Journal of Biomolecular Structure and Dynamics

Marburg virus (MARV) is a highly pathogenic filovirus that causes hemorrhagic fever with a high mortality rate, with very limited treatment options. The urgent need for targeted antiviral agents emphasizes the importance of structure-based drug discovery approaches. The present study aimed to evaluate the antiviral potential of Withaferin A (PubChem CID-265237) against three key proteins of MARV: viral protein 35 (VP35), and nucleoproteins (NP). Three-dimensional structures of these proteins were retrieved from RCSB-Protein Data Bank and docked with Withaferin A using AutoDock Vina. The ligand demonstrated favourable binding affinities towards all three viral targets, indicating strong interaction potential at functionally relevant sites. Drug-likeness and pharmacokinetic properties predicted using SwissADME and pkCSM indicated acceptable ADMET profiles that comply with key drug-like criteria. To validate the stability of the docking, molecular dynamics simulations (GROMACS, 100 nanoseconds) were conducted. The protein-ligand complexes exhibited stable root mean square deviation (RMSD), root mean square fluctuation (RMSF), and consistent hydrogen bonding patterns throughout the simulation. The MM-GBSA binding free energy analysis further supported favorable binding energetics, predominantly driven by van der Waals and electrostatic interactions. Altogether, these findings demonstrate that Withaferin A exhibits promising multi-target inhibitory potential against key MARV proteins. This study provides molecular insights into ligand-protein interactions and supports further experimental validation of Withaferin A as a potential therapeutic candidate against Marburg virus.

Glioblastoma Multiforme (GBM) is one of the most malignant forms of brain tumor in humans, with limited treatment options and poor overall survival rates. In the present study, we employed an in-silico workflow that integrated immunoinformatics and 3D structural modelling tools to design a multi-epitope vaccine against Podoplanin (PDPN), a transmembrane glycoprotein primarily involved in tumor invasion and metastasis. The differential expression of PDPN in tumor versus normal cells was investigated using transcriptomics datasets. Once the overexpression was confirmed, it was designated as a Tumor-Associated Antigen (TAA). B-cell, CTL, and HTL epitopes were predicted and screened for antigenicity, non-allergenicity, and non-toxicity. Selected epitopes were linked with appropriate adjuvant and linker sequences to construct a vaccine candidate. Codon optimization and in silico cloning was conducted to evaluate the constructs expression in a mammalian expression vector. The 3D structure of the vaccine candidate was modelled, refined, and validated before molecular docking with immune receptors and immune simulation studies. The results indicated that proposed polypeptide, RasIC-01v, could be a potential vaccine candidate for highly vigorous and dangerous cancer like GBM. Further experimental and immunological validations would be required to validate the commercial feasibility and development of RasIC-01v. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/706629v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7485b1org.highwire.dtl.DTLVardef@1f551c1org.highwire.dtl.DTLVardef@ca871eorg.highwire.dtl.DTLVardef@6cf53d_HPS_FORMAT_FIGEXP M_FIG C_FIG

