Journal of Biomolecular Structure & Dynamics最新文献

Bruton's tyrosine kinase (BTK) is a central mediator of B-cell receptor signaling and a validated therapeutic target in chronic lymphocytic leukemia (CLL). However, the clinical efficacy of both covalent and non-covalent BTK inhibitors is increasingly undermined by resistance-conferring mutations, particularly at residues C481 and T474. These mutations, alone or in combination, pose a significant challenge to sustained therapeutic response. In this study, integrative quantum mechanical and molecular modeling approaches were employed to investigate the effects of clinically relevant BTK mutations on inhibitor binding. Ten FDA-approved covalent and non-covalent inhibitors were evaluated against four single mutants (C481S, A428D, V416L, and D539G) and four compound mutants (T474A/C481S, T474I/C481S, T474M/C481S, and T474S/C481S). Density functional theory-based local and global reactivity descriptors identified nucleophilic and electrophilic hotspots within the inhibitors, with nitrogen atoms in pirtobrutinib, zanubrutinib, and spebrutinib displaying pronounced nucleophilic potential, suggesting a key role in stabilizing interactions within the BTK active site. Molecular docking analyses revealed that these inhibitors maintained strong binding affinities across multiple BTK mutants, frequently exceeding that of ibrutinib. Molecular dynamics simulations confirmed the structural stability and compactness of selected inhibitor-BTK complexes. Binding free-energy calculations further supported these observations, with several mutant complexes demonstrating enhanced affinities relative to the wild type. Collectively, these findings highlight structurally resilient inhibitors capable of overcoming compound mutation-driven resistance and underscore the importance of BTK mutational profiling in guiding precision therapeutic strategies for BTK-driven malignancies.

Lysine lactylation as a newly discovered post-translational modification of proteins, plays a key role in various cellular processes. It can be stimulated by lactate and regulates gene expression and life activities. Mass spectrometry is currently the fundamental method for identifying post-translational modification sites, but this approach is often time-consuming and labour-intensive. In this study, we propose a hybrid deep learning model, termed TCB-Kla, for predicting human lysine lactylation sites by integrating Transformer encoder, multi-scale CNN, and bidirectional LSTM. On the independent test set, our model achieves accuracy (ACC) of 82.1%, sensitivity (SN) of 82.5%, specificity (SP) of 81.7%, Matthew's correlation coefficient (MCC) of 0.642, and area under the ROC curve (AUC) of 0.898, with ACC, SN, AUC, and MCC exceeding those of the baseline model by 1.8%, 3.8%, 0.012, and 0.035, respectively. Additionally, we conduct 10-fold cross-validation and visualization analysis to validate the model's stability. To demonstrate the model's transfer learning capability, we select the datasets of anti-diabetic peptide for testing, and the AUC metric reaches 0.981, surpassing the baseline model by 0.023. Finally, to enhance the model's usability, we develop a user-friendly online web server, which can be accessed at http://sb075813.xyz. The original datasets and codes are available at https://github.com/ShengBin369/TCB_Kla.

Human Serum Albumin (HSA) plays a pivotal role in the transport, distribution, and bioavailability of pharmaceutical agents. This study investigates the interaction between HSA and a coumarin derivative, 4-((4-((benzo[d]oxazol-2-ylthio)methyl)-1H-1,2,3-triazol-1-yl)methyl)-7-methoxy-2H-chromen-2-one (C1), under physiological conditions. Binding characteristics were explored using fluorescence and absorption spectroscopy, along with molecular docking studies. Steady-state results indicate that quenching occurs via a static mechanism due to the formation of a non-fluorescent complex between HSA and C1. However, at elevated temperatures, the complex becomes destabilized, leading to a transition toward dynamic quenching as C1 interacts with the excited state of HSA. Thermodynamic parameters (ΔH, ΔG, and ΔS) confirm spontaneous binding. Circular dichroism (CD) spectroscopy demonstrated only minor changes (2-3%) in the α-helical content of HSA upon ligand binding, confirming preservation of the protein's secondary structure. Molecular docking confirms preferential binding, stabilized through hydrogen bonding and hydrophobic interactions. Importantly, a bilirubin-triggered displacement mechanism is proposed, wherein elevated bilirubin levels under pathological conditions may competitively release the bound coumarin derivative, thereby enhancing targeted therapeutic action. These findings underscore the potential of the coumarin derivative as a theranostic agent, offering biological stability through HSA binding for therapeutic applications while retaining fluorescence for bioimaging. This work advances the understanding of serum protein interactions in theranostic development.

