improve the quality of the crystals without the organic additive being incorporated into the crystal structure. Finally, crystals of one porphyrin salt were obtained by gel crystallization. These crystals were higher quality than the crystal grown by vapour diffusion, leading to a high-quality and higher-resolution X-ray structure determination. This is the first porphyrin structure to be determined from a crystal grown by gel crystallizaton. Less
UreE is a nickel chaperone required for the safe and efficient delivery of nickel to the active site of the metalloenzyme urease a key virulence factor of the urinary tract pathogen Proteus mirabilis We investigated the structural features of P mirabilis UreE using protein X-ray crystallography and its nickel-binding capacity by inductively coupled plasma-mass spectrometry Here we report a crystal structure of homodimeric PmUreE and show it has capacity to bind five nickel ions per dimer Truncation of the histidine-rich C-terminus reduced nickel binding capacity by two nickel ions per dimer and comparison with homologous UreE structures allowed the assignment ... More
UreE is a nickel chaperone required for the safe and efficient delivery of nickel to the active site of the metalloenzyme, urease; a key virulence factor of the urinary tract pathogen, Proteus mirabilis. We investigated the structural features of P. mirabilis UreE using protein X-ray crystallography and its nickel-binding capacity by inductively coupled plasma-mass spectrometry. Here, we report a 2.0 Å crystal structure of homodimeric PmUreE and show it has capacity to bind five nickel ions per dimer. Truncation of the histidine-rich C-terminus reduced nickel binding capacity by two nickel ions per dimer and comparison with homologous UreE structures allowed the assignment of putative nickel binding sites within the PmUreE structure. These findings increase our understanding of how PmUreE binds nickel and ultimately prevents this toxic metal from causing significant cellular damage in P. mirabilis. Less
To ensure safe long-term use topical products should be investigated to understand how they interact with the resident skin microbiota to mitigate potential risk Sunscreens are essential for protecting skin from UV damage but their effects on skin-resident microbes have not been well characterized We examined the impact of two sunscreen formulations containing titanium dioxide or zinc oxide on both cultured skin bacteria and the skin microbiomes of human volunteers No loss of viability was observed after a h exposure to either sunscreen in cultures of Staphylococcus epidermidis Staphylococcus capitis Staphylococcus hominis Micrococcus luteus and Corynebacterium tuberculostearicum The effects of ... More
To ensure safe, long-term use, topical products should be investigated to understand how they interact with the resident skin microbiota to mitigate potential risk. Sunscreens are essential for protecting skin from UV damage, but their effects on skin-resident microbes have not been well characterized. We examined the impact of two sunscreen formulations (containing titanium dioxide or zinc oxide) on both cultured skin bacteria and the skin microbiomes of human volunteers. No loss of viability was observed after a 2 h exposure to either sunscreen in cultures of Staphylococcus epidermidis, Staphylococcus capitis, Staphylococcus hominis, Micrococcus luteus, and Corynebacterium tuberculostearicum. The effects of the sunscreens were then studied across the skin microbiomes of 20 human participants. Skin swabs were collected before application and at 1, 6, and 24 h afterward. DNA was extracted and sequenced at the 16S rRNA V4 region, and sequences were denoised and taxonomically assigned using the nf-core/ampliseq pipeline. Across all time points, alpha diversity (Shannon index, Friedman test) and beta diversity (permutational multivariate analysis of variance) remained stable, with no significant differences in beta dispersion. Differential abundance analysis revealed minor fluctuations in some low-abundance genera, identified as likely transient due to their low prevalence, but overall resident community composition was not significantly altered. These findings suggest that short-term sunscreen application does not disrupt the skin microbiome, supporting their safe use from a microbial standpoint. Outcomes from both in vitro and in vivo experimentation point to the compositional resilience of the skin microbiota to sunscreens. Less
Human T-cell Leukemia Virus type HTLV- is an untreatable retrovirus that causes lethal malignancies and degenerative inflammatory conditions Effective treatments have been delayed by substantial gaps in our knowledge of the fundamental virology especially when compared to the closely related virus HIV A recently developed and highly effective anti-HIV strategy is to target the virus with drugs that interfere with capsid integrity and interactions with the host Importantly the first in class anti-capsid drug approved lenacapavir can provide long-acting pre-exposure prophylaxis Such a property would provide a means to prevent the transmission of HTLV- but its capsid has not previously ... More
Human T-cell Leukemia Virus type 1 (HTLV-1) is an untreatable retrovirus that causes lethal malignancies and degenerative inflammatory conditions. Effective treatments have been delayed by substantial gaps in our knowledge of the fundamental virology, especially when compared to the closely related virus, HIV. A recently developed and highly effective anti-HIV strategy is to target the virus with drugs that interfere with capsid integrity and interactions with the host. Importantly, the first in class anti-capsid drug approved, lenacapavir, can provide long-acting pre-exposure prophylaxis. Such a property would provide a means to prevent the transmission of HTLV-1, but its capsid has not previously been considered as a drug target. Here we describe the first high-resolution crystal structures of the HTLV-1 capsid protein, define essential lattice interfaces, and identify a previously unknown ligand-binding pocket. We show that this pocket is essential for virus infectivity, providing a potential target for future anti-capsid drug development. Less
