Search Results (321)

The SARS-CoV-2 Omicron variant and its descendants accumulated unprecedented numbers of spike substitutions yet remained transmissible, implying compensatory mechanisms that preserve entry while eroding humoral immunity. We analyzed 32 variants for sequence-level mutation, physicochemical profiling, and epitope disruption; 25 had growth-advantage estimates, and 18 underwent molecular dynamics/MM-PBSA simulations. We applied a systems-virology framework to the SARS-CoV-2 receptor-binding domain (RBD), integrating immunodominance-weighted epitope conservation (567 B-cell and 97 T-cell epitopes) across variants (Wuhan-Hu-1 to KP.3) with molecular dynamics, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) binding energetics, and deep mutational scanning (DMS) benchmarking. B-cell epitope conservation declined from a median of 72.7% in pre-Omicron variants to 28.8% in BA.1 and 10.6% in KP.3, and was strongly inversely associated with a breakthrough-infection proxy (Spearman ρ = −0.8246, p < 0.001), whereas RBD T-cell epitopes remained comparatively conserved (91.5% to 87.2%). Despite the loss of the ancestral K417–ACE2 D30 salt bridge, Omicron reconfigured the interface via alternative electrostatic contacts (Q493R–E35 and Q498R–D38), producing compensatory interactions captured by MM-PBSA, but with only modest agreement with DMS affinity changes (r = 0.682, p = 0.007), consistent with enthalpy–entropy compensation. Finally, mutation tolerance shifted toward stronger epistatic buffering in Omicron (two-fold higher epistasis than pre-Omicron; p = 0.0093), enabling extensive antigenic change without structural collapse. Together, these results support a multi-objective evolutionary strategy—epitope erosion, interface rewiring, and epistatic compensation—that can be operationalized to prioritize emerging lineages for surveillance and to inform vaccine designs that emphasize conserved T-cell targets. Full article

The Asian migratory locust (Oedaleus decorus asiaticus) is a major grassland pest in northern China, with outbreak dynamics closely linked to phase transition mediated by chemical communication. This study focused on a chemosensory protein, OasiCSP12, to explore its potential role in this process. We analyzed its expression patterns via qRT-PCR, purified the recombinant protein, and identified potential ligands through fluorescence competitive binding assays. Structural insights were gained through homology modeling, molecular docking, and molecular dynamics simulations, with binding energetics assessed using MM/PBSA. Results showed that OasiCSP12 expression is phase- and sex-specific, being significantly upregulated in gregarious adult antennae. The protein bound selectively to 15 locust body-surface volatiles, including aldehydes and esters. Its structure features a hydrophobic binding cavity where van der Waals interactions, primarily predicted to be mediated by residues Val86, Leu71, and Trp101, likely stabilize ligand complexes. These findings indicate that OasiCSP12 is potentially associated with both chemical perception and phase regulation in O. d. asiaticus, providing a candidate target for developing behavior-based green control strategies against this pest. Full article

Background/Objectives: The stimulator of interferon genes (STING) pathway plays a central role in innate immune signaling and represents an attractive therapeutic target for cancer immunotherapy. Amidobenzimidazole (ABZI) derivatives have emerged as promising non-nucleotide STING agonists with improved drug-like properties compared to cyclic dinucleotides. However, current ABZI compounds still exhibit limited oral bioavailability and cross-species potency discrepancies. In addition, potential systemic toxicity remains a concern, indicating the need for further structural optimization. Methods: In this study, a comprehensive computer-aided drug design strategy was employed to systematically investigate ABZI derivatives and identify novel STING agonists with enhanced activity and favorable pharmacokinetic profiles. A 3D quantitative structure–activity relationship (3D-QSAR) model was constructed using the Topomer CoMFA approach based on a dataset of 109 reported ABZI compounds. Guided by the contour map analysis, new chemical groups were introduced through a fragment growth method, generating a large virtual library. The library was subsequently filtered via molecular docking, molecular dynamics simulations, and MM-PBSA binding free energy calculations. Results: Among the newly designed ABZI compounds, five compounds displayed lower binding free energies than D59, with M13 and M44 showing reductions exceeding 6.7 kcal/mol. This work demonstrates the effectiveness of an integrated in silico design strategy for the discovery of novel STING agonists. Conclusions: The identified compounds represent promising candidates for subsequent experimental validation and may support the development of nitrogen heterocycle-based STING agonists for antitumor applications. Full article

