GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Structural and functional mapping of ion access pathways in the human K+-dependent Na+/Ca2+ exchanger NCKX2 using cysteine scanning mutagenesis, thiol-modifying reagents, and homology modelling

K+-dependent Na+/Ca2+ exchanger proteins (NCKX) are members of the CaCA superfamily with critical roles in vision, skin pigmentation, enamel formation, and neuronal functions. Despite their importance, the structural pathways governing cation transport remain unclear. To address this, we conducted a systematic study using cysteine scanning mutagenesis of human NCKX2 combined with the thiol-modifying reagents MTSET and MTSEA to probe the accessibility and functional significance of specific residues. We used homology models of outward-facing and inward-facing NCKX2 states and molecular dynamics (MD) simulations to compare and investigate residue accessibility in human NCKX2 based on the published structures of the archaeal NCK_Mj Na+/Ca2+ exchanger and the human NCX1 Na+/Ca2+ exchanger. Mutant NCKX2 proteins expressed in HEK293 cells revealed diverse effects of MTSET and MTSEA on Ca2+ transport. Of the 146 cysteine substitutions analyzed, 35 exhibited significant changes in Ca2+ transport activity upon treatment with MTSET, with 16 showing near-complete inhibition and six demonstrating increased activity. Residues within the cation binding sites and extracellular access channels were sensitive to modification, consistent with their critical role in ion transport, whereas intracellular residues showed minimal accessibility to MTSET but were inhibited by membrane-permeable MTSEA. Water accessibility maps from MD simulations corroborated these findings, providing a high-resolution view of water-accessible pathways. This study provides a comprehensive structural and functional map of NCKX2 ion access pathways, offering insights into the molecular basis of ion selectivity and transport. These findings highlight the key residues critical for cation binding and transport, advancing our understanding of the structural dynamics of NCKX2.

Comprehensive genetic analysis based on multi - omics reveals novel therapeutic targets for mitral valve prolapse and drug molecular dynamics simulation

OBJECTIVE

Mitral valve prolapse (MVP), the most prevalent primary valvular disease, serves as a direct risk factor for multiple cardiovascular disorders and exhibits a high prevalence in the general population. As no specific pharmacological therapies currently exist for MVP, the identification of precise therapeutic targets is imperative.

METHOD

We conducted comprehensive causal genetic inference by integrating genetic data from expression quantitative trait loci (eQTL) and genome-wide association studies (GWAS). Analytical approaches included Mendelian Randomization (MR), colocalization analysis, Summary-data-based Mendelian Randomization (SMR), Linkage Disequilibrium Score Regression (LDSC), and High-Definition Likelihood (HDL) analysis. Protein quantitative trait loci (pQTL) were utilized to validate gene expression. Replication analyses were performed using additional exposure datasets. Methylation quantitative trait loci (mQTL) were employed to elucidate regulatory roles of methylation sites on genes and disease pathogenesis. Phenome-Wide Association Study (PheWAS) was conducted to predict potential adverse effects of gene-targeted therapies. Drug candidates targeting identified genes were predicted via the Drug Signature Database (DSigDB) and validated through molecular docking. Core targets were identified using the STRING database, followed by molecular dynamics simulations.

RESULT

Two-sample MR analysis showed that genetically predicted 266 genes had positive or negative causal relationships with MVP. Colocalization analysis indicated that 9 genes had a posterior probability greater than 0.75. Subsequent SMR analysis excluded the gene GAPVD1. HDL analysis showed that except for the gene PTPN1, the remaining 7 genes were all significantly genetically associated with MVP, and LDSC analysis further showed that only NMB was associated with MVP. Validation using pQTL data confirmed that increased NMB protein expression reduced the risk of MVP. Replication analysis further verified this conclusion. In addition, SMR analysis of methylation sites for 8 genes indicated that multiple methylation sites played a key role in gene regulation of mitral valve prolapse. PheWAS results showed that targeted therapy for 8 genes did not detect other causal associations at the genome-wide significance level. Molecular docking showed that quercetin had good binding ability with 8 target genes. The STRING database identified 3 core target proteins, and molecular dynamics simulations further verified the binding ability of quercetin with core target proteins.

CONCLUSION

This study successfully predicted the potential of multiple druggable genes as effective therapeutic targets for MVP through genetic methods, validated the potential of quercetin as a drug, and provided new ideas for drug treatment strategies for MVP.

A comprehensive nomenclature system for cyclodextrins

Modified cyclodextrins (CDs) are cyclic oligosaccharides with many applications in drug delivery, catalysis, and as active pharmaceutical ingredients. In general, they exist as distributions of structurally diverse molecules rather than single-isomer compounds. Their performance depends on the number of glucopyranose units (GPUs), and the type, number, and position of chemical substitutions in their hydroxyl groups. Effectively targeting individual species within these distributions is essential for optimizing CDs for specific applications. Computational techniques can generate large datasets to AI-driven structural optimization, but the absence of a standardized nomenclature system for modified CDs presents a major barrier to progress in this direction. This lack of consensus limits effective communication, data sharing, automation, and collaboration. To address this, a clear and extensible nomenclature for modified CDs is proposed. In this framework, GPUs are treated like amino-acid residues, with unsubstituted GPUs as reference building-blocks and substituted ones considered as mutations. This approach precisely defines substitution types and patterns, resolves cyclic permutation ambiguities, and offers versatility for both simple and complex modifications, including chiral center alterations and covalently linked CD oligomers. By introducing this standardized nomenclature, we aim to enhance molecular design, improve reproducibility, and streamline both experimental and computational research in the CD field.