Prophages dormant bacteriophage genomes integrated within the bacterial chromosome play pivotal roles in shaping microbial communities when awakened Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers such as mitomycin C and ciprofloxacin which trigger the bacterial SOS response This study employed high-throughput screening of compounds to identify novel prophage inducers using model lambdoid prophage HK We identified multiple new inducers across diverse pharmacological classes including dietary supplements and therapeutics Despite the variety in compounds all acted through SOS-dependent pathways However bleomycin an antineoplastic antibiotic demonstrated broad-spectrum and potent prophage induction exceeding ... More
Prophages, dormant bacteriophage genomes integrated within the bacterial chromosome, play pivotal roles in shaping microbial communities when awakened. Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers, such as mitomycin C and ciprofloxacin, which trigger the bacterial SOS response. This study employed high-throughput screening of 3,921 compounds to identify novel prophage inducers using model lambdoid prophage HK97. We identified multiple new inducers across diverse pharmacological classes, including dietary supplements and therapeutics. Despite the variety in compounds, all acted through SOS-dependent pathways. However, bleomycin, an antineoplastic antibiotic, demonstrated broad-spectrum and potent prophage induction exceeding standard inducers, with activity validated across multiple phage-host pairings. These findings expand the repertoire of prophage inducers into commonly ingested xenobiotics and introduce bleomycin as a powerful, cost-effective tool for prophage research.
Around 75% of bacteria carry within them dormant viruses (prophages), which can awaken when the bacterium is stressed, killing the bacterium. Historically, this has been done using DNA-damaging antibiotics, but increasingly, more such signals have been discovered. Here, through a high-throughput screen, we identify phage-waking activity in several commonly consumed compounds, such as the SSRI Prozac, as well as a new DNA-damaging agent that is much more effective in waking phages than the previous gold standard. Less
Around 75% of bacteria carry within them dormant viruses (prophages), which can awaken when the bacterium is stressed, killing the bacterium. Historically, this has been done using DNA-damaging antibiotics, but increasingly, more such signals have been discovered. Here, through a high-throughput screen, we identify phage-waking activity in several commonly consumed compounds, such as the SSRI Prozac, as well as a new DNA-damaging agent that is much more effective in waking phages than the previous gold standard. Less
Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy StayGold a novel dimeric GFP recently monomerized through sequence engineering addresses this challenge with its high photostability There is now a focus on producing different colored StayGold derivatives to facilitate concurrent tagging of multiple targets The unnatural amino acid -aminotyrosine has previously been shown to redshift superfolder GFP upon incorporation into its chromophore via genetic code expansion Here we apply the same strategy to redshift StayGold through substitution of tyrosine- with -aminotyrosine The resultant red fluorescent protein StayRose shows an excitation wavelength maximum of nm and an ... More
Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric GFP recently monomerized through sequence engineering, addresses this challenge with its high photostability. There is now a focus on producing different colored StayGold derivatives to facilitate concurrent tagging of multiple targets. The unnatural amino acid 3-aminotyrosine has previously been shown to redshift superfolder GFP upon incorporation into its chromophore via genetic code expansion. Here, we apply the same strategy to redshift StayGold through substitution of tyrosine-58 with 3-aminotyrosine. The resultant red fluorescent protein, StayRose, shows an excitation wavelength maximum of 530 nm and an emission wavelength maximum of 588 nm. Importantly, the monomeric mStayRose retains the favorable photostability in vivo in Escherichia coli and zebrafish embryos. A high-resolution crystal structure of StayRose confirms the modified structure of the amino chromophore within an unperturbed 3D fold. Although reliant on genetic code expansion, StayRose provides an important step toward developing redshifted StayGold derivatives. Less
Heliorhodopsins HeRs the third rhodopsin family are characterized by inverted membrane topology and confinement to monoderm organisms yet their biological meaning has so far remained a mystery We report the first crystal structure of a eukaryotic HeR supported by structural modeling and comparative analyses across all domains of life A conserved carotenoid-binding site reminiscent of secondary antennae in some microbial rhodopsins is identified and found to be common among HeRs We show that inverted topology allows recruitment of exogenous xanthophylls inaccessible in diderm cells explaining HeRs distinctive orientation and distribution These findings reveal a previously unrecognized light-harvesting mechanism of HeRs ... More
Heliorhodopsins (HeRs), the third rhodopsin family, are characterized by inverted membrane topology and confinement to monoderm organisms, yet their biological meaning has so far remained a mystery. We report the first crystal structure of a eukaryotic HeR, supported by structural modeling and comparative analyses across all domains of life. A conserved carotenoid-binding site, reminiscent of secondary antennae in some microbial rhodopsins, is identified and found to be common among HeRs. We show that inverted topology allows recruitment of exogenous xanthophylls, inaccessible in diderm cells, explaining HeRs’ distinctive orientation and distribution. These findings reveal a previously unrecognized light-harvesting mechanism of HeRs, expand the known repertoire of microbial phototrophy, and suggest evolutionary constraints linking membrane topology to environmental metabolite accessibility. Less