Nme1Cas9 is an encouraging genome-editing tool with high fidelity and compactness, but its applications are limited by poor catalytic efficiency compared with SpyCas9. Understanding the dynamic activation mechanism of the HNH nuclease domain is the key to breaking the kinetic bottleneck. Here, we integrated Steered Molecular Dynamics (SMD) with the Traveling-Salesman-based automated Path Searching (TAPS) algorithm to reconstruct the atomic-level activation landscape of the L1-HNH module. The simulations suggest a complex “Lifting-Rearrangement-Sliding” pathway, revealing the critical role of a “Backbone Sliding” conformation; in this step, the HNH domain rotates across the R-loop surface. A thermodynamic analysis using free energy decomposition by MM/PBSA indicates that the intrinsic instability of the wild-type HNH/R-loop interface constitutes the predominant energetic barrier. Hyperactive variants (S593Q/W596K and S593Q/W596R) can overcome this barrier by substantially increasing binding affinity to the R-loop through a “Geometry–Electrostatics Synergism”: S593Q improves interfacial proximity, whereas W596K/R acts as an “Electrostatic Anchor.” The results of unbiased MD simulations demonstrate that strengthened interfacial interactions effectively promote spontaneous conformational drift toward the activated state. This computational study proposes a novel in silico model for “Dynamic Interface Engineering” in which reinforcing transient interfacial contacts during conformational sliding can be an effective strategy in developing high-efficiency CRISPR-Cas effectors. Full article

Background/Objectives: Breast cancer remains a leading cause of cancer-related mortality in women, with therapeutic resistance frequently arising from tumor heterogeneity and an immunosuppressive tumor immune microenvironment (TIME). While Cynomorium songaricum Rupr. (CS) has been used traditionally in Chinese medicine and exhibits preliminary anti-tumor activity, its bioactive constituents and precise mechanisms against breast cancer remain to be elucidated. Methods: The chemical constituents of CS were systematically profiled using ultra-high-performance liquid chromatography coupled with Q Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap MS/MS). Network pharmacology and functional enrichment analyses were performed to identify immuno-related targets and pathways, followed by molecular docking to prioritize component–target pairs. Molecular dynamics (MD) simulations were conducted to validate the stability of a representative docked complex and to characterize binding stability, interaction persistence, molecular mechanics/(Poisson–Boltzmann) surface area (MM/(P)BSA) energetics, and principal component analysis (PCA)-based conformational landscapes. Results: We identified 1100 compounds, of which 84 satisfied the in silico drug-likeness criteria, including 12 phenylpropanoids, 4 terpenes, 35 flavonoids, 2 quinones, 1 phenol, 3 alkaloids, and other phytochemicals. Network pharmacology analysis revealed 776 overlapping targets associated with both breast cancer and immune regulation. Functional enrichment analysis underscored significant involvement in immune-related pathways, and molecular docking studies supported high-affinity interactions between the components and their targets. MD analyses further supported a stable bound ensemble for the representative SRC–Tomentogenin complex during the equilibrated window, with persistent pocket occupancy, consistent interaction signatures, favorable MM/(P)BSA binding energetics, and a concentrated low-energy basin on the PCA-based free energy landscape. Conclusions: These findings elucidate the chemical basis of CS and uncover its immunomodulatory mechanism against breast cancer, offering a foundation for developing CS-based immunotherapeutic strategies and supporting multi-target drug discovery from traditional medicines. Full article

