HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

Comprehensive in silico characterization of nonsynonymous SNPs in the human ezrin (EZR) gene and their role in disease pathogenesis

Ezrin (EZR) is a crucial linker between the actin cytoskeleton and the plasma membrane. It interacts with proteins involved in cancer-related signaling pathways. To assess the impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on EZR structure and function, we employed bioinformatics tools (SIFT, PolyPhen-2, PROVEAN, PhD-SNP, SNPs&GO, SuSPect, and FATHMM) and identified deleterious variants. Stability analyses using MUpro, mCSM, I-Mutant 2.0, and DynaMut2 revealed six destabilizing nsSNPs (F240S, H288D, I248T, L59Q, L125S, and L225P). Structural modeling using HOPE, MutPred2, AlphaFold, Swiss-Model, and protein-protein docking using HADDOCK 2.4 assessed the impact on the EZR-EBP50 complex. Binding free energy calculations, salt bridge analysis, and interface residue mapping further confirmed that the L225P, F240S, and I248T mutations significantly impaired EZR-EBP50 interaction, potentially disrupting key signaling pathways. Molecular dynamics simulations indicated that mutant EZR proteins exhibited reduced stability, flexibility, and hydrogen bonding. This first comprehensive in silico analysis of EZR highlights pathogenic nsSNPs that may contribute to disease progression. These findings provide a foundation for experimental validation and may inform targeted therapies for EZR-related pathologies.

Multi-omics integration reveals Vha68-3 as a testicular aging-specific factor that coordinates spermatid elongation through mitochondrial metabolic homeostasis

BACKGROUND

Testicular aging has profound effects on spermatogenesis, sperm function, and the spermatogenic microenvironment, contributing to reduced male fertility. However, the precise molecular mechanisms by which mitochondria influence spermiogenesis during aging still remain largely unclear.

METHODS

Vha68-3 KO flies were generated using the CRISPR/Cas9 technique. Testicular phenotypes and functions were mainly observed through immunofluorescence staining and transmission electron microscopy. Multi-omics study was mainly conducted through single-cell RNA sequencing and transcriptome-metabolomics association analysis. Vha68-3 binding proteins were identified via liquid chromatography-tandem mass spectrometry. The therapeutic potential of modulating mitochondrial metabolism for testicular aging mainly relied on the dietary intake of related compounds in fruit flies.

RESULTS

In this study, we identified Vha68-3, a testis-specific subunit of the V-type adenosine triphosphate (ATP) synthase, predominantly localized in the tails of elongated spermatids, as a key age-related regulator of male fertility and spermatid elongation in Drosophila testes. Crucially, Vha68-3 deficiency impaired mitochondrial homeostasis in elongated spermatids during testicular aging. Through a multi-omics approach, including single-cell transcriptomics, protein interaction mapping of Vha68-3, and transcriptome-metabolome integration, we identified pyruvate metabolism as a critical pathway disrupted by Vha68-3 deficiency. Moreover, dietary supplementation with pyruvate (PA), S-lactoylglutathione (SLG), and phosphoenolpyruvate (PEP) effectively alleviated mitochondrial dysfunction and testicular aging linked to Vha68-3 deficiency.

CONCLUSIONS

Our findings uncover novel mechanisms by which mitochondrial metabolism regulates spermatid elongation and propose potential therapeutic strategies to combat mitochondrial metabolic disorders in aging testes.

HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes

Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integrated computational platform for predicting and analyzing protein-protein complexes. Over the past 6 years, HawkDock has successfully processed >234 000 computational tasks. In this study, an updated version of HawkDock was developed with the following advancements: (1) a deep learning-based flexible docking method, GeoDock, has been integrated to improve docking accuracy, particularly for apo-protein structures; (2) the VD-MM/GBSA method, which outperforms conventional MM/GBSA approaches in predicting binding affinities, has been implemented; (3) a new Mutation Analysis Module has been added to systematically evaluate the energetic impacts of amino acid mutations on protein-protein binding; (4) the server has been migrated to a high-performance cluster with Amber upgraded to version 24. Here, we describe the general protocol of HawkDock2, with a particular focus on its new features related to flexible docking, VD-MM/GBSA affinity prediction, and amino acid residue mutations. Comprehensive validation studies have demonstrated the reliability and effectiveness of these new features. HawkDock2 will remain freely accessible to all users at http://cadd.zju.edu.cn/hawkdock/.

A fast and efficient virtual screening and identification strategy for helix peptide binders based on finDr webserver: A case study of bovine serum albumin (BSA)

Peptides offer unique advantages, including strong specificity, rapid action, and low side effects, making them a prominent focus in the development of new drugs and functional materials. However, the rapid and efficient screening and identification of high-affinity peptides for specific targets remains a significant challenge. In this study, we successfully screened 12-helix candidate peptides using bovine serum albumin (BSA) as the target protein, employing the computer-aided peptide virtual screening webserver finDr. Among the top five candidate peptides, we identified E4-TP2 (GVATVVARLFLL) as the peptide capable of binding BSA with high affinity constant (KD = 39.4 nM), confirmed through an in vitro molecular interaction instrument. The interaction mode of the peptide-BSA complex was analyzed using Ligplot software, revealing that the primary interactions involved hydrophobic forces and hydrogen bonds. Additionally, molecular dynamics simulations further elucidated the molecular mechanisms underlying the high-affinity peptide interactions, the results demonstrated that the complex exhibited good conformational stability and strong binding free energy (MM/PBSA: -21.075 ± 5.471 kJ/mol). In conclusion, the finDr virtual screening strategy and the molecular interaction identification method employed in this study provide a robust technical approach for the rapid and efficient acquisition of high-affinity binding peptides for target proteins of interest.

Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility

Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision.

Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis

Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.

Development of a Novel Multi-Epitope Vaccine Against Streptococcus anginosus Infection via Reverse Vaccinology Approach

Streptococcus anginosus is an opportunistic pathogen known for its capability to cause a broad range of infections, posing a significant and growing global health concern. Alongside enhancing diagnostic capabilities and bolstering public health initiatives, developing a safe and effective vaccine represents a promising strategy to tackle this health challenge. In this paper, we employed an array of bioinformatics tools to engineer a subunit vaccine that exhibits high immunogenicity against S. anginosus. After constructing the multi-epitope vaccine, we subsequently predicted its secondary and tertiary protein structures. After refining and validating the modelled structure, we utilised advanced computational approaches, including molecular docking and dynamic simulations, to evaluate the binding affinity, compatibility, and stability of the vaccine-adjuvant complexes. Eventually, in silico cloning was conducted to optimise protein expression and production. The multi-epitope subunit vaccine we developed showed properties in antigenicity and immunity theoretically. The computational study revealed that this vaccine demonstrates significant efficacy against S. anginosus.

Immmunoinformatics-based design of T and B-cell multi-epitope vaccine to combat Borrelia burgdorferi infection

Lyme disease is one of the most common vector-borne infectious diseases globally, partly due to the absence of a vaccine for humans. Hence, in this study, an immunoinformatics method was used to design a multi-epitope vaccine (MEV) against Borrelia burgdorferi. The optimal B- and T-cell epitopes from Borrelia burgdorferi proteins (BmpA and OspC) were joined with the appropriate linkers to construct a MEV. In addition, β-defensin was included as an adjuvant in the vaccine construct. Secondary and tertiary structures of MEV were predicted, refined and validated. The developed vaccine was high antigenicity, non-allergenicity, solubility and stability. The Ramachandran plot, ProSA-web and ERRAT were employed to ensure the final model's authenticity. The immune simulation confirmed acceptable responses of both cellular and humoral immune. The vaccine's binding stability with Toll-like receptor 2 (TLR2) was confirmed using molecular docking and molecular dynamics (MD) simulation. Furthermore, MEV effectively stimulated high-level antibody production in mice, significantly promoted splenocyte proliferation in immunized mice, and markedly enhanced splenic IFN-γand IL-4 mRNA transcription levels. These results suggest that MEV, as a novel vaccine candidate, holds significant potential for future prevention and control of Borrelia burgdorferi infections.

Allosteric targeted drug delivery for enhanced blood-brain barrier penetration via mimicking transmembrane domain interactions

Current strategies for active targeting in the brain are entirely based on the effective interaction of the ligand with the orthosteric sites of specific receptors on the blood-brain barrier (BBB), which is highly susceptible to various pathophysiological factors and limits the efficacy of drug delivery. Here, we propose an allosteric targeted drug delivery strategy that targets classical BBB transmembrane receptors by designing peptide ligands that specifically bind to their transmembrane domains. This strategy prevents competitive interference from endogenous ligands and antibodies by using the insulin receptor and integrin αv as model targets, respectively, and can effectively overcome pseudotargets or target loss caused by shedding or mutating the extracellular domain of target receptors. Moreover, these ligands can be spontaneously embedded in the phospholipid layer of lipid carriers using a plug-and-play approach without chemical modification, with excellent tunability and immunocompatibility. Overall, this allosteric targeted drug delivery strategy can be applied to multiple receptor targets and drug carriers and offers promising therapeutic benefits in brain diseases.