In-silico site-directed mutagenesis and MD simulation analysis to enhance the potential of symbiont fungal chitinase of Beauveria bassiana for bioinsecticide development

The use of microbial insecticides is a promising approach to circumvent the toxic effects of chemical insecticides due to their eco-friendly nature and significant effectiveness. Beauveria bassiana strain ARSEF 2860 is a commercially used bioinsecticide that lives in a symbiont association with a variety of plants or crops. The insecticidal mechanism of this fungal strain is initiated by chitinases that degrade the chitin layer of the insects. Among these chitinases, a significant number of chitinases lack a distinct chitin-binding domain and thus have compromised catalytic efficiency. Engineering of these chitinases to enhance the chitin-binding can be a potential approach to develope high potential bioinsecticides. Present study deals with analysis of 96 mutants of the J5JGB8 chitinase of B. bassiana strain ARSEF 2860 to improve chitin-binding in the substrate binding cavity. In-silico site-directed mutagenesis revealed 30 mutations as stable, having an effective change in Gibb's free energy. Molecular docking of J5JGB8 chitinase and all stable mutants with chitin subunit proved significantly high negative binding energy of Ala127Ser mutant (-8.24 kcal/mol) compared to the wild-type enzyme (-6.75 kcal/mol). Molecular dynamic simulation analysis of Ala127Ser chitinase-chitin and wild-type chitinase-chitin complexes revealed higher number of hydrogen bonding in Ala127Ser chitinase-chitin complex, displaying high stability of chitin-binding in the substrate binding cavity of the mutant. End state free binding energy analysis showed effective change in electrostatic energy of the interactions stabilizing the binding of chitin at the substrate binding site of the Ala127Ser mutant J5JGB8 chitinase with respect to wild-type confirming improved binding of chitin with the mutant chitinase. Hence, this study provides a beneficial Ala127Ser mutant form of J5JGB8 chitinase that can itself be developed in to an effective bioinsecticide or may be used to enhance the potential of B. bassiana strain ARSEF 2860 bioinsecticide using enzyme engineering approach to encourage agricultural sustainability.

The amyloidogenic peptide stretch in human tau, tau306-311 is a promising injectable hydrogelator

A vast majority of peptide hydrogelators harbor a bulky, non-native aromatic moiety. Such foreign moieties raise safety concerns as far as biomedical applications of hydrogels are concerned. The hydrogel research, therefore, has branched to another dimension - to identify native or native-like short peptide stretches that could cause the gelation of biological fluids. Using well-defined criteria to identify native peptide stretches that could form a viscous solution in water but cause gelation of phosphate-buffered saline (PBS), we identified the hexapeptide stretch from human tau, viz. tau306-311, as a promising injectable hydrogelator. The peptide causes instant gelation of PBS and the cell culture media. Such hydrogels find applications as drug delivery vehicles, scaffolds for mammalian cell culture, wound-dressing material, etc.

Structural Insight Into the Conversion of DhNik1, A Hybrid Histidine Kinase From Debaryomyces hansenii to a Cytotoxic Phosphatase Conformation for Novel Antifungal Agent

Group III hybrid histidine kinase (HHK3) is one of the most interesting signalling molecules and a novel drug target in fungi. HHK3 is converted into a cytotoxic phosphatase form in vivo by the action of a widely used agricultural fungicide indicating that HHK3 also exhibits dual functionality by acting as kinases and phosphatases towards their substrates like many bacterial sensor histidine kinases. However, this cytotoxic form of HHK3 remained elusive for further scientific exploitation. In this study, we have isolated a cytotoxic phosphatase LOCK-IN mutant of DhNik1, a prototype HHK3, and provided structural and functional insight into this form for the first time. The mutant DhNik1CT had an in-frame deletion in the poly-HAMP domain. The fusion of the poly-HAMP domain of DhNik1CT with the histidine kinase and receiver domain of another fungal hybrid histidine kinase also created a hybrid that was cytotoxic to the fungal cell. We generated the structural model of wild-type DhNik1 and DhNik1CT using AlphaFold multimer which highlighted the differences in HAMP domain arrangement and conformation between DhNik1 and DhNik1CT. MD simulation of the modelled structure revealed crucial role of ATP lid opening and closing in regulating the activity of DhNik1 and DhNik1CT. The structure of DhNik1CT was used for virtual screening to identify a small molecule which modulates the activity of DhNik1 towards cytotoxicity. Taken together, present study shows that the conversion of HHK3 to a toxic conformation by a small molecule is a feasible approach for discovering novel antifungal drug.

Shape-Selective Separation of Model Analytes in Normal-Phase Liquid Chromatography: A Combined Simulation-Experimental Study

In this study, we demonstrate that liquid chromatographic separation can be effectively achieved based on shape differences, even for analytes of very similar chemical characters. Using a combined experimental-theoretical approach, we investigated the retention behavior of spherical buckminsterfullerene C60 and disk-shaped coronene at a hydroxylated silica stationary phase, with a mobile phase composed of toluene and n-hexane at varying compositions. High-performance liquid chromatography (HPLC) measurements revealed that increasing the n-hexane content enhances the separability of the two analytes, primarily due to coronene's stronger retention. Molecular simulations, coupled with a two-state model, attributed this effect to the structured layering of toluene at the stationary phase, which differentially influences analyte-wall interactions. Our analysis of Henry coefficients further identified the second solvent layer as the primary region governing adsorption, providing a thermodynamically consistent description of the separation process. These findings highlight the role of shape anisotropy in chromatographic retention and suggest new avenues for designing shape-selective separation strategies for molecules and nanoparticles in liquid chromatography.

Computer Integrated Dominant Epitopes Evoke Protective Immune Response Against Streptococcus pneumoniae

Streptococcus pneumoniae is a gram-positive bacterium responsible for various diseases like pneumonia, acute otitis media, sinusitis, meningitis and bacteraemia. These diseases cause a significant amount of morbidity and mortality. Although polysaccharide vaccines are available, the protection provided by these vaccines is serotype-dependent and not enough in sensitive populations like children and older people. Designing a subunit vaccine by using proteins that are responsible for the pathogenesis of diseases can provide better protection against bacterial infections. In this study, we present the design of a novel multi-epitope vaccine against Streptococcus pneumoniae using an immunoinformatic approach. More than 1170 epitopes were identified against B cells, cytotoxic T lymphocytes and helper T lymphocytes from more than 60 pneumococcal proteins. Epitopes were further screened, and potential epitopes were selected for vaccine development. Seven different vaccine combinations that harbour the 15 dominant B-cell, cytotoxic T cell and helper T cell epitopes were evaluated with linker and β-defensin adjuvant to finalise the best vaccine construct. Bioinformatics tools were used to analyse the construct's physicochemical properties, secondary and tertiary structures, allergenicity, antigenicity and immunogenicity. Docking studies with the TLR-4 receptor and molecular dynamics simulations indicated strong binding affinity and stability. In silico immune response simulations predicted robust IgG immune response generation and observed more than 200 000 IgG1 + IgG2 counts per mL. Similarly, cell-mediated immunity was also enhanced by the designed vaccine construct. The construct was codon-optimised and cloned in silico for expression in Escherichia coli. These findings suggest that the construct is a promising candidate for further experimental validation.