Cyclin-dependent kinase 2 (CDK2) plays a central role in cell cycle regulation and represents an important molecular target in anticancer drug development. In this study, a series of novel isatin derivatives substituted with a trifluoromethoxy group at the C6 position were designed and evaluated as potential CDK2 inhibitors using a comprehensive in silico approach. Density functional theory calculations were applied to analyze the electronic properties of the proposed compounds. Molecular docking and molecular dynamics simulations were used to investigate binding modes, conformational stability, and key interactions within the CDK2 active site. Binding free energies were estimated using the Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) method, while QSAR-based (Quantitative Structure–Activity Relationship) ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses were performed to assess drug-likeness and pharmacokinetic profiles. The results indicate that the investigated derivatives form stable complexes with CDK2, supported by persistent hydrogen bonds in the hinge region and favorable hydrophobic interactions. The trifluoromethoxy substituent significantly affects ligand orientation and promotes deeper insertion into the hydrophobic pocket compared with previously studied isatin analogues. ADMET predictions suggest generally favorable absorption and toxicity profiles, with moderate solubility limitations. Overall, these findings support the potential of 6-trifluoromethoxy-isatin derivatives as promising CDK2 inhibitors and provide a basis for further experimental studies. Full article

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health burden, particularly due to multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Rifampicin, a frontline anti-TB drug that inhibits RNA polymerase, has been central to therapy, but rpoB mutations compromise its efficacy. This highlights the need for Rifampicin analogues that target alternative enzymes to sustain therapeutic effectiveness. In this study, a structure-based computational approach was employed to screen Rifampicin analogues against enoylacyl carrier protein reductase (InhA), a validated enzyme in the biosynthesis of mycolic acids. A library of 399 analogues was retrieved from SwissSimilarity and evaluated using ADMET analysis, with the best candidates showing favourable pharmacokinetic profiles and compliance with Lipinski’s Rule of Five. Molecular docking identified ZINC000013629834 (−10.90 kcal/mol) and ZINC000253411694 (−10.36 kcal/mol) as superior to Rifampicin (−9.05 kcal/mol), with ILE21, SER20, and THR196 consistently stabilizing interactions. Molecular dynamics simulations confirmed the stability of the complexes, with RMSD values of 0.167 nm, 0.175 nm, and 0.297 nm for ZINC000013629834, ZINC000253411694, and Rifampicin, respectively. MM/PBSA analysis showed comparable binding free energies. These findings suggest that optimized Rifampicin analogues targeting InhA may overcome rpoB-associated resistance and serve as promising leads for next-generation anti-TB drug development. Full article

Significant advances in coronavirus immunoprophylaxis have enabled the control of the SARS-CoV-2 pandemic. However, the continued emergence of SARS-CoV-2 variants with immune escape potential highlights the need for effective direct-acting antivirals targeting conserved viral enzymes. The SARS-CoV-2 main protease (M^pro) remains one of the most promising antiviral drug targets due to its essential role in viral replication and the high conservation of its active site across coronavirus variants. Building upon the established GC373 scaffold, we designed, synthesized, and biochemically evaluated two novel GC373-like peptidomimetic inhibitors incorporated modified glutamine-mimic residues. These analogs were designed to enhance solubility and metabolic resilience while retaining key recognition features within the M^pro active site. Both compounds demonstrated micromolar inhibitory activity in enzymatic assays, supported by molecular docking and MM-PBSA analyses consistent with stable binding. The proposed inhibitors represent viable scaffolds for further optimization of electrophilic warheads and S1/S2 residue interactions. These findings contribute to the rational design of next-generation M^pro inhibitors and align with ongoing efforts to expand the chemical space of SARS-CoV-2 antiviral agents. Full article