Synthesis of an Adjuvant-Free Single Polypeptide-Based Tuberculosis Subunit Vaccine that Elicits In Vivo Immunogenicity in Rats

A novel tuberculosis subunit vaccine specific for Mycobacterium tuberculosis dual antigens, culture filtrate protein-10 (CFP-10) and antigen 85B (Ag85B) conjugated with cholera toxin non-toxic B subunit (CTB), was expressed as a single polypeptide in high amounts and cost-effectively in Escherichia coli. The recovery and purification conditions for the recombinant fusion protein were established. This simple peptide vaccine required no exogenous adjuvant as it contained CTB, a potent immune modulator. The vaccine's physiochemical, structural, and immunological properties were determined using the in-silico tools. It was highly antigenic, non-allergenic, and non-toxic. Its BlastP search with human proteomes excluded the chances of autoimmune reactions. The tertiary structure model (3D) was validated by Ramachandran plot assessment. The 3D structure docking with Toll-like receptors, TLR-1, 2, 4, and 6, showed that the binding affinity between the vaccine peptide and TLRs was high, and their complex was stable, indicating a strong immune response. The in-silico immune simulation revealed the vaccine-induced both innate and adaptive immune responses. In-vivo validation of the immunogenicity of CTB.CFP10.Ag85B in Wistar rats revealed higher activation of IgG immune response compared to either antigen protein. Similar results were also obtained using the C-ImmSim simulation online server. A comparison of immunogenicity of CTB.CFP10.Ag85B with the only available TB vaccine, Bacillus Calmette-Guérin (BCG) or as a booster after vaccination of Wistar rats with BCG, indicated that the IgG levels were the highest in rats vaccinated with BCG, followed by a booster dose of CTB.CFP10.Ag85B fusion protein. The fusion protein would be a safe potential vaccine booster candidate in BCG-primed individuals against TB.

Identification of a Novel Substrate for eEF2K and the AURKA-SOX8 as the Related Pathway in TNBC

Eukaryotic elongation factor 2 kinase (eEF2K) has been considered as a putative target for cancer therapy; however, the underlying mechanisms of eEF2K in triple-negative breast cancer (TNBC) progression remain to be fully elucidated. In this study, it is shown that eEF2K is highly expressed in TNBC and is associated with poor prognosis. In vitro, in vivo, and patient-derived organoid experiments demonstrate that knockdown of eEF2K significantly impedes progression of TNBC. Proteomic analysis and confirmation experiments reveal that eEF2K positively regulates the mRNA and protein expressions of sex-determining region Y-box 8 (SOX8). Mechanistically, eEF2K binds to and phosphorylates aurora kinase A (AURKA) at S391, a newly identified phosphorylation site critical for maintaining AURKA protein stability and kinase activity. Moreover, the compound C1, a molecular glue to degrade eEF2K, is optimized by designing and synthesizing its derivatives using reasonable structure-based optimization approach. The new compound C4 shows  better ability to degrade eEF2K and stronger anti-cancer activity than C1. These findings not only uncover the pivotal role of the eEF2K/AURKA/SOX8 axis in TNBC progression, but also provide a promising lead compound for developing novel drug for treatment of TNBC.

A Stable mRNA-Based Novel Multi-Epitope Vaccine Designs Against Infectious Heartland Virus by Integrated Immunoinformatics and Reverse Vaccinology Approaches

The Heartland virus (HRTV) is a tick-borne human pathogenic phlebovirus that primarily causes leukopenia and thrombocytopenia. It is transmitted by Amblyomma americanum type of tick, that is, notable for their aggressive biting behavior, affinity for human hosts, and high prevalence. Developing vaccines or immunizations against HRTV is gaining importance as a public-health preventive strategy. The current study was planned to prioritize a multi-epitope stable mRNA vaccine model against HRTV from lead B-cell and T-cell epitopes (with IC50 < 100 nM) of HRTV proteome following advanced immunoinformatics approaches. Model constructs were designed by linking the most potent, nonallergenic epitopes along with incorporation of human ribosomal protein adjuvant for immune response enhancement. The immunogenic potential of the coding vaccine molecule was examined via molecular docking against toll-like receptors immune receptors followed by normal mode analysis and molecular dynamics simulations-based energy minimization, molecular stability, and flexibility assessments. A robust, stable circular mRNA precursor of multi-epitopes vaccine model was designed by incorporating the Kozak consensus sequence, a start codon, and essential elements such as MHC class I trafficking domain (MITD), tPA, Goblin 5' and 3' Untranslated Region (UTRs), and a poly (A) tail. This strategic amalgamation ensures elevated immunogenicity and predicts a promising circular mRNA vaccine model against HRTV. The immune simulation predicted that the designed model vaccine is capable to elicit cell-mediated and humoral immune responses. The predicted circular mRNA vaccine precursor model is promising against HRTV to examine experimentally for its immunogenicity and safety features.

CAR T cells re-directed by a rationally designed human peptide tag demonstrate efficacy in preclinical models

Currently, only a few chimeric antigen receptor (CAR) T cell therapies have been approved by the Food and Drug Administration and European Medicines Agency for the treatment of B-cell malignancies. To enable broader application of the CAR T cell technology in other indications, improved control and flexible targeting of multiple tumor antigens are required. Here, we developed a novel adapter CAR (AdCAR) T cell platform for flexible targeting of multiple tumor antigens. This platform is based on a short peptide tag derived from an interdomain region of fibroblast growth factor receptor 2 (FGFR2), commonly mutated in cancer. To select AdCARs specific for mutated FGFR2-derived peptide tags, a multistep pooled screening approach in primary T cells was employed, incorporating MACS separation and next-generation sequencing. The resulting AdCAR was highly specific for the FGFR2-derived peptide tag. Using different in vitro and in vivo model systems, the activity of AdCAR T cells was shown to be strictly dependent on the presence of the adapter and corresponding target antigen. Moreover, AdCAR T cells could be redirected to different target antigens by the addition of respective adapter molecules (AM). Finally, in situ expression of functional AM in primary T cells under control of a drug-inducible promoter system was demonstrated, highlighting the potential for controlling the activity of AdCAR T cells by cellular micropharmacies.

Designing an optimized theta-defensin peptide for HIV therapy using in-silico approaches

The glycoproteins 41 (gp41) of human immunodeficiency virus (HIV), located on the virus's external surface, form six-helix bundles that facilitate viral entry into the host cell. Theta defensins, cyclic peptides, inhibit the formation of these bundles by binding to the GP41 CHR region. RC101, a synthetic analog of theta-defensin molecules, exhibits activity against various HIV subtypes. Molecular docking of the CHR and RC101 was done using MDockPeP and Hawdock server. The type of bonds and the essential amino acids in binding were identified using AlphaFold3, CHIMERA, RING, and CYTOSCAPE. Mutable amino acids within the peptide were determined using the CUPSAT and Duet. Thirty-two new peptides were designed, and their interaction with the CHR of the gp41 was analyzed. The physicochemical properties, toxicity, allergenicity, and antigenicity of peptides were also investigated. Most of the designed peptides exhibited higher binding affinities to the target compared to RC101; notably, peptides 1 and 4 had the highest binding affinity and demonstrated a greater percentage of interactions with critical amino acids of CHR. Peptides A and E displayed the best physiochemical properties among designed peptides. The designed peptides may present a new generation of anti-HIV drugs, which may reduce the likelihood of drug resistance.

A comprehensive strategy for the development of a multi-epitope vaccine targeting Treponema pallidum, utilizing heat shock proteins, encompassing the entire process from vaccine design to in vitro evaluation of immunogenicity

Background

Treponema pallidum, the causative spirochete of syphilis, is primarily transmitted through sexual contact and has emerged as a significant global health concern. To address this issue, enhancing diagnostic capabilities, strengthening public health interventions, and developing a safe and effective vaccine are critical strategies.

Objective

This study employed an immunoinformatics approach to design a vaccine with high immunogenic potential, targeting the heat shock proteins of T. pallidum.