Oxidative stress-induced CDO1 glutathionylation regulates cysteine metabolism and sustains redox homeostasis under ionizing radiation

Oxidative stress serves as a fundamental mechanism contributing to ionizing radiation-induced damage, which has significant implications for tissue injury. Cysteine dioxygenase type 1 (CDO1) catalyzes the rate-limiting step for cysteine oxidation pathway, thereby playing a crucial role in regulating cellular cysteine availability. However, the regulation of CDO1 activity and cysteine oxidation under ionizing radiation, as well as their subsequent effects on cell viability, remains largely unexplored. In this study, we provide evidence that CDO1 activity and cysteine oxidation are inhibited following radiation exposure. Mechanistically, ionizing radiation-induced oxidative stress triggers glutathionylation of CDO1 at cysteine (C) 164, which impairs CDO1 enzymatic activity by disrupting its interaction with the substrate cysteine. Furthermore, glutathionylation at CDO1 C164 is essential for maintaining cellular redox homeostasis and supports cell viability under ionizing radiation. These findings reveal a novel mechanism through which redox modifications of CDO1 regulate cysteine metabolism and glutathione synthesis under oxidative stress, thereby underscoring its potential as a therapeutic target for addressing radiation-induced injuries.

Maternal omega-3 polyunsaturated fatty acids improved levels of DHA-enriched phosphatidylethanolamines and enriched lipid clustering in the neuronal membranes of C57BL/6 mice fetal brains during gestation

The composition of brain lipids is crucial for neurodevelopment and brain function. Diets enriched in omega (n)-3 polyunsaturated fatty acids (PUFA) can modulate brain lipid composition. However, the influence of maternal n-3 PUFA intake on fetal brain lipidome and neuronal membrane structure during gestation is not well studied. Eight-week-old female C57BL/6 mice were fed low or high n-3 PUFA semi-purified diets for two weeks before mating and during gestation. Fetal brain lipidome and neuronal membrane structure were studied at gestation day (GD) 12.5 (mid) and 18.5 (late) using liquid chromatography high-resolution accurate mass tandem mass spectrometry and computational techniques. Maternal diets high in n-3 PUFA increased fetal brain total phosphoethanolamine, phosphoinositol, phosphoglycerol, and phosphoserine glycerophospholipids, compared to the low n-3 PUFA diet. Docosahexaenoic acid (DHA, 22:6n-3)-enriched phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylserine (PS), and lyso-PC (LPC) fatty acyl species increased as gestation progressed in the high n-3 PUFA group, compared to low n-3 PUFA. These fatty acyl species and phospholipids promote neurotransmission, memory, and cognition. A high n-3 PUFA diet increased the area per lipid in fetal neuronal membranes as gestation progressed, indicating improved membrane fluidity. Furthermore, a high n-3 PUFA diet increased the clustering of membrane lipids associated with neurotransmission, memory, and cognition (ceramide, PE, and cholesteryl ester) as gestation progressed. Our findings show for the first time that maternal diets high in n-3 PUFA before and during gestation improve fetal brain lipidome and membrane area per lipid that may enhance brain development and function.

Molecular Dynamic Study on the Structure and Thermal Stability of Mutant Pediocin PA-1 Peptides Engineered with Cysteine Substitutions

Pediocin and analogous bacteriocins, valued for thermal stability, serve as versatile antimicrobials in the food sector. Improving their resilience at high temperatures and deriving derivatives not only benefit food production but also offer broad-spectrum antimicrobial potential in pharmaceuticals, spanning treatments for peptic ulcers, women's health, and novel anticancer agents. The study aims to create mutant peptides capable of establishing a third disulfide bond or enhanced through cysteine substitutions. This involves introducing additional Cys residues into the inherent structure of pediocin PA-1 to facilitate disulfide bond formation. Five mutants (Mut 1-5) were systematically generated with double Cys substitutions and assessed for thermal stability through MD simulations across temperatures (298-394 K). The most robust mutants (Mut 1, Mut 4-5) underwent extended analysis via MD simulations, comparing their structural stability, secondary structure, and surface accessibility to the reference Pediocin PA-1 molecule. This comprehensive assessment aims to understand how Cys substitutions influence disulfide bonds and the overall thermal stability of the mutant peptides. In silico analysis indicated that Mut 1 and Mut 5, along with the reference structure, lose their helical structure and one natural disulfide bond at high temperatures, and may impacting antimicrobial activity. Conversely, Mut 4 retained its helical structure and exhibited thermal stability similar to Pediocin PA-1. Pending further experimental validation, this study implies Mut 4 may have high stability and exceptional resistance to high temperatures, potentially serving as an effective antimicrobial alternative.

Catalytic tunnel engineering of thermostable endoglucanase of GH7 family (W356C) from Aspergillus fumigatus gains catalytic rate

Tunnel engineering targets the access tunnels in enzymes, which is crucial for substrate binding and product release. Modifying the tunnels can lead to better biomass-degrading abilities of the lignocellulolytic enzymes. In this report, we have engineered the thermostable GH7 family endoglucanase from Aspergillus fumigatus (AfEgl7). The residues in the open tunnel having the highest bottleneck radius are mutated. Mutations are created (T229F, W356C) in the non-conserved region. The mutant W356C showed a 2-fold increase in product release rate (Vmax = 375.8 µM/min) and 2.5-fold higher catalytic activity (Kcat = 75.1 min-1) compared to wild-type (Vmax= 232 µM/min; Kcat = 30.9 min-1) using CM cellulose as substrate. The mutant T229F lost both catalytic activity and thermostability. Molecular dynamic simulations and docking studies of W356C revealed a change in structure near the product exit region, which may facilitate faster product release and account for the increased catalytic efficiency of the mutant. This study showed how redesigning the access pathways can be a promising strategy for protein engineering and de novo protein design by tailoring the open tunnel geometry to a ligand-specific manner.