The composition of the primordial genetic material remains uncertain Studies of duplex structure and stability and of nonenzymatic template copying chemistry provide insight into the viability of potentially primordial genetic polymers Recent work suggests that - deoxyribo-purine nucleotides may have been generated together with ribonucleotides on the early Earth Since DNA RNA duplexes are known to be less stable than RNA RNA duplexes we have examined the impact of dA dI and dG substitutions on RNA structure and nonenzymatic template copying We find that single -deoxyribo-purine substitutions reduce RNA duplex stability as expected Crystallographic studies show that such substitutions lead ... More
The composition of the primordial genetic material remains uncertain. Studies of duplex structure and stability, and of nonenzymatic template copying chemistry, provide insight into the viability of potentially primordial genetic polymers. Recent work suggests that 2′- deoxyribo-purine nucleotides may have been generated together with ribonucleotides on the early Earth. Since DNA/RNA duplexes are known to be less stable than RNA/RNA duplexes, we have examined the impact of dA, dI, and dG substitutions on RNA structure and nonenzymatic template copying. We find that single 2′-deoxyribo-purine substitutions reduce RNA duplex stability, as expected. Crystallographic studies show that such substitutions lead to minimal structural changes but point to diminished solvation as a likely reason for duplex destabilization. Kinetic studies show that dI and dG substrates exhibit slightly weaker template binding and slower rates of template-directed primer extension than the corresponding ribo-purine substrates. In contrast, dA substrates exhibit much slower reaction kinetics but higher template affinity than rA substrates. Our results suggest that a mixed RNA/DNA primordial genetic polymer would have suffered from moderately slower rates of template copying, but that this could have been offset by an advantage due to more facile strand separation or exchange. Less
C domains are ubiquitous membrane-binding modules of residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification The genome of Trichomonas vaginalis the most common non-viral sexually transmitted human pathogen encodes eight genes that contain a N-terminal C module linked to a XYPPX-repeat domain of more than four XYPPX repeats C -XYPPX While the function of the XYPPX-repeat domain remains unknown its multiple association with C domains in T vaginalis suggests it is important The C domain from one of these C -XYPPX-repeat proteins Tv-C - was structurally and physically characterized using X-ray crystallography ... More
C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. The C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca2+ showed that Tv-C2-1 bound two Ca2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with Kds of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τc, in the apo (11.1 ns) and Ca2+-bound (9.2 ns) state suggests the protein becomes more compact upon Ca2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15N heteronuclear steady-state {1H}-15N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted. Less
Spermine a pivotal player in biomolecular condensation and diverse cellular processes has emerged as a focus of investigation in aging neurodegeneration and other diseases Despite its significance the mechanistic details of spermine remain incompletely understood Here we describe the distinct modulation by spermine on Alzheimer s Tau and Parkinson s -synuclein elucidating their condensation behaviors in vitro and in vivo Using biophysical techniques including time-resolved SAXS and NMR we trace electrostatically driven transitions from atomic-scale conformational changes to mesoscopic structures Notably spermine extends lifespan ameliorates movement deficits and restores mitochondrial function in C elegans models expressing Tau and -synuclein Acting ... More
Spermine, a pivotal player in biomolecular condensation and diverse cellular processes, has emerged as a focus of investigation in aging, neurodegeneration, and other diseases. Despite its significance, the mechanistic details of spermine remain incompletely understood. Here, we describe the distinct modulation by spermine on Alzheimer’s Tau and Parkinson’s α-synuclein, elucidating their condensation behaviors in vitro and in vivo. Using biophysical techniques including time-resolved SAXS and NMR, we trace electrostatically driven transitions from atomic-scale conformational changes to mesoscopic structures. Notably, spermine extends lifespan, ameliorates movement deficits, and restores mitochondrial function in C. elegans models expressing Tau and α-synuclein. Acting as a molecular glue, spermine orchestrates in vivo condensation of α-synuclein, influences condensate mobility, and promotes degradation via autophagy, specifically through autophagosome expansion. This study unveils the interplay between spermine, protein condensation, and functional outcomes, advancing our understanding of neurodegenerative diseases and paving the way for therapeutic development. Less
Plasma and cerebrospinal fluid are complementary sources of biomarkers for neurodegenerative diseases The wide dynamic range of protein abundances particularly in plasma hampers detection of low-abundance proteins Depletion of high-abundance proteins and efficient enzymatic digestion can improve proteome coverage but must be carefully optimized for reproducibility throughput and cost-efficiency for use in large-scale clinical proteomic studies We developed a scalable sample preparation workflow for plasma and cerebrospinal fluid CSF that integrates depletion of high-abundance proteins optimized digestion using Lys-C and trypsin and compatibility with both label-free and tandem mass tag TMTpro -based quantification We systematically evaluated protein depletion and enzyme ... More
Plasma and cerebrospinal fluid are complementary sources of biomarkers for
neurodegenerative diseases. The wide dynamic range of protein abundances, particularly in
plasma, hampers detection of low-abundance proteins. Depletion of high-abundance proteins
and efficient enzymatic digestion can improve proteome coverage but must be carefully
optimized for reproducibility, throughput, and cost-efficiency for use in large-scale clinical
proteomic studies.