Methods

Based on heat shock proteins of T. pallidum, we predicted B-cell, CTL, and HTL epitopes and all the selected epitopes were linked to construct a multi-epitope vaccine. Antigenicity, toxicity, and allergenicity of epitopes were checked by VaxiJen 2.0, AllerTOP v2.0, and ToxinPred servers. After constructing the multi-epitope vaccine, we subsequently predicted its secondary and tertiary protein structures. After refining and validating the modeled structure, we utilized advanced computational approaches, including molecular docking and dynamic simulations, to evaluate the binding affinity, compatibility, and stability of the vaccine-adjuvant complexes. Eventually, in silico cloning was conducted to optimize protein expression and production.

Results

The multi-epitope subunit vaccine we developed was constructed by seven cytotoxic T lymphocyte epitopes, five helper T lymphocyte epitopes, four B cell epitopes, and adjuvant β-defensin. An adjuvant was used to enhance immune responses, all of which were linked to one another using GPGPG, AAY, and KK linkers, respectively. The population coverage of the designed vaccine was 94.41% worldwide. Molecular docking and MD simulations indicated strong binding interactions with TLR1/2, TLR-2 and TLR-4 in a stable vaccine-receptor complex. The final designed vaccine, composed of 502 amino acids, theoretically exhibits high antigenicity and immunity, capable of inducing both humoral and cellular immune responses.

Conclusion

The vaccine developed in this study theoretically represents a safe and potent multi-epitope prophylactic strategy against T. pallidum, subject to further experimental validation to ascertain its actual protective efficacy.

Leveraging core proteome data of Kingella kingae for multi-epitope vaccine design against TonB dependent receptor (TDR): an in silico approach

Kingella kingae is a Gram-negative bacterium that causes invasive infections in children and older or immunocompromised individuals, making it a significant public health concern. In this study, a pan-proteomic mediated vaccine target mining was attempted to identify potential vaccine targets in K. kingae. Currently, there is no vaccine available against this pathobiont. Therefore, we designed and validated an in silico vaccine construct by targeting the lactoferrin/transferrin-binding TonB-dependent receptor. Antigenic regions of the TonB receptor were mapped, and the predicted epitopes were anticipated to be effective in a broad range of the world population. Using their combinations with linkers and various adjuvants, 12 vaccine constructs were prepared. The best construct (C7) with no allergenicity and high antigenicity was subjected to molecular modeling, docking with important immune receptors of humans, and then molecular dynamics (MD) simulation. After binding validation and stability assessment, it was cloned into a pet-28a + plasmid vector. Immune response was also simulated, and the vaccine was observed to invoke B- and T-cell induction. These findings can help accelerate the development of a new vaccine against K. kingae or other pathogens targeting the homolog of TonB. Nevertheless, we propose additional testing of C7 construct for efficacy and safety in vitro and in vivo.

Computational Development of Allosteric Peptide Inhibitors Targeting LIM Kinases as a Novel Therapeutic Intervention

LIM Kinases (LIMKs) have emerged as critical therapeutic targets in cancer research due to their central role in regulating cytoskeletal dynamics and cell motility via cofilin phosphorylation. Allosteric inhibitors, which bind outside the ATP-binding pocket, offer distinct advantages over ATP-competitive inhibitors, such as increased specificity, reduced off-target effects, and the ability to overcome resistance. This study investigates a series of novel tetrapeptides mimicking the binding mode of TH470, an allosteric LIMK inhibitor, using in silico docking and molecular dynamics simulations to identify potential lead compounds with high specificity, binding affinity, and favorable pharmacokinetic properties. Structural analyses revealed critical interactions between TH470 and LIMKs, particularly with conserved residues such as Thr405 (gatekeeper residue), Ile408 (hinge region), and Asp469 (XDFG motif), which are essential for stabilizing inhibitor binding. Molecular dynamics simulations confirmed the stability of TH470-LIMK1 and TH470-LIMK2 complexes, with lower RMS deviations and robust interaction patterns enhancing binding affinity. From the set of tetrapeptides mimicking TH470 binding mode, only YFYW, WPHW, and YWFP for LIMK1, and PYWG, FYWV, and WFVW for LIMK2 demonstrated high binding affinities, non-toxic profiles, and promising anti-cancer, anti-angiogenic, and anti-inflammatory properties. Among the studied peptides, LIMK1-YFYW and LIMK2-WFVW exhibited the most substantial binding affinities, supported by high hydrogen bond occupancy with key residues such as Ile416 and Thr405. The findings highlight the therapeutic potential of allosteric peptide inhibitors targeting LIMK-mediated pathways in cancer progression. The study underscores the importance of specific interactions with conserved LIMK residues, providing a foundation for further developing selective inhibitors to modulate actin dynamics and combat cancer-related processes.

Atomistic Profiling of KRAS Interactions with Monobodies and Affimer Proteins Through Ensemble-Based Mutational Scanning Unveils Conserved Residue Networks Linking Cryptic Pockets and Regulating Mechanisms of Binding, Specificity and Allostery

KRAS, a historically "undruggable" oncogenic driver, has eluded targeted therapies due to its lack of accessible binding pockets in its active state. This study investigates the conformational dynamics, binding mechanisms, and allosteric communication networks of KRAS in complexes with monobodies (12D1, 12D5) and affimer proteins (K6, K3, K69) to characterize the binding and allosteric mechanisms and hotspots of KRAS binding. Through molecular dynamics simulations, mutational scanning, binding free energy analysis and network-based analyses, we identified conserved allosteric hotspots that serve as critical nodes for long-range communication in KRAS. Key residues in β-strand 4 (F78, L80, F82), α-helix 3 (I93, H95, Y96), β-strand 5 (V114, N116), and α-helix 5 (Y157, L159, R164) consistently emerged as hotspots across diverse binding partners, forming contiguous networks linking functional regions of KRAS. Notably, β-strand 4 acts as a central hub for propagating conformational changes, while the cryptic allosteric pocket centered around H95/Y96 positions targeted by clinically approved inhibitors was identified as a universal hotspot for both binding and allostery. The study also reveals the interplay between structural rigidity and functional flexibility, where stabilization of one region induces compensatory flexibility in others, reflecting KRAS's adaptability to perturbations. We found that monobodies stabilize the switch II region of KRAS, disrupting coupling between switch I and II regions and leading to enhanced mobility in switch I of KRAS. Similarly, affimer K3 leverages the α3-helix as a hinge point to amplify its effects on KRAS dynamics. Mutational scanning and binding free energy analysis highlighted the energetic drivers of KRAS interactions. revealing key hotspot residues, including H95 and Y96 in the α3 helix, as major contributors to binding affinity and selectivity. Network analysis identified β-strand 4 as a central hub for propagating conformational changes, linking distant functional sites. The predicted allosteric hotspots strongly aligned with experimental data, validating the robustness of the computational approach. Despite distinct binding interfaces, shared hotspots highlight a conserved allosteric infrastructure, reinforcing their universal importance in KRAS signaling. The results of this study can inform rational design of small-molecule inhibitors that mimic the effects of monobodies and affimer proteins, challenging the "undruggable" reputation of KRAS.

A novel immunoinformatic approach for design and evaluation of heptavalent multiepitope foot-and-mouth disease virus vaccine

BACKGROUND

Foot-and-mouth disease virus (FMDV) vaccine development can be a laborious task due to the existence of various serotypes and lineages and its quasi-species nature. Immunoinformatics provide effective and promising avenue for the development of multiepitope vaccines against such complex pathogens. In this study, we developed an immunoinformatic pipeline to design a heptavalent multi-epitope vaccine targeting circulating FMDV isolates in Egypt.

RESULT

B and T-cell epitopes were predicted and selected epitopes were proved to be non-allergenic, non-toxic, with high antigenicity, and able to induce interferon-gamma response. The epitopes were used to construct a vaccine by adding suitable linkers and adjuvant. Prediction, refinement, and validation of the final construct proved its stability and solubility, having a theoretical isoelectric point (PI) of 9.4 and a molecular weight of 75.49 kDa. The final construct was evaluated for its interaction with bovine toll-like receptor (TLR) 2 and 4 using molecular docking analysis and molecular dynamic simulation showed high binding affinity, especially toward TLR4. MM/GBSA energy calculation supported these findings, confirming favorable energetics of the interaction. Finally, the DNA sequence of the vaccine was cloned in pET-30a (+) for efficient expression in Escherichia coli.

CONCLUSION

The inclusion of computational and immunoinformatic approaches will ensure cost-effectiveness and rapid design of FMDV vaccine, decrease wet lab experimentation, and aid the selection of novel FMDV vaccines. While the vaccine demonstrates promising in-silico results, experimental assessment of vaccine efficiency is required.