Chikungunya virus (CHIKV) infection is one of the major public health concerns in several countries around the world. CHIKV non-structural protein 2 (nsP2) is a promising drug design target due to the enzymes multifunctional properties that facilities viral replication and propagation. To date, there is an evident lack of preventative and therapeutic developments that can be used against CHIKV. Drug repurposing is a time saving and cost-effective method used for the development of new drugs. In this study, drug repurposing was implemented with the use of HIV/HCV protease inhibitors to inhibit the active site of nsP2. Molecular dynamics simulations and analysis revealed the stability of two drugs, Indinavir and Paritaprevir. Indinavir forms a hydrogen bond with a major residue, which closes the flexible loop, situated in close proximity to the active site. This conformational shift in the orientation of the enzyme prevents accessibility to the active site thus disrupting the nsP2 protein from functioning effectively in viral replication. In conclusion, the findings of this study identified Indinavir was identified as a promising CHIKV nsP2 inhibitor. This study will provide the basis to further facilitate the drug repurposing strategy as an alternative approach for drug design of CHIKV inhibitors as well as other viral families.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by mutations in the TSC1 and TSC2 genes and is characterized by benign hamartoma formation in multiple organs. The TSC1-TSC2 complex regulates mTORC1 signaling in response to cellular growth conditions. This study aims to predict the structural stability and functional effects of non-synonymous single-nucleotide polymorphisms (nsSNPs) in human TSC1 and TSC2 using computational approaches. Twelve computational tools were assessed using receiver operating characteristic (ROC) analysis and applied to identify deleterious nsSNPs. Protein stability was predicted using I-Mutant 2.0 and MUpro, while evolutionary conservation was analyzed with ConSurf. NetPhos 3.1 identified potential PTM sites, and MutPred2.0 evaluated their functional impact. Project HOPE assessed mutation-induced physicochemical changes. Structural models were validated using multiple tools, visualized in ChimeraX 1.9, and further evaluated by molecular dynamics simulation to confirm wild-type and mutant stability. All twelve tools had AUC values above 0.90. A combined in silico analysis identified twelve high-risk nsSNPs in TSC1 and sixteen in TSC2, all reducing protein stability, located in conserved regions, and potentially disrupting phosphorylation sites. MutPred and Project HOPE confirmed their impact on protein function. Functional analysis showed TSC1 and TSC2 affect mTORC1 and PI3K-Akt pathways. RMSF and RMSD analyses revealed that TSC1 variants rs1846545280 (G236E), and rs2132135678 (V234E), and TSC2 variants rs45517223 (S758C), rs2151354925 (T836P), and rs45517365 (R1570W) had the largest structural fluctuations. Substitution with glutamic acid, a negatively charged and bulkier residue, may disrupt local folding of TSC1. Similarly, replacement of arginine with tyrosine at position 1570 may impair Rheb binding at the GAP domain of TSC2. These findings highlight potentially pathogenic nsSNPs in TSC1 and TSC2.

Mycobacterium tuberculosis topoisomerase I (MtbTOP1) is essential for the viability of the causative agent of TB. There are still significant unanswered questions regarding the dynamic conformations during catalysis of relaxation of negatively supercoiled DNA by MtbTOP1. We aim to study the flexible hinge residues that control the dynamics of inter-domain rearrangements involved in the enzyme conformational changes that allow the opening-closing of the topoisomerase gate. We used the online server PACKMAN to predict possible hinges from the MtbTOP1 crystal structure. The predicted region "PRO506 to LEU526" at the border between domains D2 and D4 with a p-value <0.05 was then studied as a potential hinge. The highly conserved ARG516 from this region interacts with the DNA inside the protein toroidal cavity. This arginine maintains inter-domain interaction with GLU207 of D4 and ASP691 of D5 domains. After introducing alanine substitutions, we further studied the mutant topoisomerases in biochemical experiments. The results showed a significant loss in DNA relaxation activity without affecting DNA binding and cleavage after mutating GLU207 and ARG516, consistent with their role as hinge residues in domain rearrangements.

The R2TP is a multimeric protein complex consists of RUVBL1, RUVBL2, PIH1D1, and RPAP3, and it is known to functions as a specialized co-chaperone. We hypothesize that PIH1D1 recognizes p53 and stabilizes it via R2TP complex. Upon successful completion of this study, innovative mechanism has been found for the interaction and stabilization of p53 and hence govern the cell cycle. Upon interaction between p53 and PIH1D1 protein, p53 is stabilized by PIH1D1 protein, without affecting its C-terminal domain. We have also observed that p53 protein levels were affected after the alteration in expression levels of PIH1D1. Based on the finding, we suggest that the R2TP complex stabilizes and regulates P53. Therefore, this novel method will work as a flashpoint to restore the function of p53 in cancer cells, controlling cancer and cell cycle progression.