Wee1-like protein kinase 2 (WEE2) is an oocyte-specific kinase that regulates meiotic arrest and fertilization. Its largely restricted expression in female germ cells and absence in somatic tissues make it a highly selective target for reproductive health interventions. Despite its central role in human fertility, no clinically approved WEE2 modulator is available. In this study, we employed an integrated in silico approach that combines structure-based virtual screening, molecular dynamics (MD) simulations, and MM-PBSA free-energy calculations to identify repurposed drug candidates with potential WEE2 inhibitory activity. Screening of ~3800 DrugBank compounds against the WEE2 catalytic domain yielded ten high-affinity hits, from which Midostaurin and Nilotinib emerged as the most mechanistically relevant based on kinase-targeting properties and pharmacological profiles. Docking analyses revealed strong binding affinities (−11.5 and −11.3 kcal/mol) and interaction fingerprints highly similar to the reference inhibitor MK1775, including key contacts with hinge-region residues Val220, Tyr291, and Cys292. All-atom MD simulations for 300 ns demonstrated that both compounds induce stable protein–ligand complexes with minimal conformational drift, decreased residual flexibility, preserved compactness, and stable intramolecular hydrogen-bond networks. Principal component and free-energy landscape analyses further indicate restricted conformational sampling of WEE2 upon ligand binding, supporting ligand-induced stabilization of the catalytic domain. MM-PBSA calculations confirmed favorable binding free energies for Midostaurin (−18.78 ± 2.23 kJ/mol) and Nilotinib (−17.47 ± 2.95 kJ/mol), exceeding that of MK1775. To increase the translational prioritization of candidate hits, we place our structure-based pipeline in the context of modern machine learning (ML) and deep learning (DL)-enabled virtual screening workflows. ML/DL rescoring and graph-based molecular property predictors can rapidly re-rank docking hits and estimate absorption, distribution, metabolism, excretion, and toxicity (ADMET) liabilities before in vitro evaluation. Full article

Background: Due to chronic venous insufficiency, venous leg ulcers (VLUs) develop as chronic wounds characterized by impaired healing, persistent inflammation, and endothelial dysfunction. Nitrosative stress, mitochondrial damage, and tissue apoptosis caused by excess nitric oxide (NO) produced by iNOS in macrophages and fibroblasts are contributing factors in the chronic wound environment; therefore, pharmacological modulation of iNOS presents an attractive mechanistic target in chronic wound pathophysiology. Methods: Herein, we present the use of a structure-based computational strategy to assess the inhibition of tavaborole, a boron-based antifungal agent, against iNOS using human iNOS crystal structure (PDB ID: iNOS) by molecular docking using AutoDock 4.2, 500 ns simulation of molecular dynamics (MD), with equilibration within ~50 ns and analyses over full trajectory and binding free energy calculations through the MM-PBSA approach. Results: Docking studies showed favorable binding of tavaborole (–6.1 kcal/mol) in the catalytic domain, which stabilizes contacts with several key residues (CYS200, PRO350, PHE369, GLY371, TRP372, TYR373, and GLU377). MD trajectories for 1 ns showed stable structural configurations with negligible deviations (RMSD ≈ 0.44 ± 0.10 nm) and hydrogen bonding, and MM-PBSA analysis confirmed energetically favorable complex formation (ΔG_binding ≈ 18.38 ± 63.24 kJ/mol) similar to the control systems (L-arginine and 1400W). Conclusions: Taken together, these computational findings indicate that tavaborole can stably occupy the iNOS active site and interact with key catalytic residues, providing a mechanistic basis for further in vitro and ex vivo validation of its potential as an iNOS inhibitor to reduce nitrosative stress and restore endothelial homeostasis in venous leg ulcers, rather than direct therapeutic proof. Full article

Background: Intrinsically disordered regions (IDRs) within proteins often act as pivotal linkage units for the interaction of functional domains. The p53 tumor suppressor protein contains intrinsically disordered N-terminal and C-terminal domains (NTD and CTD), playing crucial regulatory roles in cellular processes. Furthermore, experimental approaches have encountered challenges in elucidating the structural regulation by the IDRs. Methods: In this work, we employed microsecond-scale molecular dynamics simulations to explore the allosteric regulation mechanism of the p53 DNA binding domain (DBD) induced by the CTD and the DNA binding. Subsequently, we integrated dynamic cross-correlation analysis with binding free energy calculations to evaluate the interaction between the CTD and DNA. Results: The free energy landscapes (FELs) were utilized to identify the conformational ensemble of the p53 DBD. The FELs revealed that the CTD enhances the allosteric regulatory mechanisms. Conclusions: Firstly, the conformation of DBD changes on the S6-S7 loop and L1 upon DNA binding. Then the CTD directly interacts with DNA and further regulates the allosteric network (involving the S6-S7 loop, L1 loop, S4, S10, H1, and H3) to promote the binding of DBD to DNA. The allosteric mechanisms presented in this work will provide new insights into the functional mechanisms of the p53 CTD and inform the rational design of p53-targeted drugs. Full article