MERS-CoV remains a significant global health challenge due to sporadic outbreaks. The ongoing emergence of new viral variants, particularly among betacoronaviruses, underscores the importance of understanding mutations in structural proteins. The membrane (M) protein, a highly conserved structural component essential for viral assembly, is a promising target for therapeutic intervention, and any mutations in this protein are particularly concerning as they may compromise antiviral efficacy. Despite its critical role, the structural consequences of M protein mutations remain poorly characterised. This study investigates six conserved amino-acid substitutions (F27L, A62T, V69L, I82T, T127I, and R162H) identified in the M- protein across bat coronaviruses, SARS-related coronaviruses, and MERS-CoV. Using atomistic molecular dynamics simulations, we examined how these substitutions affect MERS-CoV M protein stability, dimerisation, and interaction with the N protein. All mutants largely preserved native-like structural stability relative to the wild type, indicating that the M protein is resilient to mutation-induced alterations at conserved sites. Although the R162H substitution within the β-sheet domain induced localised flexibility, it did not result in substantial global conformational changes. Notably, the I82T mutant identified exhibited structural stability similar to the wild-type protein, supporting its evolutionary persistence. Furthermore, the mutant M proteins maintained favourable dimeric interactions and stable binding with the N protein. Collectively, these findings elucidate how conserved-site mutations modulate M-protein dynamics while preserving structural and functional integrity, potentially contributing to coronavirus adaptability.

Human serum albumin (HSA) is a key transport protein whose ability to bind multiple endogenous and exogenous ligands is governed by site heterogeneity and long-range conformational coupling; however, the mechanisms underlying ligand redistribution among binding sites, particularly in nanoparticulate HSA, remain poorly understood. To address this, we systematically examined the binding of ANS, DAUDA, palmitic acid (PA), and the anticancer lipopeptide PA-EQRPR to monomeric HSA (mHSA) and HSA nanoparticles (HSA-NPs) using steady-state and time-resolved fluorescence spectroscopy complemented by molecular modeling. In mHSA, three spectroscopically distinct binding species were resolved, with fluorescence lifetimes of ∼22.7, 14.5, and 1.6 ns and dissociation constants of 0.33, 9.0, and 3.3 μM, revealing multiple binding environments with distinct affinities and dynamics. Competitive binding experiments demonstrated cooperative PA binding and showed that PA-EQRPR not only displaces ANS or DAUDA but also promotes their redistribution to alternative, more hydrophobic sites, consistent with ligand-induced allosteric site-site communication. Lifetime-resolved analysis of DAUDA further revealed that PA stabilizes long-lived, high-affinity binding states, while PA-EQRPR shifts ligand populations toward deeper hydrophobic environments, enhancing fluorescence. HSA-NPs prepared using ethanol or acetone exhibited markedly different binding behaviors from mHSA, highlighting the impact of protein organization on ligand accessibility. Ethanol-induced HSA-NPs favored long-lifetime, hydrophobic binding species, whereas acetone-induced particles showed reduced site heterogeneity. Docking and molecular dynamics simulations revealed ligand-driven conformational rearrangements that reshape HSA's hydrophobicity landscape. Together, these findings introduce an allosteric population-shift framework that rationalizes multisite ligand binding and redistribution in both monomeric and nanoparticulate HSA.

Casein kinase I isoform epsilon (CK1ε) demonstrates significant implications in cancer pathogenesis, influencing key cellular processes linked to oncogenesis. Its regulatory roles in cell survival, proliferation, and modulation of oncogenic pathways highlight CK1ε as a potential target for therapeutic strategies in diverse cancer types. In this research, a virtual screening of phytoconstituents from the IMPPAT2.0 database was conducted to find potential inhibitors targeting CK1ε. Initially, compounds adhering to Lipinski's rule of five were retrieved, followed by filtering based on binding affinities and subsequent interaction analyses to refine the selection. Finally, two compounds, Chrysin-7-O-Glucuronide and Rhodiolin, demonstrated considerable affinities with specific interactions at the CK1ε ATP binding site (involving SER17, SER19, and LYS38), forming hydrogen bonds, and were identified for further analysis via PASS server. Employing all-atom molecular dynamic (MD) simulations for 200 ns, structural deviation, residual fluctuation, compactness by radius of gyration, solvent accessible surface area calculation, principal component analysis, and free energy landscapes, were conducted. These findings suggest that Chrysin-7-O-Glucuronide and Rhodiolin warrant further investigation in experimental and clinical research as potential candidates for developing anticancer therapeutics targeting CK1ε kinase.