Synaptic vesicle glycoproteins 2 (SV2) are integral membrane proteins essential for neurotransmitter release and are implicated in neurological disorders including epilepsy and Parkinsons disease. In the attempt to develop a ligand selective for SV2C, and in collaboration with UCB, UCB-F was identified as a potential candidate. However, the affinity of UCB-F to SV2C was found to be temperature dependent, decreasing by about 10-fold from +4 to 37 degrees. UCB1A was subsequently identified as SV2C ligand displaying in vitro a 100-fold selectivity for SV2C compared with SV2A. In this study we investigated whether the binding of UCB-1A to SV2A and SV2C was affected by the temperature. A combination of experimental binding assay data and molecular dynamics (MD) simulations were used. The binding studies revealed that UCB1A affinity for SV2A decreased significantly at 37 {degrees}C compared with 4 {degrees}C, whereas binding to SV2C remained largely unchanged. MD simulations reproduced these observations, namely that ligand RMSD values at 310 K showed that UCB1A binding fluctuated markedly in the SV2A complex, with many trajectories exceeding the 3.0 [A] stability cutoff, whereas UCB1A remained relatively well-anchored in SV2C under the same conditions. Structural analysis showed that, while UCB1A adopts a conserved binding pose across all isoforms stabilized by {pi}- {pi} stacking and a hydrogen bond with Asp, SV2C possesses a unique stabilizing feature. In SV2C, Tyr298 is less exposed to the solvent and engages in a persistent hydrogen bond with Asparagine, a structural feature that reinforces pocket stability and limits temperature-induced destabilization. This interaction is absent in SV2A, consistent with its greater temperature sensitivity. Together, these findings provide a mechanistic explanation for the experimentally observed temperature independence of UCB1A binding to SV2C. More broadly, the results highlight the importance of incorporating physiologically relevant temperatures into SV2 ligand evaluation and demonstrate how combining experiments with simulations can uncover isoform-specific mechanisms of ligand recognition and stability.

Globally, about 264 million individuals across all age groups are impacted by depression, a prevalent central nervous system (CNS) condition. Chronic and enduring depression might result in significant health consequences. Numerous pharmaceutical antidepressants exist for the management of mild to severe depression, largely functioning by modifying neurotransmitter levels in the brain. Nevertheless, these drugs frequently induce a variety of side effects, such as insomnia, constipation, exhaustion, drowsiness, and anxiety. Saffron (Crocus sativus L.) is widely acknowledged as a natural antidepressant with little adverse effects. This study investigated the potential antidepressant mechanisms of saffrons principal bioactive compounds safranal, crocin, and picrocrocin via molecular docking against critical target proteins associated with depression, namely the dopamine transporter (DAT), serotonin transporter (SERT), and monoamine oxidase B (MAO-B). Molecular docking was conducted with AutoDock 4.2 to assess the binding affinity and interaction energy of these drugs with the target proteins. Furthermore, Discovery Studio facilitated the viewing and study of both interacting and non-interacting residues at the docking sites, juxtaposing these interactions with those of established inhibitors in crystal structures. The permeability of the blood-brain barrier (BBB), pharmacokinetic characteristics, and toxicity profiles of saffron components were evaluated using SWISS ADME, DataWarrior, and Osiris Molecular Property Explorer. Among the evaluated elements, safranal had the greatest potential as a competitive inhibitor of the dopamine transporter, according to its notable blood-brain barrier permeability, robust binding affinity, and analogous interaction residues in comparison to nortriptyline, a recognized inhibitor. Our findings indicate that safranal may be a viable natural alternative to traditional antidepressants, with minimized adverse effects.

Ribociclib, a selective cyclin-dependent kinase (CDK) 4/6 inhibitor, is approved as a first-line therapy for HR-positive/HER2-negative advanced breast cancer. Emerging evidence suggests that Ribociclib may exert immunomodulatory effects. However, its role in cytokine regulation remains largely unexplored. This study presents a comprehensive in silico investigation of Ribociclibs interactions with eight key pro-inflammatory cytokines--IL-6, TNF-, IL-17A, IL-17F, IL-17A/F, IL-1{beta}, MCP-1, and IFN-{gamma}. Computational assessments included molecular docking, molecular dynamics (MD) simulations, MM-GBSA binding free energy calculations, principal component analysis (PCA), and dynamic cross-correlation matrix (DCCM) analyses. Molecular docking and MD simulations indicated strong and stable complex formation with TNF-, IL-6, MCP-1, IL-1{beta}, and IL-17A/F. MM-GBSA results further showed that Ribociclib formed the most stable complexes with IL-17A/F ({Delta}Gbind = -25.94 kcal/mol) and MCP-1 ({Delta}Gbind = -25.88 kcal/mol), comparable to binding with the CDK-6 ({Delta}Gbind = -36.23 kcal/mol) control protein. PCA and DCCM analyses further supported the stabilizing influence of Ribociclib on these cytokine conformations. Moderate interactions were observed with TNF-, IL-6, and IFN-{gamma}. Collectively, these findings suggest that Ribociclib may function as a multi-target inhibitor capable of modulating diverse inflammatory pathways, providing a computational foundation for its repurposing as a cost-effective anti-inflammatory therapeutic candidate.