We developed a scalable sample preparation workflow for plasma and cerebrospinal fluid (CSF)
that integrates depletion of high-abundance proteins, optimized digestion using Lys-C and
trypsin, and compatibility with both label-free and tandem mass tag (TMTpro)-based
quantification. We systematically evaluated protein depletion and enzyme digestion conditions,
and the effect of deoxycholate on digestion, monitoring the number of detectable proteins and
the quantitation precision. Less
neurodegenerative diseases. The wide dynamic range of protein abundances, particularly in
plasma, hampers detection of low-abundance proteins. Depletion of high-abundance proteins
and efficient enzymatic digestion can improve proteome coverage but must be carefully
optimized for reproducibility, throughput, and cost-efficiency for use in large-scale clinical
proteomic studies.
We developed a scalable sample preparation workflow for plasma and cerebrospinal fluid (CSF)
that integrates depletion of high-abundance proteins, optimized digestion using Lys-C and
trypsin, and compatibility with both label-free and tandem mass tag (TMTpro)-based
quantification. We systematically evaluated protein depletion and enzyme digestion conditions,
and the effect of deoxycholate on digestion, monitoring the number of detectable proteins and
the quantitation precision. Less
The Maternal-to-Zygotic transition MZT is a reprograming process encompassing zygotic genome activation ZGA and the clearance of maternally-provided mRNAs While some factors regulating MZT have been identified there are thousands of maternal RNAs whose function has not been ascribed yet Here we have performed a proof-of-principle CRISPR-RfxCas d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT Bckdk mRNA knockdown caused epiboly defects ZGA deregulation H K ac reduction and a partial impairment of miR- processing Phospho-proteomic analysis revealed that Phf Baf a a chromatin remodeling factor is ... More
The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation. Less
High-grade serous ovarian cancer HGSOC is a devastating disease that is frequently detected at an advanced and incurable stage Advances in ultrasensitive mass spectrometry-based spatial proteomics have provided a unique opportunity to uncover early molecular events in tumorigenesis and common dysregulated pathways with high therapeutic potential Here we present a comprehensive proteomic analysis of serous tubal intraepithelial carcinoma STIC the HGSOC precursor lesion covering more than proteins from ultralow input archival tissue We discovered that STICs and concurrent invasive carcinomas were indistinguishable at the global proteome level revealing a similar level of phenotypic and molecular heterogeneity Using cell-type resolved tissue ... More
High-grade serous ovarian cancer (HGSOC) is a devastating disease that is frequently detected at an advanced and incurable stage. Advances in ultrasensitive mass spectrometry-based spatial proteomics have provided a unique opportunity to uncover early molecular events in tumorigenesis and common dysregulated pathways with high therapeutic potential. Here, we present a comprehensive proteomic analysis of serous tubal intraepithelial carcinoma (STIC), the HGSOC precursor lesion, covering more than 10,000 proteins from ultralow input archival tissue. We discovered that STICs and concurrent invasive carcinomas were indistinguishable at the global proteome level, revealing a similar level of phenotypic and molecular heterogeneity. Using cell-type resolved tissue proteomics, we revealed strong cell-of-origin signatures preserved in STICs and invasive tumors and identified early dysregulated pathways of therapeutic relevance. These include proliferation and DNA damage repair signatures, as well as onco-metabolic changes, such as increased cholesterol biosynthesis. Finally, we uncovered substantial remodeling of the co-evolving tumor microenvironment, affecting approximately one-third of the stromal proteome, and derived a common signature associated with progressive immunosuppression and ECM restructuring. In summary, our study highlights the power of spatially resolved quantitative proteomics to dissect the molecular underpinnings of early carcinogenesis and provides a rich proteomic resource for future biomarker and drug target discovery. Less
The increase in multidrug-resistant bacteria underscores an urgent need for additional antibiotics Here we integrate small-molecule high-throughput screening with a deep-learning-based virtual screening approach to uncover new antibacterial compounds We screen million small molecules against a sensitized Escherichia coli strain yielding thousands of hits We use these data to train a deep learning model GNEprop to predict antibacterial activity retrospectively validating robustness with respect to out-of-distribution generalization and activity cliff prediction Virtual screening of over billion synthetically accessible compounds identifies potential candidates of which exhibit antibacterial activity on the same strain illustrating a -fold improved hit rate over the high-throughput ... More