Nematode serine protease inhibitor SPI-I8 negatively regulates host NF-κB signalling by hijacking MKRN1-mediated polyubiquitination of RACK1

Parasitic roundworms are remarkable for their ability to manipulate host immune systems and ameliorate inflammatory diseases. Although much is known about the nature of nematode effectors in immune modulation, little is known about the action mode of these molecules. Here, we report that a serine protease inhibitor SPI-I8 in the extracellular vesicles of blood-feeding nematodes like Ancylostoma ceylanicum, Haemonchus contortus and Nippostrongylus brasiliensis, effectively halts excessive inflammatory responses in vitro and in vivo. We demonstrate that H. contortus SPI-I8 promotes the role of a negative regulator of RACK1 and enhances the effects of RACK1 on tumor necrosis factor (TNF)-α-IκB kinases (IKKs)-nuclear factor kappa beta (NF-κB) axis in mammalian cells, by hijacking E3 ubiquitin protein ligase MKRN1-mediated polyubiquitination of RACK1. Administration of recombinant N. brasiliensis SPI-I8 effectively protects mice from dextran sulfate sodium (DSS)-induced colitis and lipopolysaccharide (LPS)-induced sepsis. Considering the structural and functional conservation of SPI-I8s among Strongylida nematodes and the conservation of interactive mediators (i.e., MKRN1 and RACK1) among mammals, our findings provide insights into the host-parasite interface where parasitic roundworms secret molecules to suppress host inflammatory responses. Harnessing these findings should underpin the exploitation of nematode's immunomodulators to relief excessive inflammation associated diseases in animals and humans.

Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach

BACKGROUND

Acquired Immunodeficiency Syndrome (AIDS) is a critical global health issue caused by the human immunodeficiency virus (HIV). It has different strains and subtypes; among these, Subtype C accounts for higher infection rates than others. Despite its high prevalence, the molecular interactions with host receptors, specifically CD4, have not yet been explored.

METHODS

This study investigates the molecular interactions between HIV subtype C and the CD4 receptor via docking and dynamics approach. Four HIV targets were examined, and their structure was modelled. Subsequently, these models were docked with the CD4 to analyze their binding interaction. The stability was examined over 200 simulations via Desmond software, and trajectories were analyzed, followed by Root mean square deviation (RMSD), root mean square fluctuation (RMSF), and the radius of gyration (Rg), PCA (principal component analysis), etc., to assess their stability and interaction dynamics.

RESULTS

The four target structures were modelled, and their quality was validated. Further, the docking analysis with CD4 revealed that the Envelope glycoprotein has -13.6 kcal/mol, protease has -11.2 kcal/mol, Reverse transcriptase has -12.4 kcal/mol, and integrase has -13.1 kcal/mol binding affinity towards it, followed by the number of hydrogen bond, such as 9, 6, 11, 6. The simulation over 200 ns demonstrated that the average RMSD for each complex started stabilizing within the 0.9 Å - 3.4 Å, followed by 25-50 ns, whereas the RMSF, Rg and PCA revealed the relative compactness and flexibility varied across different viral targets.

CONCLUSIONS

The study successfully identified the interactive residues of HIV subtype C toward the CD4 receptor. The binding affinities and stability data provide valuable insights into Subtype C's molecular interactions with the host, and these findings underscore the potential for developing treatments that disrupt these interactions to combat HIV more effectively.

Multi-epitope-based vaccine models prioritization against Astrovirus MLB1 using immunoinformatics and reverse vaccinology approaches

Astrovirus MLB1 (HAstV-MLB1) is non-enveloped RNA virus that cause acute gastroenteritis infection. Despite research progress about infection and pathogenesis of HAstV-MLB1, Currently, no vaccine has been developed to effectively combat this pathogen. The current study is based on immunoinformatics and reverse vaccinology approaches to design next-generation, multi-epitope-based vaccine models against HAstV-MLB1. Genome-wide whole proteome data of HAstV-MLB1 strain was retrieved, and a series of analyses were conducted to explore effective B and T-cell epitopes that hold significant antigenic nature with no toxicity and allergenicity. A set of vaccine constructs were designed by different combination of lead B and T-cell epitopes with diverse linkers and adjuvants sequences. The model vaccine structures were analyzed via rigorous criteria of physiochemical properties, antigenicity, and molecular docking with HLA and TLR4 immune receptors to ensure their efficacy and safety. Based on the lowest binding energy of -82.48 kcal/mol against the HLA receptor, the MLB1-C2 vaccine model with β-definsin adjuvant was prioritized for molecular dynamic and immune simulations analyses to assess its stability and immunogenic potential. These analyses revealed that the MLB1-C2 construct has feasible molecular stability and potential to boost strong immune responses in the host cell. Besides, the model was predicted to be non-toxic, non-allergenic, and antigenic, ensuring broad population coverage and capable to elicit a robust immune response. The in-silico cloning analysis highlighted a possible gene expression potential of the MLB1-C2 construct in E.coli commercial recombinant vector molecule. The findings of the current study provide an essential template for the development of a advanced next-generation effective vaccine against HAstV-MLB1.

Identification of the therapeutic potential of novel TIGIT/PVR interaction blockers based advanced computational techniques and experimental validation

The inhibition of the TIGIT/PVR interaction demonstrates considerable anticancer properties by enhancing the cytotoxic activity of natural killer (NK) and CD8+ T cells. However, the development of small molecule inhibitors that target TIGIT is currently limited. In this study, small molecules with the capacity to bind TIGIT and block the TIGIT/PVR interaction were screened through an advanced computational process, subsequently confirmed by blocking assays. Combined machine learning model XGBOOST and centroid-based molecular docking were employed to expeditiously exclude negative molecules, thereby reducing the chemical space. Subsequently, a blockade assay targeting the TIGIT/PVR interaction was conducted on 14 candidate molecules along with positive control, wherein compound MCULE-5547257859 exhibited the most potent inhibitory effect. Molecular dynamics simulations and binding free energy analyses revealed that compound MCULE-5547257859 possesses a thermodynamically stable conformation, indicative of a stronger binding affinity to TIGIT. In conclusion, our investigation has delineated that compound MCULE-5547257859 effectively impedes the TIGIT/PVR interaction, thereby offering a novel therapeutic modality for oncology.

Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches

Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.

A potential therapeutic strategy by fungal laccase targeting novel binding sites on human cytomegalovirus DNA polymerase

Human cytomegalovirus (HCMV) is a common herpesvirus that can severely affect transplant recipients, those with AIDS, and newborns. Existing synthetic medications face limitations, including toxicity, processing issues, and viral resistance. As part of this study, the efficacy of the extracellular enzyme laccase isolated from a widely available mushroom (Pleurotus pulmonarius) was compared to that of ganciclovir, a common antiviral, used against HCMV. The study found that laccase can synergistically inhibit HCMV replication by targeting new inhibitory sites on the UL54 protein. Viral replication requires significant energy, increasing cellular respiration. The antiviral effect of laccase was linked to reduced expression of genes regulating cellular respiration, which coincided with decreased viral DNA copies. Additionally, in silico analysis has identified a novel binding site for the laccase enzyme in the C-terminal region of HCMV DNA polymerase specifically between amino acids 1004 and 1242, which effectively obstructs the binding of the essential viral replication regulatory accessory protein UL44, thereby hindering successful replication. Molecular dynamics simulations were performed under standardized conditions mimicking a cellular environment, revealing a stable protein-protein docking complex. This study may aid in developing novel antiviral strategies by utilizing laccase's target specificity to regulate host cellular pathways against Herpesviridae.

Targeting the E Prostanoid Receptor EP4 Mitigates Cardiac Fibrosis Induced by β-Adrenergic Activation

Sustained β-adrenergic activation induces cardiac fibrosis characterized by excessive deposition of extracellular matrix (ECM). Prostaglandin E2 (PGE2) receptor EP4 is essential for cardiovascular homeostasis. This study aims to investigate the roles of cardiomyocyte (CM) and cardiac fibroblast (CF) EP4 in isoproterenol (ISO)-induced cardiac fibrosis. By crossing the EP4f/f mice with α-MyHC-Cre or S100A4-Cre mice, this work obtains the CM-EP4 knockout (EP4f/f-α-MyHCCre+) or CF-EP4 knockout (EP4f/f-S100A4Cre+) mice. The mice of both genders are subcutaneously injected with ISO (5 mg kg-1 day-1) for 7 days. Compared to the control mice, both EP4f/f-α-MyHCCre+ and EP4f/f-S100A4Cre+ mice show a significant improvement in cardiac diastolic function and fibrosis as assessed by echocardiography and histological staining, respectively. In the CMs, inhibition of EP4 suppresses ISO-induced TGF-β1 expression via blocking the cAMP/PKA pathway. In the CFs, inhibition of EP4 reversed TGF-β1-triggers production of ECM via preventing the formation of the TGF-β1/TGF-β receptor complex and blocks CF proliferation via suppressing the ERK1/2 pathway. Furthermore, double knockout of the CM- and CF-EP4 or administration of EP4 antagonist, grapiprant, markedly improves ISO-induced cardiac diastolic dysfunction and fibrosis. Collectively, this study demonstrates that both CM-EP4 and CF-EP4 contribute to β-adrenergic activation-induced cardiac fibrosis. Targeting EP4 may offer a novel therapeutic approach for cardiac fibrosis.