The process of DNA transcription leads to the generation of torsional stress, which must be resolved for smooth progression of the transcription machinery. In Saccharomyces cerevisiae, DNA topoisomerase I (Top1), a type IB topoisomerase, plays a critical role in relaxing supercoils and mitigating the topological strain associated with transcription. While several proteins from the transcription machinery have been reported to interact with yeast Top1, detailed characterization and functional relevance of these interactions have remained underexplored. This gap is partly due to the absence of a complete three-dimensional structure of the full-length enzyme, which hinders structure-based computational analyses of its interactome. In this study, we present a template-based model of full-length yeast Top1. Leveraging this model, we investigated its molecular interaction with Rpc82, a key subunit of RNA polymerase III enzyme, responsible for transcribing small non-coding RNAs such as tRNAs and 5S rRNA. Through molecular docking and molecular dynamics simulations, critical residues at the Top1-Rpc82 interface were identified that likely mediate their interaction. Our findings provide new insights into the structural basis of Top1s association with RNA polymerase III and its potential role in regulating Pol III-mediated transcription. The Top1 model developed here offers a valuable framework for future in silico studies aimed at elucidating the broader interactome and regulatory mechanisms of this essential enzyme.

Malaria is one of the deadliest diseases in sub-Saharan Africa and Southeast Asia. The majority of the fatalities occur mostly in children under 5 years and pregnant women and this is due to infection by Plasmodium spp, of which Plasmodium falciparum is the most virulent and is responsible for most of the morbidity and mortality. Despite various public health interventions such as use of insecticide-treated bed nets, spraying of homes with insecticides and use of WHO recommended artemisinin-based combination therapies (ACT), malaria prevention still faces major setback due to drug and insecticide resistance by P. falciparum and mosquitoes respectively. The study uses molecular docking and immunoinformatics to screen various Plasmodium spp antigens and evaluate their antigenicity and suitability as vaccine candidates. The P. falciparum antigens and T-cell receptor (TCR) structures were obtained from Protein Data Bank (PDB) based on a range of factors related to their role in the lifecycle of the parasite and their status as vaccine targets. Protein structures not available in the PDB were predicted using AlphaFold. The 3D structures of selected P. falciparum antigens and TCR structures were downloaded in PDB format then all water molecules, Hetatm, and bound ligands were deleted from the protein structures using BIOVIA Discovery Studio Visualizer. Subsequently, molecular docking was done using ClusPro v2.0 server and docked complexes were compared. The findings of this study gave valuable insights into the interaction of human immune response with P. falciparum antigens. The best three ranked antigen complexes are PfCyRPA, PfMSP10 and PfCSP and this confirm their use as potential candidates for vaccine development. This study highlights the usefulness of computational docking in identifying P. falciparum antigens of excellent immunogenic potential as vaccine candidates.