Background/Objectives: Necroptosis is a critical process in the pathogenesis of myocardial ischemia–reperfusion injury (MIRI). Tilianin (Til), a natural flavonoid glycoside derived from Dracocephalum moldavica L., exhibits significant therapeutic potential in cardiovascular diseases. However, its efficacy and mechanisms in mitigating necroptosis-induced MIRI remain incompletely understood. This study aimed to elucidate the molecular mechanisms by which Til regulates cardiomyocyte necroptosis to alleviate MIRI. Methods: A rat model of MIRI was established by ligating the left anterior descending coronary artery. Necroptosis in H9c2 cardiomyocytes was induced by oxygen–glucose deprivation/reoxygenation (H/R) combined with Z-VAD-FMK. Myocardial infarct size was assessed using 2,3,5-triphenyltetrazolium chloride (TTC) staining. Histopathological injury in cardiac tissue was examined by hematoxylin–eosin (HE) staining. Fluorescent probes were used to detect reactive oxygen species (ROS) and mitochondria. The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method was used to predict the binding energy between Til and RIP3. Furthermore, RIP3 overexpression and knockdown, along with inhibition of the downstream protein CaMKII, were used to further investigate the mechanism. Results: Til treatment significantly reduced MIRI in rats, decreased myocardial infarct size, histopathological injury, and regulated myocardial enzyme levels. Til pretreatment effectively inhibited necroptosis in H9c2 cells induced by H/R and Z-VAD-FMK, as evidenced by reduced necroptosis rates, decreased inflammatory cytokine release, improved mitochondrial function, and suppressed phosphorylation of the necroptosis marker MLKL. Molecular docking and dynamics simulation demonstrated stable binding of Til to RIP3, which was verified through Western blot. The protective effects of Til on necroptosis were reversed by RIP3 overexpression. Furthermore, the CaMKII inhibitor KN93 abolished Til’s effect on mitochondria. Conclusions: Til alleviates MIRI by targeting RIP3 to inhibit the necroptosis pathway and mPTP opening. These findings provide a new therapeutic strategy for MIRI and necroptosis-related diseases. Full article

The COVID-19 pandemic exposed critical vulnerabilities in single-target antiviral strategies, highlighting the urgent need for multi-mechanism therapeutic approaches against emerging viral threats. Here, we present an integrated computational framework systematically evaluating natural fatty acids as potential dual ACE2 (Angiotension Converting Enzyme 2)-inflammatory modulators; compounds simultaneously disrupting SARS-CoV-2 viral entry through allosteric ACE2 binding while suppressing host inflammatory cascades; through allosteric binding mechanisms rather than conventional competitive inhibition. Using molecular docking across eight ACE2 regions, 100 ns molecular dynamics simulations, MM/PBSA free energy calculations, and multivariate statistical analysis (PCA/LDA), we computationally assessed nine naturally occurring fatty acids representing saturated, monounsaturated, and polyunsaturated classes. Hierarchical dynamics analysis identified three distinct binding regimes spanning fast (τ < 50 ns) to slow (τ > 150 ns) timescales, with unsaturated fatty acids demonstrating superior binding affinities (ΔG = −6.85 ± 0.27 kcal/mol vs. −6.65 ± 0.25 kcal/mol for saturated analogs, p = 0.002). Arachidonic acid achieved optimal SwissDock affinity (−7.28 kcal/mol), while oleic acid exhibited top-ranked predicted binding affinity within the computational hierarchy (ΔG_bind = −24.12 ± 7.42 kcal/mol), establishing relative prioritization for experimental validation rather than absolute affinity quantification. Energetic decomposition identified van der Waals interactions as primary binding drivers (65–80% contribution), complemented by hydrogen bonds as transient directional anchors. Comprehensive ADMET profiling predicted favorable safety profiles compared to synthetic antivirals, with ω-3 fatty acids showing minimal nephrotoxicity risks while maintaining excellent intestinal absorption (>91%). Multi-platform bioactivity analysis identified convergent anti-inflammatory mechanisms through eicosanoid pathway modulation and kinase inhibition. This computational investigation positions natural fatty acids as promising candidates for experimental validation in next-generation pandemic preparedness strategies, integrating potential therapeutic efficacy with sustainable sourcing. The framework is generalizable to fatty acids from diverse biological origins. Full article