A Computational Approach to Characterize the Protein S-Mer Tyrosine Kinase (PROS1-MERTK) Protein-Protein Interaction Dynamics

Protein S (PROS1) has recently been identified as a ligand for the TAM receptor MERTK, influencing immune response and cell survival. The PROS1-MERTK interaction plays a role in cancer progression, promoting immune evasion and metastasis in multiple cancers by fostering a tumor-supportive microenvironment. Despite its importance, limited structural insights into this interaction underscore the need for computational studies to explore their binding dynamics, potentially guiding targeted therapies. In this study, we investigated the PROS1-MERTK interaction using advanced computational analyses to support immunotherapy research. High-resolution structural models from ColabFold, an AlphaFold2 adaptation, provided a baseline structure, allowing us to examine the PROS1-MERTK interface with ChimeraX and map residue interactions through Van der Waals criteria. Molecular dynamics (MD) simulations were conducted in GROMACS over 100 ns to assess stability and conformational changes using RMSD, RMSF, and radius of gyration (Rg). The PROS1-MERTK interface was predicted to contain a heterogeneous mix of amino acid contacts, with lysine and leucine as frequent participants. MD simulations demonstrated prominent early structural shifts, stabilizing after approximately 50 ns with small conformational shifts occurring as the simulation completed. In addition, there are various regions in each protein that are predicted to have greater conformational fluctuations as compared to others, which may represent attractive areas to target to halt the progression of the interaction. These insights deepen our understanding of the PROS1-MERTK interaction role in immune modulation and tumor progression, unveiling potential targets for cancer immunotherapy.

BCOR-rearranged sarcomas: In silico insights into altered domains and BCOR interactions

BCOR (BCL-6 corepressor) rearranged small round cell sarcoma (BRS) represents an uncommon soft tissue malignancy, frequently characterized by the BCOR::CCNB3 fusion. Other noteworthy fusions include BCOR::MAML3, BCOR::CLGN, BCOR::MAML1, ZC3H7B::BCOR, KMT2D::BCOR, CIITA::BCOR, RTL9::BCOR, and AHR::BCOR. The BCOR gene plays a pivotal role in the Polycomb Repressive Complex 1 (PRC1), essential for histone modification and gene silencing. It interfaces with the Polycomb group RING finger homolog (PCGF1). This study employed comprehensive in silico methodologies to investigate the structural and functional effects of BCOR fusion events in BRS. The analysis revealed significant alterations in the domain architecture of BCOR, which resulted in the loss of BCL6-regulated transcriptional repression. Furthermore, IUPred3 prediction indicated a significant increase in disorder in the C-terminal regions of the BCOR in the fusion proteins. A detailed analysis of the physicochemical properties by ProtParam revealed a decrease in isoelectric point, stability, and hydrophobicity. The analysis of protein structures predicted by AlphaFold3 using the PRODIGY algorithm revealed statistically significant deviations in binding affinities for BCOR-PCGF1 dimers and a non-canonical PRC1 variant tetramer compared to the wild-type BCOR. The findings provide a comprehensive summary and elucidation of the fusion proteome associated with BRS, suggesting a substantial impact on the stability and functionality of the fusion proteins, thereby contributing to the oncogenic mechanisms underlying BRS. In this study, we provide the first compilation and comparative analysis of the known BCOR fusions of BRS and introduce a new in silico approach to enhance a better understanding of the molecular basis of BRS.

Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study

In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.

Computational discovery of novel PI3KC2α inhibitors using structure-based pharmacophore modeling, machine learning and molecular dynamic simulation

PI3KC2α is a lipid kinase associated with cancer metastasis and thrombosis. In this study, we present a novel computational workflow integrating structure-based pharmacophore modeling, machine learning (ML), and molecular dynamics (MD) simulations to discover new PI3KC2α inhibitors. Key innovations include the generation of diverse pharmacophores from both crystallographic and docking-derived complexes, coupled with data augmentation via ligand conformational sampling to enhance ML robustness. The optimal model, developed using XGBoost with genetic function algorithm (GFA) and Shapley additive explanations (SHAP), identified four critical pharmacophores and three descriptors governing bioactivity. Virtual screening of the NCI database using these pharmacophores yielded three hits, with H_1 (NCI: 725847) demonstrating MD-derived binding stability and affinity comparable to the potent inhibitor PITCOIN1 (IC50 = 95 nM). This study represents the first application of a conformation-augmented ML framework to PI3KC2α inhibition, offering a blueprint for targeting underexplored kinases with limited structural data.

Mechanistic insights into Sanbi Decoction for osteoarthritis treatment based on network pharmacology and experimental validation

Sanbi Decoction (SBD) has demonstrated promising therapeutic potential in osteoarthritis (OA) treatment, yet its precise mechanisms remain unclear. This research combined computational and experimental approaches, including bioinformatics analysis, network pharmacology, molecular docking, molecular dynamics simulations, and laboratory validation, to investigate the mechanisms of action of SBD. A total of 114 active compounds and 113 intersecting targets were identified through TCMSP and multiple screening strategies. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these targets are primarily involved in key signaling pathways, including the AGE-RAGE signaling pathway, IL-17 signaling pathway, and TNF signaling pathway. Among the active components, Shinflavanone, Gancaonin L, Xambioona, Phaseol, Gancaonin O, and Licoisoflavanone exhibited strong binding affinity and structural stability with core targets, as validated by molecular docking and molecular dynamics simulations. Experimental results confirmed that SBD alleviates oxidative stress, reduces inflammation, and protects cartilage by inhibiting the AGE-RAGE/JNK pathway. These findings highlight SBD's potential as a promising therapeutic agent for OA treatment.

Insights into Ligand-Specific Activation Dynamics of Dopamine D2 Receptor Explored by MD Simulations

The human G protein-coupled receptor (GPCR) dopamine 2 receptor (D2R) is an essential target of antipsychotic drugs. The modulation of downstream GPCR signaling induced by different agonists, termed functional selectivity, has potentially a great impact on drug discovery and control of side effects. The molecular origin of this modulation is, however, not fully understood. Here, the structural determinants underlying the response of D2R to binding of the endogenous agonist dopamine, the partial agonist aripiprazole, and the antagonist sulpiride are investigated at full atomistic resolution by molecular dynamics simulations. Multiple replicas covering 18 μs per system allow us to model binding mode and long-range effects of ligands and specifically modulation at the transmembrane helices (TMs) and at the intracellular interface. The dopamine-bound complex maintains the interaction points on TM3, TM5, and TM6 that lead to partial opening of the ionic lock required for the outward movement of TM6, whereas the binding mode of sulpiride disrupts the toggle switch, thereby globally altering the TM dynamics, which is conserved in the other two ligands. Moreover, we predict a significant impact of the partial agonist aripiprazole both on the extracellular loop EL2, on the N-terminal conformation of TM5, and on the dynamics of TM4, which in turn induces the perturbation of intracellular loop IL2 at the intracellular side. The latter loses its helical conformation, leading to a structure that is not competent for arrestin binding in a protein-protein docking computational experiment. These structural changes are accompanied by a modulation of cholesterol interactions with the receptor. Our model suggests that aripiprazole might cause poor arrestin recruitment by modulating TM4 and TM5 down to the intracellular side through the destabilization of a hydrophobic binding pocket at TM5, in agreement with previous mutational data.