Antimicrobial resistance (AMR) in plant pathogenic bacteria poses a serious threat to global agriculture, necessitating the development of novel antibacterial agents targeting virulence mechanisms. This study presents an integrated bioinformatics-driven framework for the rational design and computational validation of Solres, a newly designed small molecule targeting key virulence proteins in phytopathogenic bacteria. Approximately 10,000 active compounds from PubChem BioAssay (AID: 588726) were analyzed using structural clustering and scaffold mining to identify conserved molecular motifs associated with antibacterial activity. Guided by high-frequency substructures, Solres was designed de novo and screened for structural novelty against PubChem, ChEMBL, and WIPO databases. Drug-likeness evaluation using Lipinskis Rule of Five confirmed favorable physicochemical properties. Molecular docking was performed against essential virulence regulators, including PhcA, PhcR, HrpB, PehA, and Egl from Ralstonia solanacearum and Xanthomonas spp., with active sites predicted using CaspFold. Docking analyses revealed strong binding affinities and stable interactions with key catalytic and regulatory residues. Complex stability and conformational integrity were further validated through molecular dynamics simulations. Quantum chemical descriptors, including HOMO-LUMO energy gap and dipole moment, supported the electronic suitability and reactivity profile of Solres. Collectively, this study demonstrates the effective integration of cheminformatics, structural bioinformatics, molecular simulations, and quantum chemical analyses for plant-focused antibacterial discovery. The compound Solres represents a promising lead candidate for mitigating bacterial wilt disease and provides a computational framework for future experimental validation and sustainable crop protection strategies against AMR-driven phytopathogens.

It has been recognized a long time ago that the hedgehog (Hh) and Wnt signaling pathways have numerous similarities that suggest their common evolutionary origin. Although the Hh and Wnt proteins are unrelated they are similar in as much as they carry lipid modifications that are critical for their interaction with their receptors. In our earlier work we have shown that Wnt inhibitory factor 1 (WIF1), originally identified as a Wnt antagonist also binds to and inhibits the signaling activity of sonic hedgehog (Shh), raising the possibility that the lipid moieties of these unrelated morphogens play a dominant role in their interaction with WIF1. In the present work we have compared the interactions of human WIF1 protein with lipidated and non-lipidated forms of human sonic hedgehog (Shh) using Surface Plasmon Resonance spectroscopy and reporter assays monitoring the signaling activity of human Shh. Our studies have shown that human WIF1 protein has significantly higher affinity for lipidated than non-lipidated Shh, indicating that lipid modifications of Hhs are important for interactions with WIF1.

Exposure to cigarette smoke is one of the major risk factors for developing various diseases such as chronic obstructive pulmonary disease (COPD), cardiovascular disorders, and cancer mediated via cellular oxidative stress and organelle dysfunction. To this end, the current study investigated how cigarette smoke extract (CSE) affects vacuole structure and function in Saccharomyces cerevisiae, as vacuole plays a crucial role in handling oxidative stress-induced misfolded proteins. Our results showed that CSE exposure causes transient vacuolar fragmentation up to 1 h to increase its surface area to facilitate microautophagy in clearing CSE-mediated misfolded protein and promoting cell survival. However, excessive fragmentation or vacuolar fusion sensitizes cells towards CSE-mediated cellular toxicity. Towards understanding the underlying mechanism, the current study demonstrated the involvement of PI3P and PI (3,5) P2-mediated signaling and phospholipase-driven remodeling of lipid moieties. Moreover, the current study also showed the importance of mitochondrial activity in CSE-mediated vacuolar fragmentation. Prolonged exposure to CSE impairs mitochondrial function and thus disrupts fragmentation, the adaptive survival strategy against CS. It results in proteostasis collapse, which is a characteristic shared by many inflammatory and degenerative disorders. Taken together, the current study reveals a previously unrecognized cellular protection mechanism induced by cigarette smoke and highlights potential therapeutic targets for mitigating CS-mediated diseases

GPI-anchored proteins are crucial cell surface proteins with diverse, organism-specific functions, in eukaryotes. They are produced when the GPI transamidase (GPIT), a five-subunit membrane-bound enzyme complex, attaches a pre-formed GPI anchor to the C-terminal end of nascent proteins on the lumenal face of the endoplasmic reticulum. This process requires the removal of a C-terminal signal sequence (SS) on the substrate protein by the action of an endopeptidase subunit of the GPIT, Gpi8/ PIG-K. Using an AMC-tagged peptide in a cell free (post-mitochondrial fraction) assay, this manuscript studies the steady state kinetics of enzymatic cleavage of the substrate by GPIT of the human pathogenic fungus, C. albicans. We show that Mn+2 enhances activity by improving substrate binding but plays no direct role in substrate cleavage per se. Molecular dynamics simulations suggest that the divalent cation binds at a site away from the active site but provides compactness and stability to Gpi8. It also enables a conformation in which a flexible loop (219-244 residues) in the vicinity of the catalytic pocket is able to interact with and position the scissile bond for cleavage by Cys202. Steady state kinetics also indicate that peptides of lengths 7-mer to 9-mer are better bound than 4-mer or 15-mer peptide substrates. A bulky residue at the site of cleavage reduces the catalytic activity of the GPIT. This is the first detailed steady state kinetics study on the endopeptidase activity of a GPIT from any organism.