The enzyme Asparaginyl Endopeptidase (AEP) is associated with proteinopathy-related pathologies such as Alzheimer's disease (AD) and Frontal Temporal Dementia (FTD). The onset of pathologies by AEP is due to cleaved fragments forming protein aggregates resulting in neurodegeneration. Unfortunately, there are no clinically approved small molecule inhibitors for AEP, and therefore, it serves as an unmet medical need for the design and development of potential novel small molecules. In developing potential inhibitors for proteolytic activity, a structured approach utilizing structure-based computer-aided drug design (SB-CADD) parameters was employed. This involved virtual high throughput screening (vHTS) across various CNS-focused databases enriched with diverse functionality. We identified the top sixty ligands based on the glide XP-docking score out of 10 million ligands. The free binding energy was then calculated using MM-GBSA for all top selected molecules which resulted in discovering that AEPI-1 to AEPI-6 (Asparaginyl Endopeptidase inhibitors) displayed high affinity towards the catalytic triad. Further investigation determined that all top six hits form stable complexes during 50 ns molecular dynamic simulations. We also observed that AEPI-2 demonstrated the highest stability within the binding pockets. Post-MD analyses such as DCCM, PCA, PDF, and ADMET properties were also evaluated. By bridging all the observations, we observed these six molecules occupy the active site of the β-helix (β1, β3, and β4) of the S1 pocket and additional binding sites in α1 and β5, suggesting its suitability as a potential candidate for drug discovery against Asparaginyl Endopeptidase.

The global dengue outbreak is a significant public health concern, with the World Health Organization recording over 3 million cases and a 0.04% case fatality rate until July 2023. The infection rate is anticipated to rise in vulnerable regions worldwide. While live-attenuated vaccines are the current standard, their effectiveness in certain populations is debated. Furthermore, the presence of four closely related dengue virus serotypes can lead to antibody-dependent enhancement, compromising vaccine efficacy. In response, we propose the development of a therapeutic subunit-vaccine based on epitopes from all four serotypes to induce robust cross-protective cellular immunity. Our approach involves designing a multi-epitope chimeric immunogen using the envelope protein of the dengue virus. MHC-I and MHC-II binding T-cell epitopes were selected based on their antigen processing criteria. The most potent and immunodominant epitopes for each serotype, considering immunogenicity, population coverage, and prediction scores, were combined using AAY linker peptides to create a stable multi-epitope polypeptide. Predicted to be both antigenic and non-allergenic, the protein design exhibits a stable and soluble tertiary structure with a half-life of 4.4 h in mammalian systems. In addition, we employed an agonist to toll-like receptor-4 at the N-terminal of the vaccine design to induce downstream immunostimulatory response, validated through docking and molecular dynamics simulations. This multi-epitope construct shows promise in eliciting an effective cellular immune response against all dengue virus serotypes.

The present study aimed to screen small molecular compounds such as human noroviruses (HuNoV) inhibitors/modulators that could potentially be responsible for exhibiting some magnitude of inhibitory/modulatory activity against HuNoV 3CLPro. The structural similarity-based screening against the ChEMBL database is performed against known chemical entities that are presently under pre-clinical trial. After the similarity search, remaining molecules were considered for molecular docking using SCORCH and PLANTS. On detailed analyses and comparisons with the control molecule, three hits (CHEMBL393820, CHEMBL2028556, and CHEMBL3747799) were found to have the potential for HuNoV 3CLpro inhibition/modulation. The binding interaction analysis revealed several critical amino acids responsible to hold the molecules tightly at the close proximity site of the catalytic residues of HuNoV 3CLpro. Further, MD simulation study was performed in triplicate to understand the binding stability and potentiality of the proposed molecule toward HuNov 3CLpro. The binding free energy based on MM-GBSA has revealed their strong interaction affinity with 3CLpro.

Alcohol oxidase (AOx) enzymes have gained significant attention for their potential in industrial applications due to their unique ability to catalyze irreversible oxidation of diverse alcohol substrates without external co-factors. This study revisits and enhances in-silico work on Aspergillus terreus MTCC6324 recombinant AOx (rAOx) enzyme, combining artificial intelligence (AlphaFold), molecular docking (AutoDock Vina) techniques and Molecular dynamics (MD) simulations (Desmond). Comprehensive sequence analysis revealed a high degree of conservation among 23 AOx amino acid sequences from various Aspergillus species highlights conserved regions, affirming its GXGXXG Rossmann fold motif. AlphaFold-predicted 3D structure of rAOx demonstrated improved stereo-chemical stability compared to I-TASSER predicted structure with 87.6% amino acid residues in most favourable region of Ramachandran plot compared to 79.5%, respectively. Molecular docking revealed the binding affinities of co-factors FAD and diverse alcohol substrates, with cinnamyl alcohol exhibiting robust interaction with rAOx holoenzyme. MD simulations further elucidate the stability and dynamics of rAOx-FAD-cinnamyl alcohol complex over 100 nanoseconds. The simulations showcase FAD's stable binding within the protein core and highlights transient substrate interactions, dissociating within the active site after 75 ns suggesting a substrate sequestration mechanism. The study unveils substrate sequestration mechanism wherein cinnamyl alcohol exhibits temporary binding, leading to quick detachment from active site, mimicking reported exponential kinetics. This study not only validates previous findings but also offers a comprehensive understanding of intricate dynamics governing rAOx enzymatic activity. The improved sequence-to-structure prediction and detailed molecular insights into substrate sequestration provide a valuable foundation for future experimental investigations and rational design of bio-catalytic processes.