The increase in multidrug-resistant bacteria underscores an urgent need for additional antibiotics. Here, we integrate small-molecule high-throughput screening with a deep-learning-based virtual screening approach to uncover new antibacterial compounds. We screen ~2 million small molecules against a sensitized Escherichia coli strain, yielding thousands of hits. We use these data to train a deep learning model, GNEprop, to predict antibacterial activity, retrospectively validating robustness with respect to out-of-distribution generalization and activity cliff prediction. Virtual screening of over 1.4 billion synthetically accessible compounds identifies potential candidates, of which 82 exhibit antibacterial activity on the same strain, illustrating a 90-fold improved hit rate over the high-throughput screening experiment used for training. Many newly identified compounds exhibit high dissimilarity to known antibiotics, potency beyond the training bacterial strain and selectivity. Biological characterization identifies specific, validated targets, indicating promising avenues for further exploration in antibiotic discovery. Less
Abstract Background Recombinant human NELL- rhNELL- is a potent osteogenic protein with therapeutic potential in regenerative medicine A stable formulation is essential to prevent aggregation during production filling storage and clinical use Methodology A four-stage rational formulation strategy was used identify intrinsic aggregation risks of rhNELL- screen polysorbate- and cyclodextrin-based formulations to enhance colloidal and conformational stability test lead candidates under agitation freeze thaw pH shifts and elevated temperature Analytical techniques included PEG challenge differential scanning fluorimetry DSF isothermal chemical denaturation ICD and dynamic light scattering DLS Aggregation was assessed via visible particles VP opalescence subvisible particles SVP Micro Flow ... More
Abstract
Background
Recombinant human NELL-1 (rhNELL-1) is a potent osteogenic protein with therapeutic potential in regenerative medicine. A stable formulation is essential to prevent aggregation during production, filling, storage, and clinical use.
Methodology
A four-stage rational formulation strategy was used: (1) identify intrinsic aggregation risks of rhNELL-1; (2) screen polysorbate- and cyclodextrin-based formulations to enhance colloidal and conformational stability; (3–4) test lead candidates under agitation, freeze/thaw, pH shifts, and elevated temperature. Analytical techniques included PEG challenge, differential scanning fluorimetry (DSF), isothermal chemical denaturation (ICD), and dynamic light scattering (DLS). Aggregation was assessed via visible particles (VP), opalescence, subvisible particles (SVP, Micro Flow Imaging), SDS-PAGE, and ultra-high performance size exclusion chromatography (UP-SEC).
Results
rhNELL-1 was prone to self-association via hydrophobic and electrostatic interactions. Polysorbate 20 (PS20) and hydroxypropyl beta cyclodextrin (HPB-LB-BCD) improved protein stability. PS20 markedly reduced VP and SVP formation. While HPB-LB-BCD alone did not further reduce SVP beyond PS20, it enhanced thermal stress resistance. PS20 was more effective under agitation.
Conclusions
Two lead formulations containing potassium phosphate/Tris buffer, sorbitol, PS20, and HPB-LB-BCD demonstrated strong resistance to aggregation under multiple stresses. PS20 mitigated interfacial stress, while HPB-LB-BCD suppressed solution-phase aggregation, especially at high temperatures. This systematic approach offers a framework for stabilizing other aggregation-prone proteins. Less
Background
Recombinant human NELL-1 (rhNELL-1) is a potent osteogenic protein with therapeutic potential in regenerative medicine. A stable formulation is essential to prevent aggregation during production, filling, storage, and clinical use.
Methodology
A four-stage rational formulation strategy was used: (1) identify intrinsic aggregation risks of rhNELL-1; (2) screen polysorbate- and cyclodextrin-based formulations to enhance colloidal and conformational stability; (3–4) test lead candidates under agitation, freeze/thaw, pH shifts, and elevated temperature. Analytical techniques included PEG challenge, differential scanning fluorimetry (DSF), isothermal chemical denaturation (ICD), and dynamic light scattering (DLS). Aggregation was assessed via visible particles (VP), opalescence, subvisible particles (SVP, Micro Flow Imaging), SDS-PAGE, and ultra-high performance size exclusion chromatography (UP-SEC).