Soybean Lectin Cross-Links Membranes by Binding Sulfatide in a Curvature-Dependent Manner

Soybean (Glycine max) is a key source of plant-based protein, yet its nutritional value is impacted by antinutritional factors, including lectins. Whereas soybean lectin is known to bind N-acetyl-d-galactosamine (GalNAc), its lipid interactions remain unexplored. Using a novel purification method, we isolated lectin from soybean meals and characterized its interactions with GalNAc and the glycosphingolipid sulfatide. Isothermal titration calorimetry revealed micromolar affinity for GalNAc, whereas most GalNAc derivatives displayed weak or no binding. Lectin exhibited high-affinity binding to sulfatide in a membrane curvature-dependent manner. Binding of lectin to sulfatide promoted cross-linking of sulfatide-containing vesicles. Whereas sulfatide interaction was independent of GalNAc binding, suggesting distinct binding sites, vesicle cross-linking was inhibited by the sugar. Molecular dynamics simulations identified a consensus sulfatide-binding site in lectin. These findings highlight the dual ligand-binding properties of soybean lectin and may provide strategies to mitigate its antinutritional effects and improve soybean meal processing.

Computational investigations on the anaesthetic drug, tetracaine (TCA) by DFT, TD-DFT, molecular docking, and molecular dynamic simulation analysis

The current investigation deals with the theoretical exploration of tetracaine (TCA) employing density function theory (DFT), time-dependent density function theory (TD-DFT), molecular docking (MD), and molecular dynamic simulation (MDS). The B3LYP method was utilised for this study in conjunction with a 6-31++G(d,p) basis set. We computed the charge distribution of the molecule tetracaine using molecular electrostatic potential (MEP) analysis, which indicate how molecules interact and what kinds of chemical bonds they have. Additionally, population analysis and Fukui function analysis have explored charges on the atoms. This comprehensive study also includes an assessment of various parameters such as chemical hardness, chemical softness, and electrophilicity index through the Frontier Molecular Orbital (FMO) investigation. The molecule's non-linear optical (NLO) properties were conducted to ascertain the hyperpolarizability and polarity values. Lastly, molecular docking was used to look at how a ligand and two protein receptors, named monoamine oxidase A (code: 2BXR) and monoamine oxidase B (code: 1OJD), interact with a ligand. The resulting binding energies were determined to be -7.7 and -7.6 kcal/mol, respectively. Following the completion of the docking process, an investigation of conformational behaviour was conducted with the assistance of molecular dynamic simulation (MDS). These findings indicate the possible applicability of this interaction in the field of medicine. This study has the potential to be utilized in the future to advance the creation of amphiphilic drugs.

Gut opportunistic pathogens contribute to high-altitude pulmonary edema by elevating lysophosphatidylcholines and inducing inflammation

Gut microbiota have been found to promote hypoxia-induced intestinal injury. However, the role of gut microbiota in high-altitude pulmonary edema (HAPE), the preventive effect of synbiotic on HAPE, and the mechanisms by which they might work remain unknown. In this study, we aimed to investigate the role of gut microbiota in the pathogenesis of HAPE and to explore the underlying mechanisms involved. We performed a fecal microbiome analysis and found a significant decrease in intestinal Klebsiella and Escherichia-Shigella, along with a notable increase in intestinal Bifidobacterium and Lactobacillus, as volunteers recovered from acute mountain sickness (AMS). Gavage colonization with Klebsiella pneumoniae and Escherichia coli induced plasma inflammation, increased plasma lysophosphatidylcholine (LPC) levels, and contributed to HAPE in rats at a simulated altitude of 6,500 m. Conversely, a synbiotic containing Bifidobacterium, Lactiplantibacillus, fructooligosaccharides, and isomaltose-oligosaccharides significantly reduced the severity of HAPE. Cellular experiments and molecular dynamics simulations revealed that LPCs can cause damage and permeability to human pulmonary microvascular endothelial cell (HPMEC) and human pulmonary alveolar epithelial cell (HPAEpiC) monolayers under hypoxic conditions by disrupting cell membrane integrity. In addition, tail vein injection of LPCs promoted HAPE in mice at a simulated altitude of 6,500 m. In conclusion, this study describes a gut microbiota-LPCs/inflammation-HAPE axis, an important new insight into HAPE that will help open avenues for prevention and treatment approaches.

IMPORTANCE

The role of the gut microbiota in high-altitude pulmonary edema (HAPE) is currently unknown. This study found that intestinal Klebsiella pneumoniae and Escherichia coli contribute to HAPE by inducing inflammation and increasing lysophosphatidylcholine (LPC) levels under hypoxic conditions. Conversely, a synbiotic containing Bifidobacterium, Lactiplantibacillus, fructooligosaccharides, and isomaltose-oligosaccharides significantly reduced the severity of HAPE. Further investigation revealed that LPCs can cause damage and permeability to human pulmonary microvascular endothelial cell (HPMEC) and human pulmonary alveolar epithelial cell (HPAEpiC) monolayers under hypoxic conditions by disrupting cell membrane integrity. These findings contribute to the understanding of the pathogenesis of HAPE and will benefit populations living at high altitude or traveling from low to high altitude.

Structural and mechanistic profiling of Nurr1 modulation by vidofludimus enables structure-guided ligand design

The neuroprotective transcription factor nuclear receptor related 1 (Nurr1, NR4A2) is in the focus of biomedical research for its promising neuroprotective role in Parkinson's disease, Alzheimer's disease, and multiple sclerosis. Its activity can be controlled by ligands offering access to pharmacological Nurr1 modulation. However, the binding epitope(s) and molecular activation mechanisms of synthetic Nurr1 activators remained elusive but are essential to advance Nurr1 ligands towards new medicines. Here we characterized Nurr1 dimer dissociation and coregulator release as molecular contributions to Nurr1 activation by vidofludimus and locate its binding in an allosteric surface pocket lined by helices 1, 5, 7, and 8 by mutagenesis and molecular dynamics simulation. Structure-guided ligand design using these insights resulted in an optimized Nurr1 agonist with substantially enhanced potency and binding affinity. Our results provide a structural and molecular basis for Nurr1 activation by a synthetic agonist which was lacking for rational ligand design.