The proteasome β5 subunit plays a central role in protein degradation and is an established therapeutic target in glioblastoma. Marizomib (MZB), a natural β5 inhibitor, has shown promising anticancer activity, yet suboptimal pharmacological properties limit its clinical translation. Using a comprehensive computational approach, this study aimed to identify and characterize novel MZB analogs with improved binding affinity, stability, and drug-like profiles. An integrative in silico study was performed, including molecular docking, frontier molecular orbital (FMO) analysis, pharmacophore modeling, molecular dynamics (MD) simulations over 200 ns, MM/PBSA binding free energy calculations, and per-residue energy decomposition. ADMET profiling evaluated the pharmacokinetic and safety properties of MZB and top-performing analogs. Docking and pharmacophore modeling revealed strong complementarity between MZB analogs and the β5 catalytic pocket. MD simulations showed that MZBMOD-77 and MZBMOD-79 exhibited exceptional structural stability with low RMSD values (0.40–0.42 nm), persistent binding within the active site cavity, and significant disruption of hydrogen-bond networks in the active loop regions Ala19–Lys33 and Val87–Gly98. MM/PBSA analysis confirmed their superior binding free energies (−19.99 and −18.79 kcal/mol, respectively), surpassing native MZB (−6.26 kcal/mol). Per-residue decomposition highlighted strong contributions from Arg19, Ala20, Lys33, and Ala50. ADMET predictions indicated improved oral absorption, reduced toxicity, and favorable pharmacokinetics compared to native MZB. This integrative computational study identifies MZBMOD-77 and MZBMOD-79 as promising next-generation proteasome β5 inhibitors. These analogs mimic and enhance the inhibitory mechanism of native MZB, offering potential candidates for further optimization and preclinical development in glioblastoma therapy. Full article

β-site amyloid precursor protein cleaving enzyme 1 (BACE1) is a central therapeutic target in Alzheimer’s disease, as it catalyzes the rate-limiting step in amyloid-β production. Verubecestat (VER), a clinical BACE1 inhibitor, failed in late-stage trials due to limited efficacy and safety concerns. This study employed an integrative computational approach to design VER derivatives with improved binding affinity, stability, and pharmacokinetic profiles. Structural similarity analysis, Molecular docking, frontier molecular orbital (FMO) analysis, pharmacophore modeling, 200 ns molecular dynamics (MD) simulations, MM/PBSA free energy calculations, and per-residue decomposition were performed. In silico ADMET profiling assessed drug-likeness, absorption, and safety parameters. Docking and pharmacophore analyses identified derivatives with stronger complementarity in the BACE1 catalytic pocket. MD simulations revealed that VERMOD-33 and VERMOD-57 maintained low root mean square deviations (RMSDs) and stable binding orientations and induced characteristic flexibility in the flap and catalytic loops surrounding the catalytic dyad (Asp93 and Asp289), consistent with inhibitory activity. MM/PBSA confirmed the superior binding free energies of VERMOD-33 (−51.12 kcal/mol) and VERMOD-57 (−43.85 kcal/mol), both outperforming native VER (−35.33 kcal/mol). Per-residue decomposition highlighted Asp93, Asp289, and adjacent flap residues as major energetic contributors. ADMET predictions indicated improved oral absorption, BBB penetration, and no mutagenicity or toxicity alerts. Rationally designed VER derivatives, particularly VERMOD-33 and VERMOD-57, displayed enhanced binding energetics, stable inhibitory dynamics, and favorable pharmacokinetic properties compared with native VER. These findings provide a computational framework for rescuing VER and support further synthesis and experimental validation of next-generation BACE1 inhibitors for Alzheimer’s disease. Full article