Results
rhNELL-1 was prone to self-association via hydrophobic and electrostatic interactions. Polysorbate 20 (PS20) and hydroxypropyl beta cyclodextrin (HPB-LB-BCD) improved protein stability. PS20 markedly reduced VP and SVP formation. While HPB-LB-BCD alone did not further reduce SVP beyond PS20, it enhanced thermal stress resistance. PS20 was more effective under agitation.
Conclusions
Two lead formulations containing potassium phosphate/Tris buffer, sorbitol, PS20, and HPB-LB-BCD demonstrated strong resistance to aggregation under multiple stresses. PS20 mitigated interfacial stress, while HPB-LB-BCD suppressed solution-phase aggregation, especially at high temperatures. This systematic approach offers a framework for stabilizing other aggregation-prone proteins. Less
Macromolecular crystallography provides mechanistic understanding of biological processes and can be applied in drug design Nowadays the use of robotic systems for crystal growth and diffraction analysis is widespread and high throughput protein-to-structure pipelines for ligand and fragment screening are revolutionizing the field However the identification of crystals is still largely carried out through manual inspection sometimes involving tens of thousands of images which represents a bottleneck in an otherwise highly automated process Here we describe AXIS an AI-based Crystal Identification System combining the DINOv computer vision model state-of-the-art transfer learning and MARCO the largest crystallization dataset available to date ... More
Macromolecular crystallography provides mechanistic understanding of biological processes and can be applied in drug design. Nowadays, the use of robotic systems for crystal growth and diffraction analysis is widespread and high throughput protein-to-structure pipelines for ligand and fragment screening are revolutionizing the field. However, the identification of crystals is still largely carried out through manual inspection, sometimes involving tens of thousands of images, which represents a bottleneck in an otherwise highly automated process. Here we describe AXIS, an AI-based Crystal Identification System combining the DINOv2 computer vision model, state-of-the-art transfer learning and MARCO, the largest crystallization dataset available to date, for automated crystal detection. AXIS can operate both with visible and UV light images and integrates a Lab-In-The-Loop approach combining ML and expert inputs for continuous learning and specialization. AXIS enables automated annotation of large crystallization image datasets with performance and accuracy comparable to that of human experts and the Lab-In-The-Loop approach introduced here enables efficient adaptation to local conditions facilitating widespread application, which has been a major limitation to date. AXIS can help correct human errors in image annotation and removes critical bottlenecks, particularly in the context of extensive crystallization screens or high throughput applications like fragment and ligand screening unlocking the potential for higher levels of automation that are key both in fundamental and translational research. Less
Thrombin is generated from prothrombin through cleavage at two sites by the enzyme prothrombinase composed of factor Xa fXa and fVa The affinity of fXa for fVa is low with assembly and function dependent on phospholipid PL membranes Some snakes have evolved venom versions of fXa that bind to fVa with high affinity and efficiently activate prothrombin in the absence of PL We created a similar high-affinity PL-independent human prothrombinase with mutations to human fXa M The increase in affinity enabled cryogenic electron microscopy cryo-EM structure determination of M -prothrombinase to a resolution of All protein domains were well resolved ... More
Thrombin is generated from prothrombin through cleavage at two sites by the enzyme prothrombinase, composed of factor Xa (fXa) and fVa. The affinity of fXa for fVa is low, with assembly and function dependent on phospholipid (PL) membranes. Some snakes have evolved venom versions of fXa that bind to fVa with high affinity and efficiently activate prothrombin in the absence of PL. We created a similar high-affinity, PL-independent human prothrombinase with 17 mutations to human fXa (M17). The increase in affinity enabled cryogenic electron microscopy (cryo-EM) structure determination of M17-prothrombinase to a resolution of 3.3 Å. All protein domains were well resolved in the map, except for the Gla domain of fXa. The main contacts involve the serine protease and EGF2 domains of fXa and the A2 and A3 domains of fVa, resulting in the burying of a total surface area of 4,900 Å2. The map is of sufficient quality to resolve side chain interactions, including several key M17 mutations. To aid in the placement of the loop Cterminal to the A2 domain (a2-loop), we solved a high-resolution crystal structure of fXa in complex with a synthetic a2 peptide. The acidic a2-loop interacts with the basic heparin binding site of fXa, involving a conserved antiparallel -strand interaction. The M17-prothrombinase structure is compatible with data from biochemical and mutagenesis research and provides important new insights into the assembly and function of the prothrombinase complex. Less
Severe acute respiratory syndrome coronavirus SARS-CoV- continues to threaten global health This underpins the need for novel therapeutics against this virus Nonstructural protein Nsp of SARS-CoV- is a multifunctional protein with an essential role in viral replication As such it presents itself as an attractive target for drug discovery Here we describe two crystallographic fragment-screening campaigns against Nsp one using the established F X-Entry Screen and one using a new chemically and structurally diverse fragment library which we call the KIT library Together hits could be identified from screened fragments which constitutes the highest hit rate reported for Nsp to ... More