Antibody-induced TREM2 ectodomain shedding inhibits TREM2 signaling in macrophage

Antibody-based therapy targeting triggering receptor expressed on myeloid cells 2 (TREM2) is a promising tumor immunotherapy strategy that blocks the TREM2 signaling pathway. How to develop inhibitory antibodies with better performance is the current challenge. Here, we aimed to explore how TREM2's stalk region (136-172 aa) protects the ectodomain from shedding and develop antibodies to promote TREM2 shedding and inhibit signal activation. Molecular dynamics simulations indicated a self-folding conformation in the stalk region of TREM2. The TREM2 risk variant (H157Y) reduces the stability of this conformation by affecting hydrogen bond formation. Histidine 154 (H154) also participated in maintaining the stability of the self-folding conformation and preventing shedding of TREM2. The screened antibody test-2 could target stalk region of TREM2, induce the shedding of TREM2 and regulate the expression of inflammatory factors in THP1 cells. These results suggest that antibodies targeting the stalk region of TREM2 have the potential to serve as inhibitory antibodies.

Exploring the structural and dynamical features of bacterial-tubulin FtsZ

FtsZ, a bacterial tubulin, plays a crucial role in the cytokinesis process. It shares structural similarities with tubulin, as it consists of two domains-N-terminal and C-terminal domains. The protein assembles to form single-stranded protofilaments that exhibit a dynamic phenomenon known as treadmilling where the FtsZ filaments appear to execute a unidirectional movement even though individual monomers constituting the filament do not move. Despite forming protofilaments, an FtsZ molecule requires a conformational switch to form stable contacts with neighboring subunits in a filament. Therefore, FtsZ has two well-characterized conformations based on its polymerization propensity: 1) R state, preferred by the monomeric FtsZ and 2) T state, preferred by the polymeric FtsZ. The treadmilling ability of FtsZ is coupled with the conformational switch and the GTPase activity of the protein as hydrolysis-deficient mutants of FtsZ do not treadmill. We employ all-atom molecular dynamics simulations to investigate certain structural and dynamical features of the protofilaments by considering FtsZ heptamers as our model system. We simulated FtsZ filaments in three nucleotide states-GTP, GDP, and GDP-Pi-to understand the conformational states of the terminal monomers, interface dynamics of the filaments, and important interactions at the protein interdomain and interface regions. Our study reveals that the γ-phosphate binding loop T3 prompts the structural rearrangements at the interface post hydrolysis.

Comparative analysis of Polyethylene-Degrading Laccases: Redox Properties and Enzyme-Polyethylene Interaction Mechanism

Laccases that oxidize low-density polyethylene (LDPE) represent a promising strategy for bioremediation purposes. To rationalize or optimize their PE-oxidative activity, two fundamental factors must be considered: the enzyme's redox potential and its binding affinity/mode towards LDPE. Indeed, a stable laccase-PE complex may facilitate a thermodynamically unfavorable electron transfer, even without redox mediators. In this study, we compared the redox potential and the LDPE-binding properties of three different PE-oxidizing laccases: a fungal high-redox potential laccase from Trametes versicolor, a bacterial low-redox potential laccase from Bacillus subtilis, and the recently characterized LMCO2 from Rhodococcus opacus R7. First we found that LMCO2 is a low-potential laccase (E°=413 mV), as reported in other bacterial variants. Using computational tools, we simulated the interactions of these laccases with a large LDPE model and highlighted the key role of hydrophobic residues surrounding the T1 site. Notably, a methionine-rich loop in LMCO2 appears to enhance the formation of a stable complex with LDPE, potentially facilitating electron transfer. This study underscores the necessity for comprehensive computational strategies to analyze enzyme-polymer interactions beyond simplistic models, uncovering critical binding determinants and informing future mutagenesis experiments, in order to enhance laccase performance and rationalize variations in enzymatic activity.

In-silico design strategies for tubulin inhibitors for the development of anticancer therapies

INTRODUCTION

Microtubules, composing of α, β-tubulin dimers, are important for cellular processes like proliferation and transport, thereby they become suitable targets for research in cancer. Existing candidates often exhibit off-target effects, necessitating the quest for safer alternatives.

AREA COVERED

The authors explore various aspects of computer-aided drug design (CADD) for tubulin inhibitors. The authors review various techniques like molecular docking, QSAR analysis, molecular dynamic simulations, and machine learning approaches for predicting drug efficacy and modern computational methods utilized in the design and discovery of agents with anticancer potential. This article is based on a comprehensive search of literature utilizing Scopus, PubMed, Google Scholar, and Web of Science, covering the period from 2018 to 2025.

EXPERT OPINION

CADD is crucial in the pursuit of new cancer treatments, particularly by merging computer algorithms with experimental data. CADD predicts small molecule activity against tubulin related targets, expediting drug candidate identification and optimization for enhanced efficacy with reduced toxicity. Challenges include limited predictive models and the need for sophisticated ones to capture complex interactions among targets and pathways. Despite relying on cancer cell line transcriptome profiles, CADD remains pivotal for future anticancer drug discovery efforts.

Promoted Li+ Desolvation by the Reconstruction of Hydrogen-Bond Network in Functional Separator to Stabilize the Lithium Metal Anode Interface

High energy density lithium metal batteries (LMBs) are challenged by unstable interface reactions, leading to the continuous deterioration of parasitic reactions. To overcome this problem, here, new strategies are designed for promoting Li+ desolvation (PLD) separators with modulated hydrogen-bond network to stabilize the interfacial reaction. Experimental and computational results show that the difference in the electron cloud density distribution on the separator surface not only breaks the hydrogen-bond network of the conventional carbonate electrolyte, thus capturing the strongly dissolved ethylene carbonate (EC) but also realizes the promoted desolvation process of the outer Helmholtz plane (OHP). As a result, the Li+ desolvation barrier of the PLD separator decreases from 81.15 kJ to 73.01 kJ mol-1. The long cycle life of the assembled Li/Li symmetric cell with PLD separator can be extended to 4500 h at 3 mA cm-2/1.5 mAh cm-2. Notably, the LFP/Li full cell with the PLD separator even achieves a specific capacity of 94.2 mAh g-1 at a high rate of 7C. These results demonstrate that the PLD separator is capable of stabilizing interfacial reactions and enhancing the performance of high-rate LMBs, providing new ideas for further rational development in this field.