Macromolecular interaction mechanism of the bacteriocin EntDD14 with the receptor binding domain (RBD) for the inhibition of SARS-CoV-2 and the JN.1 variant: Biomedical study based on elastic networks, stochastic Markov models, and macromolecular volumetric analysis

Bacteriocins, a class of molecules produced by bacteria, exhibit potent antimicrobial properties, including antiviral activities. The urgent need for treatments against SARS-CoV-2 has proposed bacteriocins such as enterocin DD14 (EntDD14) as potential therapeutic agents. However, the mechanism of macromolecular interaction of EntDD14 for the inhibition of SARS-CoV-2 is not yet fully understood, and its efficacy against variants like JN.1 has not been completely established. To address these knowledge gaps, biocomputational analyses were employed using a diverse set of tools, including Markov state models and volumetric analyses. This analysis revealed a favorable interaction between EntDD14 and the receptor-binding domain (RBD) of SARS-CoV-2. Furthermore, it was found that EntDD14 induces changes in the flexibility of the RBD and alters the distribution and size of its internal cavities, particularly in the JN.1 variant. These findings align with experimental observations and support the inhibitory mechanism of EntDD14 against SARS-CoV-2. Additionally, they suggest that EntDD14 may possess a broader spectrum of action, encompassing the JN.1 variant. This study paves the way for future investigations and therapeutic applications, encouraging further exploration of the antiviral activity of bacteriocins like EntDD14 against variants of concern like JN.1. However, additional experimental demonstrations are warranted to substantiate these findings.

Abnormal Expression of Proteolytic Stress-Related Proteins and Protective Effect of Fibrinolytic Enzymes in Prion Diseases

Prion diseases are fatal, irreversible, and infectious neurodegenerative diseases caused by proteinase K-resistant prion protein (PrPSc). Against PrPSc, several endogenous proteases involved in cellular degradation mechanisms can be activated to remove PrPSc. However, since PrPSc shows proteinase K resistance, we presumed that undegradable PrPSc induces positive feedback on the overactivation of the cellular degradation mechanisms and is correlated with proteolytic stress and exacerbation of the progression of prion diseases. We investigated the expression pattern of proteolytic stress-related proteins in the brains of ME7 scrapie-infected mice at 7 months postinfection and sporadic Creutzfeldt-Jakob disease (CJD) patients using western blotting and immunohistochemistry (IHC). In addition, we analyzed the 3D structure and binding complexes of prion protein (PrP) with nattokinase and lumbrokinase using in silico programs, including SWISS-MODEL and HawkDock. To fundamentally reduce proteolytic stress by the degradation of PrPSc, we performed an in vitro evaluation of the PrPSc degradation abilities of fibrinolytic enzymes, including nattokinase and lumbrokinase. Furthermore, we assessed the protective effects of nattokinase and lumbrokinase in ME7 scrapie-infected mice. We observed an abnormal accumulation of proteolytic stress-related proteins, including CD10, cathepsin B, cathepsin D, and matrix metalloproteinase 9 (MMP9), in the brains of ME7 scrapie-infected mice and sporadic CJD patients. In addition, we identified that nattokinase and lumbrokinase can stably bind to PrP. Furthermore, we identified significant in vitro degradation of PrPSc derived from ME7 scrapie-infected mice and sporadic CJD patients by nattokinase and lumbrokinase. Last, we found in vivo protective effects of nattokinase and lumbrokinase against prion disease in ME7 scrapie-infected mice. To the best of our knowledge, this is the first report on the identification of proteolytic stress-related novel potential biomarkers and the therapeutic potential of nattokinase and lumbrokinase for prion diseases.

Molecular dynamics simulation shows enhanced stability in scaffold-based macromolecule, designed by protein engineering: a novel methodology adapted for converting Mtb Ag85A to a multi-epitope vaccine

CONTEXT

Multi-epitope vaccine (MEV) construction is a technique which combines multiple epitopes, both B cell epitopes and T cell epitopes which have the potential to elicit a much stronger immune response compared to a subunit vaccine. Therefore, recently, a lot of research has been focused on development and improvement of multiepitope vaccines. The strategy of designing a MEV in silico lies in a few basic steps, including procuring the amino acid sequence of the B cell and T cell epitopes from literature search, bioinformatics approach, to construct a potent immunogen capable of eliciting both humoral and cell-mediated response and finally joining these epitopes by linkers. However, a vaccine constructed by merely joining the epitopes may not always result in a stable globular structured protein. In this study, we have focused on developing a strategy where a potential vaccine candidate of Mycobacterium tuberculosis has been used as a scaffold and the low complexity regions of this scaffold have been replaced by the predicated epitopes. Essentially, instead of joining the epitopes by linkers, they have been carefully positioned on a scaffold of a protein that is itself a vaccine candidate to derive a MEV against Mycobacterium tuberculosis.

METHOD

In this study, a methodology has been detailed to tackle this great challenge using a simple approach of protein engineering. A scaffold-based MEV has been designed against Mtb by converting a vaccine candidate protein, Ag85A, into a scaffold by truncating its low complexity non-immunogenic regions, and the gaps were supplemented by the highly immunogenic epitopes. Replicated 500 ns molecular dynamics simulation at different temperatures (300 K and 310 K) and principal component analysis proved that MEV built on the scaffold is more stable than the conventional one.

Unlocking the potential of in silico approach in designing antibodies against SARS-CoV-2

Antibodies are naturally produced safeguarding proteins that the immune system generates to fight against invasive invaders. For centuries, they have been produced artificially and utilized to eradicate various infectious diseases. Given the ongoing threat posed by COVID-19 pandemics worldwide, antibodies have become one of the most promising treatments to prevent infection and save millions of lives. Currently, in silico techniques provide an innovative approach for developing antibodies, which significantly impacts the formulation of antibodies. These techniques develop antibodies with great specificity and potency against diseases such as SARS-CoV-2 by using computational tools and algorithms. Conventional methods for designing and developing antibodies are frequently costly and time-consuming. However, in silico approach offers a contemporary, effective, and economical paradigm for creating next-generation antibodies, especially in accordance with recent developments in bioinformatics. By utilizing multiple antibody databases and high-throughput approaches, a unique antibody construct can be designed in silico, facilitating accurate, reliable, and secure antibody development for human use. Compared to their traditionally developed equivalents, a large number of in silico-designed antibodies have advanced swiftly to clinical trials and became accessible sooner. This article helps researchers develop SARS-CoV-2 antibodies more quickly and affordably by giving them access to current information on computational approaches for antibody creation.

Designing of a multiepitope-based vaccine against echinococcosis utilizing the potent Ag5 antigen: Immunoinformatics and simulation approaches

Echinococcosis is a significant parasitic zoonotic disease with severe implications for human and animal health. To date, there has been no effective vaccine candidate available for echinococcosis. Therefore, we employed computational approaches to develop a multiepitope-based vaccine using the most potent epitopes of MHC-I, MHC-II, and B-cell derived from the Ag5 protein of Echinococcus spp. The final vaccine construct containing the epitopes, linkers, and adjuvant exhibited potent antigenicity (score > 0.1) with no evidence of allergenicity (score < 0) and toxicity (score < 0) in several computational platforms. The vaccine also exhibited favorable physicochemical characteristics such as being highly soluble (SOLpro score of 0.781243) and hydrophilic (Grand average of hydropathy of -0.433). Moreover, the tertiary structure of the vaccine was also found to be structurally stable, with a Z score of -5.71. Further, the molecular docking analysis confirmed the vaccine's significant binding affinity to the RP-105 (docking score of -1252.7) and TLR-9 (docking score of -970.9). The molecular dynamic simulations confirmed the structural stability of the docked complexes under a virtual physiological system. The negative ΔTOTAL values derived from the MM-PBSA and MM-GBSA analyses confirmed a spontaneous and thermodynamically favorable binding process between the vaccine and receptors. Moreover, the vaccine demonstrated high potentiality to elicit both innate (natural killer cell, dendritic and macrophage) and adaptive (B-cell, helper T cell and cytotoxic T cell) immune responses with sustained humoral immune responses evidenced by increased IFN-γ and IL-2 levels. Following codon optimization and in silico cloning, the vaccine was successfully expressed (CAI value of 0.9607 and average GC content of 52.34%) after being inserted into the pET-28a (+) plasmid of E. coli. These findings highlight the potential of the designed vaccine candidate to combat echinococcosis and lay the groundwork for future preclinical and clinical studies.

Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A-D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key binding hotspots, and explored the evolutionary strategies employed by the virus to evade neutralization. The residue-based decomposition analysis revealed energetic mechanisms and thermodynamic factors underlying the effect of mutations on antibody binding. The results demonstrate excellent qualitative agreement between the predicted binding hotspots and the latest experiments on antibody escape. These findings provide valuable insights into the molecular determinants of antibody binding and viral escape, highlighting the importance of targeting conserved epitopes and leveraging combination therapies to mitigate the risk of immune evasion.

TREM-1 as a Potential Coreceptor in Norovirus Pathogenesis: Insights from Transcriptomic Analysis and Molecular Docking

Norovirus (NoV) is a major cause of acute diarrheal disease in humans. However, due to complications in cultivating this virus, bioinformatics aids in elucidating the virus-host relationship. One of the molecules that has been associated with the burden of viral diseases is TREM-1, mainly due to its role in amplifying the inflammatory response. Thus, we hypothesized that TREM-1 may be involved in NoV infection. Analysis of public transcriptomic data sets showed an increased expression of Trem1 and Trem3 during murine NoV (MNoV) infection. Then, molecular docking was performed between murine TREM-1 and the P domain of the MNoV VP1 protein. The viral antigenic segment C'-D' was recognized by the murine TREM-1 CDR1 region. Subsequently, based on phylogenetic criteria, NoV VP1 proteins from the GII.4 genotype sequenced in different years (1987, 2010, 2012, 2014, 2016, and 2019) were modeled. Using docking and molecular dynamics simulations, a stable interaction was observed between the human TREM-1 Ig-like domain and the conserved S and P segments of the NoV VP1 protein. Notably, this interaction was conserved over the years and was mainly dictated by the TREM-1 CDR3 region. Also, coexpression between Trem1 with genes involved in apoptosis and pyroptosis pathways was surveyed during viral infection by MNoV. It was found that Trem1 is primarily expressed with genes from the pyroptosis pathway. These simulations strongly suggest the involvement of TREM-1 in NoV pathogenesis and its potential contribution as a coreceptor.

Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies

A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning of SARS-CoV-2 spike residues, and binding free energy computations for two distinct groups of broadly neutralizing antibodies: the E1 group (BD55-3152, BD55-3546, and BD5-5840) and the F3 group (BD55-3372, BD55-4637, and BD55-5514). Using these approaches, we examined the energetic determinants by which broadly potent antibodies can largely evade immune resistance. Our analysis revealed the emergence of a small number of immune escape positions for E1 group antibodies that correspond to the R346 and K444 positions in which the strong van der Waals and interactions act synchronously, leading to the large binding contribution. According to our results, the E1 and F3 groups of Abs effectively exploit binding hotspot clusters of hydrophobic sites that are critical for spike functions along with the selective complementary targeting of positively charged sites that are important for ACE2 binding. Together with targeting conserved epitopes, these groups of antibodies can lead expand the breadth and resilience of neutralization to the antigenic shifts associated with viral evolution. The results of this study and the energetic analysis demonstrate excellent qualitative agreement between the predicted binding hotspots and critical mutations with respect to the latest experiments on average antibody escape scores. We argue that the E1 and F3 groups of antibodies targeting binding epitopes may leverage strong hydrophobic interactions with the binding epitope hotspots that are critical for the spike stability and ACE2 binding, while escape mutations tend to emerge in sites associated with synergistically strong hydrophobic and electrostatic interactions.

Impact of African-Specific ACE2 Polymorphisms on Omicron BA.4/5 RBD Binding and Allosteric Communication Within the ACE2-RBD Protein Complex

Severe acute respiratory symptom coronavirus 2 (SARS-CoV-2) infection occurs via the attachment of the spike (S) protein's receptor binding domain (RBD) to human ACE2 (hACE2). Natural polymorphisms in hACE2, particularly at the interface, may alter RBD-hACE2 interactions, potentially affecting viral infectivity across populations. This study identified the effects of six naturally occurring hACE2 polymorphisms with high allele frequency in the African population (S19P, K26R, M82I, K341R, N546D and D597Q) on the interaction with the S protein RBD of the BA.4/5 Omicron sub-lineage through post-molecular dynamics (MD), inter-protein interaction and dynamic residue network (DRN) analyses. Inter-protein interaction analysis suggested that the K26R variation, with the highest interactions, aligns with reports of enhanced RBD binding and increased SARS-CoV-2 susceptibility. Conversely, S19P, showing the fewest interactions and largest inter-protein distances, agrees with studies indicating it hinders RBD binding. The hACE2 M82I substitution destabilized RBD-hACE2 interactions, reducing contact frequency from 92 (WT) to 27. The K341R hACE2 variant, located distally, had allosteric effects that increased RBD-hACE2 contacts compared to WThACE2. This polymorphism has been linked to enhanced affinity for Alpha, Beta and Delta lineages. DRN analyses revealed that hACE2 polymorphisms may alter the interaction networks, especially in key residues involved in enzyme activity and RBD binding. Notably, S19P may weaken hACE2-RBD interactions, while M82I showed reduced centrality of zinc and chloride-coordinating residues, hinting at impaired communication pathways. Overall, our findings show that hACE2 polymorphisms affect S BA.4/5 RBD stability and modulate spike RBD-hACE2 interactions, potentially influencing SARS-CoV-2 infectivity-key insights for vaccine and therapeutic development.

Identification and Validation of B-Cell Epitopes on the VP1 Protein of Parvovirus B19 through Molecular Docking and Dynamics Simulation

This study aimed to identify B-cell epitope candidates using multiple epitope identification software and in silico analysis of the modeled B19 V protein against specific antibodies using molecular docking and dynamics simulation. Materials and Methods : Full-length amino acid sequences of the VP1 protein of B19 V were retrieved from NCBI. A consensus sequence was generated using CLC sequence viewer. Linear B cell epitopes were identified using Bepipred 2.0, ABCpred, and LBTope. The linear epitope was synthesized and validated against B19 V-specific antibodies. A 3D model of the B19 V VP1 consensus protein was generated using the ITASSER server. Discontinuous B cell epitopes were identified using Discotope 2.0 and Ellipro. Molecular docking and molecular dynamics simulation was performed to investigate the interaction between the modeled B19 V protein and specific anti-B19 V antibody. Results : The identified epitope was 100% conserved and similarly identified through ABCpred and LBTope. The HADDOCK score and MDS analysis, such as hydrogen bond interactions and MMPBSA analysis, revealed that the VP1 and mAb H chains formed a significantly stable complex. The MDS demonstrated that the VP1-mAb H chain complexes had lower RMSF values around 130 to 200 residues, a region responsible for the catalytic network for enzyme activity; as a result, the flexibility of the antibody-bound VP1 decreased when compared to Apo-VP1. Conclusion: A viable epitope identified through this process was synthesized and validated using ELISA, which highlighted the role of the epitope identification process in diagnostics. This study also sheds light on the complex interplay between VP1 and the mAb H chain and highlights key binding specificity and stability determinants.

Characterization and kinetics of a cathepsin B-inhibiting protein from Musa acuminata Colla peel

Hyperexpression of cathepsin B caused by an imbalance of endogenous inhibitors is involved in multiple pathologies, hence making it a key therapeutic target. Protease inhibitors are effective biomolecules that regulate protease activities and are considered potential therapeutic agents in various diseases. Plant protease inhibitors have been reported as an effective complementary alternative drug. A proteinaceous cathepsin B inhibitor (CBI-BP) has been isolated from Musa acuminata Colla (banana) peel with a molecular weight of 27.9 kDa on SDS-PAGE. The purity of the CBI-BP was confirmed on the native- PAGE. The isolated CBI-BP showed an IC50 value of 8.14 μg and a Ki value of 10.59 μg (0.19 μM). Cathepsin B inhibition kinetics indicated that CBI-BP follows a mixed-type of cathepsin B inhibition. Its inhibition activity was also confirmed by reverse zymography. The inhibitor was stable from pH 2.6-10.0 with maximum activity at pH 7.2, temperature 25-100 °C and exhibited thermostability for 60 min at 70 °C. MALDI/TOF/MS analysis of CBI-BP showed 40 % similarity to the GH18 domain-containing protein (A0A4S8JRM9) from Musa balbisiana. Although in-silico docking studies showed binding of A0A4S8JRM9 to cathepsin B affects the binding energy of the substrate to cathepsin B but is not reported for any anti-cathepsin B activity. This suggests that isolated CBI-BP might be a novel protein with anti-cathepsin B activity. Thus the isolated CBI-BP may be further explored as possible anti-cathepsin B drug.