The intracellular transport system is pivotal for cellular function and integrity, facilitated by cytoskeletal motor proteins such as dynein, which traverse along microtubules (MTs). The heterogeneity of the tubulin isotypes composing MTs introduces functional diversity, potentially affecting cytoskeletal motor proteins interactions with the MT. This in silico study investigated the influence of amino acid sequence variations in the C-terminal tails (CTTs) of six different Homo sapiens tubulin isotypes, TUBB2A, TUBB2B, TUBB2C, TUBB3, TUBB4A, and TUBB5, highly expressed in human brain tumors, and assessed the isotypes effect on the binding of motor protein dynein to MT. Among these isotypes, TUBB2A, TUBB2B, and TUBB2C were found to affect conformational motions of the dyneins microtubule-binding domain (MTBD) and stalk domain. The investigation highlighted the novel role of isotype-specific variations in lateral interactions between tubulin protofilaments (PFs) in determining the proximity of the {beta}-CTT of the adjacent PF to the MTBD, potentially affecting dyneins motility and suggesting how changes in isotype expression directly influence dyneins velocity and processivity and contribute to transport defects associated with neurological disorders and cancers. Isolating specific tubulin isotypes experimentally is challenging due to their high sequence similarity and complex interactions with other microtubule-associated proteins. This makes it challenging to distinguish between different tubulin isotypes and their effects, particularly in tissues where multiple isotypes are co-expressed. Additionally, these isotypes are heavily modified in vivo by post-translational modifications, which further complicate the isolation of a single, unmodified tubulin isotype. As a result, computational approaches have been necessary in this study for exploring these effects in a controlled, isotype-specific manner.

In siRNA-based applications, cellular delivery remains one of the main hurdles. Many formulations are tested for the same and peptides came up as one of the optimal options. The latter have various advantages like natural biological presence, high specificity, and natural metabolism etc. siRNA in conjugation with peptides have exhibited enhanced mRNA silencing. Peptides aid siRNAs in condensation to smaller volumes, enhance nuclease protection, increase half-life, promote cell specific binding as well as endosomal escape and release in cytosol. Despite its prime importance, no resource is available for the peptide-based delivery of siRNAs, therefore to fill the gap we developed PEPsRNA web server. It includes 2266 entries of 270 different kinds of peptides, 106 different types of siRNAs and shRNAs along with more than 80 conjugate molecules targeting 55 different genes, experimentally tested for the delivery of the siRNAs. To provide the detailed insights of the procedure, we have incorporated analysis of the peptides (e.g. secondary structure, amino acid composition, polarity, hydrophobicity etc.), siRNAs (e.g. secondary structures with minimum free energies etc.) and associated conjugate molecules (e.g. structure, SMILES, Inchl). We have derived these values using various other tools and resources to make the web server comprehensive. We further compared various physicochemical properties with the efficacy of the peptide based on the target gene silencing, but these properties do not shown any distinct conclusive relationship. The data is available for browsing, searching and downloading freely on the web server with URL: http://bioinfo.imtech.res.in/manojk/pepsirna. Highlights PEPsRNA is the first database of experimentally tested peptides for siRNA delivery It comprised of 2266 entries with 270 peptides and about 80 conjugate molecules Analysis of peptides, siRNAs and details of conjugate molecules are provided Browse, search and various tools are incorporated for data retrieval and usage