Tryptophan Metabolism as a Key Target in PFOS-Mediated Decline of Porcine Oocyte Quality

Perfluorooctanesulfonate (PFOS) is a persistent environmental endocrine disruptor that poses severe threats to mammalian reproductive health upon accumulation in organisms. Therefore, elucidating the mechanisms of PFOS-induced damage and identifying effective protective strategies are of critical importance. In this study, an untargeted metabolomic analysis revealed that PFOS exposure significantly disrupted metabolic homeostasis in oocytes. Using public databases to predict potential target proteins of PFOS and performing KEGG pathway enrichment analysis, we identified the tryptophan metabolism pathway as a key target of PFOS. Molecular docking and molecular dynamics simulations demonstrated specific binding between PFOS and proteins involved in the tryptophan metabolism pathway, leading to dynamic structural alterations in these proteins. Furthermore, supplementation with tryptophan was shown to significantly enhance mitochondrial function in oocytes, regulate the glutathione (GSH)/oxidized glutathione (GSSG) ratio, reduce reactive oxygen species (ROS) levels, and alleviate oxidative stress, thereby mitigating the decline in oocyte quality caused by PFOS exposure. These findings provide novel theoretical insights and research directions for using tryptophan as a protective agent against PFOS-induced reproductive toxicity.

A combined in silico and MD simulation approach to discover novel LpxC inhibitors targeting multiple drug resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa), a member of the ESKAPE family, is the major cause of infections leading to increased morbidity and mortality due to multidrug resistance (MDR). One of the main proteins involved in the Raetz pathway is LpxC, which plays a significant role in anti-microbial resistance (AMR). Our study aimed to identify a novel compound to combat MDR due to the LpxC protein. It involved in silico methods comprising molecular docking, simulations, ADMET profiling, and DFT calculations. First, an ADMET and bioactivity evaluation of the 25 top-hit compounds retrieved from ligand-based virtual screening was performed, followed by molecular docking. The results revealed compound P-2 as the lead compound, which was further subjected to DFT analysis and molecular dynamics (MD) simulations. With these analyses, our in silico study identified P-2, 3-[(dimethylamino)methyl]-N-[(2 S)-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide as a potential lead compound that may behave as a very potent inhibitor of LpxC for the development of targeted therapies against MDR P. aeruginosa.

Synthesis of 3-Carboxy-6-sulfamoylquinolones and Mefloquine-Based Compounds as Panx1 Blockers: Molecular Docking, Electrophysiological and Cell Culture Studies

The membrane channel protein Panx1 is a promising therapeutic target since its involvement was demonstrated in a variety of pathologies such as neuropathic pain, ischemic stroke and cancer. As a continuation of our previous work in this field, we report here the synthesis and biological evaluation of two classes of compounds as Panx1 blockers: 3-carboxy-6-sulphonamidoquinolone derivatives and new Mefloquine analogs. The series of 3-carboxy-6-sulphonamidoquinolones gave interesting results, affording powerful Panx1 channel blockers with 73.2 < I% < 100 at 50 µM. In particular, 12f was a more potent Panx1 blocker than the reference compound CBX (IC50 = 2.7 µM versus IC50 = 7.1 µM), and its profile was further investigated in a cell culture model of polycystic kidney disease. Finally, interesting results have been highlighted by new molecular modeling studies.

Phosphorylation Changes SARS-CoV-2 Nucleocapsid Protein's Structural Dynamics and Its Interaction With RNA

The SARS-CoV-2 nucleocapsid protein, or N-protein, is a structural protein that plays an important role in the SARS-CoV-2 life cycle. The N-protein takes part in the regulation of viral RNA replication and drives highly specific packaging of full-length genomic RNA prior to virion formation. One regulatory mechanism that is proposed to drive the switch between these two operating modes is the phosphorylation state of the N-protein. Here, we assess the dynamic behavior of non-phosphorylated and phosphorylated versions of the N-protein homodimer through atomistic molecular dynamics simulations. We show that the introduction of phosphorylation yields a more dynamic protein structure and decreases the binding affinity between the N-protein and RNA. Furthermore, we find that secondary structure is essential for the preferential binding of particular RNA elements from the 5' UTR of the viral genome to the N-terminal domain of the N-protein. Altogether, we provide detailed molecular insights into N-protein dynamics, N-protein:RNA interactions, and phosphorylation. Our results corroborate the hypothesis that phosphorylation of the N-protein serves as a regulatory mechanism that determines N-protein function.

Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2

Schizophrenia is a severe brain disorder that usually produces a lifetime of disability. Related research shows activating metabotropic glutamate receptors holds therapeutic potential. Agonist-positive allosteric modulations (ago-PAMs) not only activate metabotropic glutamate receptors but also enhance glutamate-induced responses, offering a promising treatment strategy. However, the molecular mechanisms by which ago-PAM enhances glutamate-induced responses remain unclear, as does the potential influence of glutamate on ago-PAM. In this study, Gaussian accelerated molecular dynamics and tau random acceleration molecular dynamics simulations were employed to investigate the molecular mechanism between ago-PAM and glutamate in full-length mGlu2. Results suggest that the ago-PAM JNJ-46281222 enhances the binding affinity and residence time of glutamates in the Venus flytrap (VFT) domains by initiating a variant reverse communication from the heptahelical transmembrane (7TM) domains to VFTs via the cysteine-rich domains. Meanwhile, glutamate facilitates the interaction between Trp676 and Glu701 to further induce the relaxation of TM5, promoting the opening of the PAM-binding pocket. Glutamate can also promote the upward rotation of the cyclopropylmethyl group of the JNJ-46281222 to bring the TM6-TM6 distance closer. Nevertheless, it remains uncertain how the binding between mGlu2 and G protein differs when induced by small molecules binding in allosteric sites, orthosteric sites, or both. In conclusion, this study shed new light on the positive coordination relationship between ago-PAM and glutamate in the full-length mGlu2 receptor, which could help develop novel and more effective ago-PAM to treat schizophrenia.

Analysis of Multi-Target Synergistic Mechanism of Coix Seed Therapy for Herpes Zoster Based on Machine Learning and Network Pharmacology

OBJECTIVE

To explore the efficacy and mechanism of Coix seeds in treating herpes zoster (HZ) using an integrated computational approach.