Citrullination at the N-terminal region of MDM2 by the PADI4 enzyme

PADI4 is one of the human isoforms of a family of enzymes involved in the conversion of arginine to citrulline. MDM2 is an E3 ubiquitin ligase that is critical for degradation of the tumor suppressor gene p53. We have previously shown that there is an interaction between MDM2 and PADI4 in cellulo, and that such interaction occurs through the N-terminal region of MDM2, N-MDM2, and in particular through residues Thr26, Val28, Phe91, and Lys98. Here, by using a "divide-and-conquer" approach, we have designed and synthesized peptides comprising these two polypeptide stretches (residues Ala21-Lys36, and Lys94-Val108), either in the wild-type species or in their citrullinated versions. Some of the citrullinated peptides were aggregation-prone, as suggested by DOSY-NMR experiments, but the wild-type versions of both fragments were monomeric in solution. We found out that wild-type and modified peptides were disordered in all cases, as also tested by far-UV circular dichroism (CD), and citrullination mainly affected the NMR chemical shifts of adjacent residues. Isothermal titration calorimetry (ITC) in the absence and presence of GSK484, an enzymatic PADI4 inhibitor, indicated that this compound blocked binding of the peptides to the enzyme. Binding to the active site of the N-MDM2 fragments was also confirmed by in silico experiments. The affinities of PADI4 for the wild-type peptides were more favorable than those of the corresponding citrullinated ones, but all measured values were within the micromolar range, indicating that there were no major variations in the thermodynamics of binding due to sequence effects. The kinetic dissociation rates, koff, measured by biolayer interferometry (BLI), were always one-order of magnitude faster for the citrullinated peptides than for the wild-type ones. Taken together, all these findings indicate that MDM2 is a substrate for PADI4 and is prone to citrullination in the identified (and specific) positions of its N-terminal region.

Design and assessment of two broad-spectrum multi-epitope vaccine candidates against bovine viral diarrhea virus based on the E0 or E2 envelope glycoprotein

Bovine viral diarrhea virus (BVDV) is a significant pathogen that exerts substantial economic influence on the global cattle industry. Developing a safe and effective novel vaccine targeting various BVDV subtypes is critical for controlling BVDV infection. In the study, we created two distinct multi-epitope vaccines by linking highly conserved and dominant cytotoxic T-lymphocytes (CTL), helper T-lymphocytes (HTL), and B-cell epitopes from either the E0 or E2 envelope glycoprotein of diverse BVDV subtypes. To enhance immunogenicity, β-defensin-3 was fused to the N-terminus of these constructs as an adjuvant. Using multiple immunoinformatics tools, we conducted an analysis and assessment of the vaccine constructs' physicochemical properties and immunological features. Consequently, two prospective vaccine candidates named BVDV-M1 and BVDV-M2 were successfully designed and shown to be stable, antigenic, non-allergenic, and non-toxic. The optimized vaccine 3D models exhibit excellent structural quality. Molecular docking revealed a strong interaction between the vaccines with bovine TLR2 and TLR4. The stability of the docked vaccine-TLR complexes was confirmed through molecular dynamics simulation. Immune simulation analyses indicated that both vaccines have the potential to induce high levels of antibodies IgM, IgG and the cytokines IFN-γ and IL-2. Furthermore, the vaccine's efficient expression in the E.coli system was secured through codon optimization coupled with in silico cloning. Summarily, the designed multi-epitope vaccines have the potential to elicit robust humoral and cellular immune responses, positioning them as hopeful broad-spectrum vaccine candidates against the currently prevalent BVDV subtypes.

Accurate Characterization of the Allosteric Energy Landscapes, Binding Hotspots and Long-Range Communications for KRAS Complexes with Effector Proteins : Integrative Approach Using Microsecond Molecular Dynamics, Deep Mutational Scanning of Binding Energetics and Allosteric Network Modeling

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Oncogenic mutations in KRAS, including G12V, G13D, and Q61R, drive constitutive activation and hyperactivation of signaling pathways, contributing to cancer progression. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS binding and allostery by which oncogenic mutations enhance KRAS-RAF1 binding and signaling remain incompletely understood. In this study, we employ microsecond molecular dynamics simulations, Markov State Modeling, mutational scanning and binding free energy calculations together with dynamic network modeling to elucidate the effect of KRAS mutations and characterize the thermodynamic and allosteric drivers and hotspots of KRAS binding and oncogenic activation. Our simulations revealed that oncogenic mutations stabilize the open active conformation of KRAS by differentially modulating the flexibility of the switch I and switch II regions, thereby enhancing RAF1 binding affinity. The G12V mutation rigidifies both switch I and switch II, locking KRAS in a stable, active state. In contrast, the G13D mutation moderately reduces switch I flexibility while increasing switch II dynamics, restoring a balance between stability and flexibility. The Q61R mutation induces a more complex conformational landscape, characterized by the increased switch II flexibility and expansion of functional macrostates, which promotes prolonged RAF1 binding and signaling. Mutational scanning of KRAS-RAF1 complexes identified key binding affinity hotspots, including Y40, E37, D38, and D33, and together with the MM-GBSA analysis revealed the hotspots leverage synergistic electrostatic and hydrophobic binding interactions in stabilizing the KRAS-RAF1 complexes. Network-based analysis of allosteric communication identifies critical KRAS residues (e.g., L6, E37, D57, R97) that mediate long-range interactions between the KRAS core and the RAF1 binding interface. The central β-sheet of KRAS emerges as a hub for transmitting conformational changes, linking distant functional sites and facilitating allosteric regulation. Strikingly, the predicted allosteric hotspots align with experimentally identified allosteric binding hotspots that define the energy landscape of KRAS allostery. This study highlights the power of integrating computational modeling with experimental data to unravel the complex dynamics of KRAS and its mutants. The identification of binding hotspots and allosteric communication routes offers new opportunities for developing targeted therapies to disrupt KRAS-RAF1 interactions and inhibit oncogenic signaling. Our results underscore the potential of computational approaches to guide the design of allosteric inhibitors and mutant-specific therapies for KRAS-driven cancers.

Designing a broad-spectrum multi-epitope subunit vaccine against leptospirosis using immunoinformatics and structural approaches

Introduction

Leptospirosis, caused by Leptospira interrogans, is a neglected zoonotic disease that poses a significant global health risk to both humans and animals. The rise of antimicrobial resistance and the inefficacy of existing vaccines highlight the urgent need for new preventive strategies.

Methods

An immunoinformatics approach was employed to design a multi-epitope subunit vaccine (MESV) against leptospirosis. B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes were selected from five key Leptospira proteins. These epitopes were fused with a heparin-binding hemagglutinin (HBHA) adjuvant and appropriate linkers to construct the broad-spectrum vaccine. The physicochemical properties of the vaccine were assessed, including antigenicity, immunogenicity, allergenicity, and conservation. The vaccine's 3D structure was modeled, optimized, and validated. Molecular docking, molecular dynamics simulations, and MM-GBSA analysis were performed to assess the vaccine's binding interactions with Toll-like receptors (TLR2 and TLR4). Immune simulations and in silico cloning were also conducted to evaluate the vaccine's immune response and expression potential.

Results

The MESV demonstrated high antigenicity, immunogenicity, non-allergenicity, and conservation across different Leptospira strains. Population coverage analysis revealed that T-cell epitopes significantly interacted with HLA molecules, covering 95.7% of the global population. Molecular docking showed strong and stable binding with TLR2 and TLR4, with binding energies of -1,357.1 kJ/mol and -1,163.7 kJ/mol, respectively. Molecular dynamics simulations and MM-GBSA analysis confirmed the stability of these interactions and accurately calculated the intermolecular binding free energies. Immune simulations indicated robust B and T cell responses, and in silico cloning demonstrated that the vaccine could be successfully expressed in E. coli.

Discussion

These findings suggest that MESV is a promising candidate for leptospirosis prevention, providing robust immune responses and broad population coverage. However, further in vivo studies are necessary to validate its efficacy and safety.