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to threaten global health. This underpins the need for novel therapeutics against this virus. Nonstructural protein 1 (Nsp1) of SARS-CoV-2 is a multifunctional protein with an essential role in viral replication. As such, it presents itself as an attractive target for drug discovery. Here, we describe two crystallographic fragment-screening campaigns against Nsp1, one using the established F2X-Entry Screen and one using a new, chemically and structurally diverse fragment library, which we call the KIT library. Together, 21 hits could be identified from 192 screened fragments, which constitutes the highest hit rate reported for Nsp1 to date. Many hits bind to a key functional region and interact with residues involved in cellular mRNA cleavage, ribosome binding and viral RNA recognition. Furthermore, most of the identified fragments share a common binding mode, providing promising starting points for further optimization into drug-like compounds that can disrupt the role of Nsp1 in viral replication. Less
Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic
Current clinical antibiotics are largely broad-spectrum agents that can alter the gut microbiome and promote colonization by Enterobacteriaceae which are often drug resistant This includes adherent-invasive Escherichia coli AIEC particularly in patients with inflammatory bowel disease in which dysbiosis creates a niche for this pathogen to colonize There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics Here we screened bioactive small molecules for antibacterial activity against AIEC and discovered enterololin an antibacterial compound with targeted activity against Enterobacteriaceae species Enterololin could overcome intrinsic and acquired resistance mechanisms in clinical isolates when combined with a subinhibitory concentration ... More
Current clinical antibiotics are largely broad-spectrum agents that can alter the gut microbiome and promote colonization by Enterobacteriaceae, which are often drug resistant. This includes adherent-invasive Escherichia coli (AIEC), particularly in patients with inflammatory bowel disease, in which dysbiosis creates a niche for this pathogen to colonize. There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics. Here we screened 10,747 bioactive small molecules for antibacterial activity against AIEC and discovered enterololin, an antibacterial compound with targeted activity against Enterobacteriaceae species. Enterololin could overcome intrinsic and acquired resistance mechanisms in clinical isolates when combined with a subinhibitory concentration of SPR741, a polymyxin B analogue used here to increase outer membrane permeability in Gram-negative bacteria. Molecular substructure- and deep learning-guided mechanism-of-action investigations revealed that enterololin perturbs lipoprotein trafficking through a mechanism involving the LolCDE complex, laboratory-evolved resistant mutants predominantly mapped to lolC and lolE, with an in vitro frequency of resistance of ~10-8 to 10-7. Enterololin showed low mammalian cytotoxicity (HEK293 half-maximal inhibitory concentration ~100 µg ml-1) and suppressed AIEC infection in mouse models when administered in combination with SPR741, while largely preserving the overall microbiome composition. This study highlights the utility of deep learning methods for predicting molecular interactions and identifies a promising Enterobacteriaceae-specific antibacterial candidate for further development. Less
Antibody-drug conjugates ADCs are a promising therapeutic modality that enables the delivery of cytotoxic drugs to the target cells that express the corresponding antigen However the purification of ADCs while ensuring product safety homogeneity and stability is a challenging task due to their complex and fragile structure Size exclusion chromatography SEC the conventional method for ADC purification is time-consuming as it requires multiple column washes and equilibration steps Moreover subsequent formulation of ADCs typically using dead-end filtration DEF further complicates the production workflow We compared SEC DEF with the Pulse a miniaturized and automated tangential flow filtration system for purification ... More
Antibody-drug conjugates (ADCs) are a promising therapeutic modality that enables the delivery of cytotoxic drugs to the target cells that express the corresponding antigen. However, the purification of ADCs while ensuring product safety, homogeneity, and stability is a challenging task due to their complex and fragile structure. Size exclusion chromatography (SEC), the conventional method for ADC purification, is time-consuming as it requires multiple column washes and equilibration steps. Moreover, subsequent formulation of ADCs, typically using dead-end filtration (DEF), further complicates the production workflow. We compared SEC+DEF with the µPulse®, a miniaturized and automated tangential flow filtration system, for purification and formulation of ADCs. Quality analysis revealed that both approaches were equally gentle as comparable drug-to-antibody ratios (DARs) and monomer purities were observed in the purified samples. Most importantly, both methods exhibited equivalent cleanup efficiency with a 99.8% reduction in free linker-drug concentration. The endotoxin loads comprised 0.11 EU mg-1 for the µPulse and 0.07 EU mg-1 for SEC+DEF, ensuring validation of the safe application of purified ADCs in living systems. However, the µPulse performed purification and formulation of ADCs simultaneously as compared to SEC+DEF, which required multiple manual interventions. Our results indicate that the µPulse is a gentle, single-step, and walk-away approach for the purification of ADCs. Less