Purpose/ObjectiveThis study aimed to design and computationally evaluate a synthetic GluN1-mimetic peptide as a decoy to bind and neutralize pathogenic autoantibodies in anti-NMDA receptor (NMDAR) encephalitis, a severe autoimmune neurological disorder affecting approximately 1.5 per million individuals annually. MethodsKey GluN1 epitope residues (351-390 of the amino-terminal domain) were identified from crystallographic evidence and patient-derived antibody binding studies. Multiple peptide variants were rationally designed to mimic the antibody-binding interface. AlphaFold2 was used to predict peptide structures. Rigid-body docking simulations were conducted with HADDOCK 2.4 to model peptide-antibody complexes, and binding affinities were quantified using PRODIGY. A scrambled peptide control was included to establish docking specificity. ResultsThe top-performing peptide demonstrated favorable predicted binding ({Delta}G = -21.5 kcal/mol, Kd = 1.7 x 10-{superscript 1} M) with an average pLDDT score of 90%, a buried surface area of 3,255.5 [A]{superscript 2}, and 18 intermolecular hydrogen bonds. Relative to the scrambled control ({Delta}G = -8.3 kcal/mol), the designed peptide showed substantially stronger predicted binding. Conclusion/ImplicationsThese results support the validity of an epitope-mimicry design strategy and establish a scalable computational framework for prioritizing peptide decoy candidates applicable to other antibody-mediated autoimmune disorders. Experimental validation remains necessary to confirm real-world efficacy.

Drug promiscuity is a double-edged sword where a small molecule acts on multiple biological targets to induce toxicological or therapeutic benefits. It is possible to exploit promiscuity to expand treatment options without the prohibitive costs of designing a new drug. Imatinib is a representative case, exhibiting varied affinities and inhibitions to different kinases. It binds most favorably to Abl and Kit kinases, intermediately to Chk1 and Lck kinases, and least favorably to p38 and Src kinases. The strongly conserved features of the ATP-binding site render imatinibs molecular binding determinants unclear despite over 25 years of interrogation. To address this question, molecular thermodynamics, force distribution analysis, residue sidechain dihedral correlations, and principal component analysis were computed using trajectories from all-atom molecular dynamics simulations in explicit solvent. The results of these simulations agree with experimental affinity and binding data, enabling highly predictive factors for imatinibs binding specificity from free- and bound-state simulations through a global protein network of protein-ligand interactions, changes in sidechain dihedral correlations, and shifts in the secondary motifs modulating binding site access corresponding with well-characterized kinase "breathing motions." The sidechain dihedral correlation network also identifies distal mutants known to reduce patients imatinib sensitivity. Higher imatinib-kinase affinity trends with a loss in sidechain dihedral correlations and diminished secondary motif migration following binding, corresponding with more restricted configurations, to reduce solvent approach and ATP competition. Lower-affinity proteins show enhanced sidechain dihedral correlation and exaggerated secondary motif motions. This is consistent with a tendency to expose the protein pocket, facilitate solvent entrance, and increase ATP competition. Using imatinib as a model system, this study shows residue correlation, force interaction, and essential principal components can effectively forecast imatinib-kinase binding specificity and introduces an effective approach to repurpose and design high-affinity binders for off-target applications more generally.

Glucan-water-dikinase 1 (GWD1) plays an essential role in regulating starch metabolism in plants via O-6 phosphorylation of amylopectin. Here, we used biochemical characterization, AlphaFold2 modeling, X-ray crystallography and Small-Angle X-ray Scattering (SAXS) experiments to study its structure and catalytic mechanism. The protein is organized into five domains with two carbohydrate-binding modules (CBMs) at its N-terminal end followed by a central domain, whose structure was solved by X-ray crystallography in open and closed conformations. Next comes the domain carrying the catalytic histidine and the ATP-binding domain. We studied the spatial arrangement of the full enzyme and of several truncated forms by SAXS-driven modeling and identified a pivoting movement of the Histidine domain consistent with the enzymes autophosphorylation and subsequent phosphate transfer to a glucan. Our data suggest important residues at the domain interfaces that might assist catalysis and we hypothesize that the second CBM helps maintaining the catalytic domain close to the glucan chain for productive phosphate transfer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/704335v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1b860e5org.highwire.dtl.DTLVardef@1e172dcorg.highwire.dtl.DTLVardef@3c03edorg.highwire.dtl.DTLVardef@25c0d4_HPS_FORMAT_FIGEXP M_FIG C_FIG