Computational epitope-based vaccine design with bioinformatics approach; a review

The significance of vaccine development has gained heightened importance in light of the COVID-19 pandemic. In such critical circumstances, global citizens anticipate researchers in this field to swiftly identify a vaccine candidate to combat the pandemic's root cause. It is widely recognized that the vaccine design process is traditionally both time-consuming and costly. However, a specialized subfield within bioinformatics, known as "multi-epitope vaccine design" or "reverse vaccinology," has significantly decreased the time and costs of the vaccine design process. The methodology reverses itself in this subfield and finds a potential vaccine candidate by analyzing the pathogen's genome. Leveraging the tools available in this domain, we strive to pinpoint the most suitable antigen for crafting a vaccine against our target. Once the optimal antigen is identified, the next step involves uncovering epitopes within this antigen. The immune system recognizes particular areas of an antigen as epitopes. By characterizing these crucial segments, we gain the opportunity to design a vaccine centered around these epitopes. Subsequently, after identifying and assembling the vital epitopes with the assistance of linkers and adjuvants, our vaccine candidate can be formulated. Finally, employing computational techniques, we can thoroughly evaluate the designed vaccine. This review article comprehensively covers the entire multi-epitope vaccine development process, starting from obtaining the pathogen's genome to identifying the relevant vaccine candidate and concluding with an evaluation. Furthermore, we will delve into the essential tools needed at each stage, comparing and introducing them.

Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease

This study evaluates the performance of various structure prediction tools and molecular docking platforms for therapeutic peptides targeting coronary artery disease (CAD). Structure prediction tools, including AlphaFold 3, I-TASSER 5.1, and PEP-FOLD 4, were employed to generate accurate peptide conformations. These methods, ranging from deep-learning-based (AlphaFold) to template-based (I-TASSER 5.1) and fragment-based (PEP-FOLD), were selected for their proven capabilities in predicting reliable structures. Molecular docking was conducted using four platforms (HADDOCK 2.4, HPEPDOCK 2.0, ClusPro 2.0, and HawDock 2.0) to assess binding affinities and interactions. A 100 ns molecular dynamics (MD) simulation was performed to evaluate the stability of the peptide-receptor complexes, along with Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) calculations to determine binding free energies. The results demonstrated that Apelin, a therapeutic peptide, exhibited superior binding affinities and stability across all platforms, making it a promising candidate for CAD therapy. Apelin's interactions with key receptors involved in cardiovascular health were notably stronger and more stable compared to the other peptides tested. These findings underscore the importance of integrating advanced computational tools for peptide design and evaluation, offering valuable insights for future therapeutic applications in CAD. Future work should focus on in vivo validation and combination therapies to fully explore the clinical potential of these therapeutic peptides.

NLS-binding deficient Kapβ2 reduces neurotoxicity via selective interaction with C9orf72-ALS/FTD dipeptide repeats

Arginine-rich dipeptide repeat proteins (R-DPRs) are highly toxic proteins found in patients with C9orf72-linked amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). R-DPRs can cause toxicity by disrupting the natural phase behavior of RNA-binding proteins (RBPs). Mitigating this abnormal phase behavior is, therefore, crucial to reduce R-DPR-induced toxicity. Here, we use FUS as a model RBP to investigate the mechanism of R-DPR-induced aberrant RBP phase transition. We find that this phase transition can be mitigated by Kapβ2. However, as a nuclear import receptor and phase modifier for PY-NLS-containing RBPs, the function of WT Kapβ2 could lead to undesired interaction with its native substrates when used as therapeutics for C9-ALS/FTD. To address this issue, it is crucial to devise effective strategies that allow Kapβ2 to selectively target its binding to the R-DPRs, instead of the RBPs. We show that NLS-binding deficient Kapβ2W460A:W730A can indeed selectively interact with R-DPRs in FUS assembly without affecting normal FUS phase separation. Importantly, Kapβ2W460A:W730A prevents enrichment of poly(GR) in stress granules and mitigates R-DPR neurotoxicity. Thus, NLS-binding deficient Kapβ2 may be implemented as a potential therapeutic for C9-ALS/FTD.

Ligand docking in the sigma-1 receptor compared to the sigma-1 receptor-BiP complex and the effects of agonists and antagonists on C. elegans lifespans

Model organisms are commonly used to study human diseases; we set out to understand the relevance of several model organisms with relation to the σ1R protein. The study explored the interactions of σ1R with various agonists, antagonists across different species. Ligand and protein-protein (σ1R-BiP) docking approaches were used to understand the significance of σ1R in modulating neuroprotective mechanisms and its potential role in Alzheimer's. Ligand docking revealed that common σ1R antagonists generally exhibited stronger σ1R binding than commonly used agonists. Human σ1R showed high binding affinity for S1RA and NE100. Orthologs in yeast, slime mold, and C. elegans displayed varied binding affinities, indicating evolutionary adaptation in their binding pockets. We evaluated the relevance of σ1R-ligand interactions in C. elegans, measuring life-spans showing the impact of ligands on lifespan depends on genetic background and amyloid-beta pathology. Haloperidol (5-10 mM) extended wild-type worms' lifespan, but this effect was absent in the σ1R-KO, suggesting at least a partial role for the σ1R. Fluoxetine (5-10 mM) also promoted a small increase in longevity in wild-type worms but was not seen in the σ1R-KO strain. BD1047 (5 & 10 mM) reduced the lifespan of amyloid-beta-expressing transgenic worms, whereas dipentylamine (DPA) (5 mM) significantly increased the lifespan in a σ1R antagonist-sensitive manner. These findings highlight the importance of the σ1R in neurodegeneration and suggest that ligand interactions are modulated by BiP. Further research using in-vitro and in-vivo models is needed to clarify σ1R's therapeutic potential in neurodegenerative diseases, where modulating σ1R could provide neuroprotective effects.

Insect Brain Proteomics: A Case Study of Periplaneta americana

Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.

Exploring B-cell epitope conservation and antigenicity shift in current COVID-19 variants: Analyzing spike-antibody interactions for therapeutic uses

SARS-CoV-2, responsible for the global COVID-19 pandemic, has undergone significant genetic changes, leading to various variants impacting transmissibility, severity, and vaccine efficacy. The methodology involved evaluating SARS-CoV-2 variants designated by WHO as Variants of Interest (VOIs) and Variants Under Monitoring (VUMs). Several noteworthy mutations including G446S, K417N, T478K, E484A, N501Y, and Y505H exhibit a strong pattern of convergent evolution across all these variants, particularly at antigenic sites within the spike protein. Conformational epitopes mapping and antigenicity shift analyses implicated epitope changes which were compared for therapeutic purposes. VUMs BA.2.86 and XBB.2.3 show significant antigenicity changes and epitope dynamics, correlating with high root mean square deviation values and epitope expansions or contractions. Nonsynonymous mutations are predominant in all variants, suggesting functional changes affecting transmissibility and immune evasion. VOIs XBB.1.5, BA.2.86, and CH.1.1 show high solvent-accessible surface area and radius of gyration, indicating structural expansion and increased epitope availability. In contrast, stable VOI EG.5.1 displays minimal structural changes and moderate epitope expansions. We evaluated two classes of antibodies for their effectiveness in neutralizing SARS-CoV-2 variants. Antibodies CC12.1 and P4A1 from Class I, alongside CV07-250, P5A-2G9, and MW05 from Class II, display strong binding across multiple variants, indicating broad neutralizing capabilities. Specifically, P4A1 shows the highest affinity for EG.5 and EG.5.1, while MW05 exhibits the strongest binding to XBB.1.5, CH.1.1, and XBB.2.3, highlighting their potent neutralization potential. This study aims to elucidate epitope variations in evolving SARS-CoV-2 strains, offering critical insights for developing targeted interventions against current challenges posed by the virus.

Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies

The growing body of experimental and computational studies suggested that the cross-neutralization antibody activity against Omicron variants may be driven by balance and tradeoff of multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with the epitope residues remain scarcely characterized. In this study, we performed molecular dynamics simulations, ensemble-based deep mutational scanning of SARS-CoV-2 spike residues and binding free energy computations for two distinct groups of broadly neutralizing antibodies : E1 group (BD55-3152, BD55-3546 and BD5-5840) and F3 group (BD55-3372, BD55-4637 and BD55-5514). Using these approaches, we examine the energetic determinants by which broadly potent antibodies can largely evade immune resistance. Our analysis revealed the emergence of a small number of immune escape positions for E1 group antibodies that correspond to R346 and K444 positions in which the strong van der Waals and interactions act synchronously leading to the large binding contribution. According to our results, E1 and F3 groups of Abs effectively exploit binding hotspot clusters of hydrophobic sites critical for spike functions along with selective complementary targeting of positively charged sites that are important for ACE2 binding. Together with targeting conserved epitopes, these groups of antibodies can lead to the expanded neutralization breadth and resilience to antigenic shift associated with viral evolution. The results of this study and the energetic analysis demonstrate excellent qualitative agreement between the predicted binding hotspots and critical mutations with respect to the latest experiments on average antibody escape scores. We argue that E1 and F3 groups of antibodies targeting binding epitopes may leverage strong hydrophobic interactions with the binding epitope hotspots critical for the spike stability and ACE2 binding, while escape mutations tend to emerge in sites associated with synergistically strong hydrophobic and electrostatic interactions.