Ferritins are a widespread family of proteins involved in iron homeostasis While classic ferritins consist of four -helices and form -meric nanocages related ferritin-like proteins display other types of assemblies and sometimes lack any iron storage capacity Here by analyzing the available genomic data we identify a family of double ferritin-like proteins DFLPs composed of two four-helical domains which arose by duplication of a ferritin fold protein We characterize representative DFLPs from Thermocrinis minervae and Caldanaerovirga acetigignens TmDFLP and CaDFLP and show that they form homodimers and bind heme We determine the X-ray structure of TmDFLP and demonstrate its ferroxidase ... More
Ferritins are a widespread family of proteins involved in iron homeostasis. While classic ferritins consist of four α-helices and form 24-meric nanocages, related ferritin-like proteins display other types of assemblies and sometimes lack any iron storage capacity. Here, by analyzing the available genomic data, we identify a family of double ferritin-like proteins (DFLPs) composed of two four-helical domains, which arose by duplication of a ferritin fold protein. We characterize representative DFLPs from Thermocrinis minervae and Caldanaerovirga acetigignens, TmDFLP and CaDFLP, and show that they form homodimers and bind heme. We determine the X-ray structure of TmDFLP and demonstrate its ferroxidase activity. Furthermore, we show that some DFLPs, including TmDFLP and CaDFLP, are highly likely to be targeted into encapsulin shells. Our work expands the range of known iron metabolism systems and highlights the power of genome mining for discovery of new proteins. Less
Flap endonuclease FEN is a long-standing target of interest in the DNA damage response DDR field due to its therapeutic potential in BRCA mutant cancers To-date there have only been a handful of FEN inhibitors reported in the literature most of which display modest selectivity and or weak cellular activity As such there is a need for more advanced pharmacological tools to probe the biology of FEN Here we report the discovery of MSC the first potent selective and orally bioavailable FEN inhibitor We describe our metal-chelating fragment screening approach and structure-based optimization to identify MSC using structural insights to ... More
Flap endonuclease 1 (FEN1) is a long-standing target of interest in the DNA damage response (DDR) field due to its therapeutic potential in BRCA mutant cancers. To-date there have only been a handful of FEN1 inhibitors reported in the literature, most of which display modest selectivity and/or weak cellular activity. As such, there is a need for more advanced pharmacological tools to probe the biology of FEN1. Here, we report the discovery of MSC778, the first potent, selective, and orally bioavailable FEN1 inhibitor. We describe our metal-chelating fragment screening approach and structure-based optimization to identify MSC778, using structural insights to drive design. Consistent with FEN1 inhibition, MSC778 selectively kills BRCA2-deficient cells and potentiates the activity of PARPi niraparib in vivo to induce tumor stasis in a BRCA2 KO DLD-1 mouse xenograft. Furthermore, we illustrate how development of this approach has the potential for addressing nucleases as a target class. Less
The enzymatic degradation of polyethylene terephthalate PET offers a sustainable solution for PET recycling Over the past two decades more than PETases have been characterized primarily exhibiting similar sequences and structures Here we report new PET-degrading hydrolases including HaloPETase from the marine Halopseudomonas lineage thereby extending the narrow sequence space by novel features at the active site The crystal structure of HaloPETase was determined to a resolution of revealing a unique active site architecture and a lack of the canonical -stacking clamp found in PETases so far Further variations in active site composition and loop structures were observed Additionally we ... More
The enzymatic degradation of polyethylene terephthalate (PET) offers a sustainable solution for PET recycling. Over the past two decades, more than 100 PETases have been characterized, primarily exhibiting similar sequences and structures. Here, we report new PET-degrading α/β hydrolases, including HaloPETase1 from the marine Halopseudomonas lineage, thereby extending the narrow sequence space by novel features at the active site. The crystal structure of HaloPETase1 was determined to a resolution of 1.16 Å, revealing a unique active site architecture and a lack of the canonical π-stacking clamp found in PETases so far. Further, variations in active site composition and loop structures were observed. Additionally, we found five more enzymes from the same lineage, two of which have a high similarity to type IIa bacterial PETases, while the other three resemble HaloPETase1. All these enzymes exhibited high salt tolerance ranging from 2.5 to 5 M NaCl leading to higher total product releases upon PET degradation at 40 or 50 °C. Based on these findings, we propose an extension of the existing PETase classification system to include type III PETases. Less