METHODS

Network pharmacology, molecular docking, and machine learning were employed. Disease-related targets were collected from multiple databases, and intersection targets with Coix seed were analyzed via PPI, GO, and KEGG enrichment. A "TCM-Ingredient-Target" network was constructed using Cytoscape. Molecular docking and dynamics simulations were performed for validation.

RESULTS

Fifty-five overlapping targets were identified, with core targets including TNF, EGF, and GAPDH. Enrichment analysis revealed key pathways such as inflammation and immune regulation. Molecular docking confirmed strong binding affinity between active compounds and targets.

CONCLUSIONS

This study demonstrates that Coix seed exerts anti-HZ effects through multi-target mechanisms, providing a theoretical basis for developing novel multi-pathway treatment strategies.

Multiscale modeling of charge transfer in hole-transporting materials: Linking molecular morphology to charge mobility

Hole-transporting materials (HTMs) play a pivotal role in the performance and stability of organic electronic devices by enabling efficient hole transport. This study employs a multiscale approach to explore the relationship between molecular morphology and charge transfer properties in four HTM molecules. By combining quantum mechanical calculations, molecular dynamics simulations, and kinetic Monte Carlo modeling, we analyze key structural features such as radial distribution functions, principal axis orientations, and non-covalent interactions. Our findings reveal that molecular size and substituent effects significantly influence non-covalent interactions and molecular alignments, thereby affecting charge transport pathways. Charge transfer rates and energetic disorder were modeled using the master equation, and mobilities were computed, showing satisfactory agreement with experimental data. This comprehensive analysis provides valuable insights into the design of HTMs for organic electronic devices, emphasizing the importance of molecular architecture in optimizing charge mobility and minimizing energy losses.

A Set of Quantum-Mechanically Derived Force Fields for Natural and Synthetic Retinal Photoswitches

The diverse biological functions of rhodopsins are all triggered by the photoexcitation of retinal protonated Schiff base chromophores. This diversity can be traced back not only to variations in protein scaffolds in which the chromophore is embedded, but also to the different isomeric forms of the chromophore itself, whose role is crucial in several processes. Although most computational approaches for these systems often require classical molecular dynamics, efforts in providing a set of parameters able to accurately and consistently model several isomeric chromophores are lacking in the literature. The most recent efforts entail either refinements of general purpose force fields lacking in accuracy, or parametrization strategies that include environmental effects, which makes the resulting parameters not transferable to a different embedding. In this work, we provide accurate intramolecular force fields based on data purposely computed using Møller-Plesset second order perturbation theory, specifically tailored for varied natural retinal protonated Schiff bases and synthetic analogues often employed in retinal-based photoswitches. We demonstrate the quality of our quantum-mechanically derived force fields (QMD-FFs) through a wide set of validation tests. These consistently indicate that QMD-FFs outperform in all cases transferable, general-purpose FFs, delivering an excellent description of each chromophore in terms of equilibrium geometries, conformational landscapes, and optical properties in comparison to literature data, experimental measurements, and reference QM calculations. Our intramolecular QMD-FFs, distributed in electronic format, can be adopted to describe these chromophores in complex environments, exploiting intermolecular parameters compatible with those available in the literature for biological macromolecules.

Microscopic effects of proline co-solvent on alanine homopeptide structure, solvation and helix folding dynamics

We present a computational investigation to explore the influence of the protective osmolyte proline as a co-solvent on peptide structure and dynamics for a series of alanine-based peptides, (ALA)n of length n = 5, 8, 15, and 21 residues. Applying multi-microsecond molecular dynamics simulations in a 2 M proline solution, we evaluate peptide structure, solvation and helix folding dynamics and compare to behavior in pure water. Proline addition enhances helix content and significantly slows folding and unfolding times, correlating with a 1.9-fold increase in solvent viscosity. Notably, ALA15 helix content increases from 25% to 49% and relaxation time rises from 110 ns to 540 ns in proline relative to water. Microscopic solvation effects of proline include peptide compaction and dehydration, exclusion of proline from the backbone, formation of weak interactions with the ALA methyl sidechains, and strong interactions with water. The differences of these effects on the helix and coil states drive helix stabilization by proline. Low-dimensional kinetic modeling with Optimal Dimensionality Reduction predicts distinct folding mechanisms: shorter peptides (ALA5-ALA15) exhibit direct helix-coil transitions, and only the longest ALA21 follows a more complex folding pathway involving intermediates. Statistically, enhanced stability of hydrogen bonds in the peptide centers and strong correlation between transitions on neighboring residues are shared between water and proline solutions. However, there is a preference for helix initiation at the N-terminus under proline influence. Our analysis describes the molecular mechanisms of how proline modulates peptide behavior, offering atomistic insights into helix stabilization and folding mechanisms mediated by osmolytes.

Tailoring Epoxy Network Architecture and Stiffness-Toughness Balance Using Competitive Short- and Long-Chain Curing Agents: A Multiscale Simulation Study

Designing high-performance crosslinked polymers requires overcoming the inherent stiffness-toughness trade-off through precise control of the network topology. Using epoxy resin as a model system, we establish a multiscale simulation framework to investigate curing reaction kinetics, network evolution, and structure-property relationships. By employing m-phenylenediamine (mPDA) and 1,3-bis(3-aminophenoxy)benzene (DABPB) as competing short- and long-chain curing agents, we demonstrate how network architecture dictates mechanical performance. Simulations reveal that mPDA produces a dense, heterogeneous network with enhanced stiffness, whereas DABPB forms a more uniform structure with greater chain mobility, leading to improved toughness. Through stoichiometric tuning, we achieve fine control over crosslink density and mechanical properties. Furthermore, we decouple cavity formation mechanisms into pendant chain slippage and bond rupture, offering molecular-level insights for the rational design of epoxy resins with programmable mechanical behavior.

Revealing thermophysical and mechanical responses of graphene-reinforced polyvinyl alcohol nanocomposites using molecular dynamics simulations

The effects of graphene (G) nanofiller content on enhancing the mechanical and thermal resistance of the polyvinyl alcohol (PVA) matrix are disentangled by performing all-atom classical molecular dynamics (MD) simulations. The crux of the computational work is to assess several key performance-limiting factors of the functional hybrid material, including the strain rate, temperature, and the size and distribution of the graphene nanofiller. Adding graphene nanofiller to the polymer results in more compact polymer chains, with the most significant impact observed in the 2% graphene composite. Uniaxial compression MD simulations revealed that the yield strength of the material is impacted by the proportion of nanofiller present. Specifically, the calculated stress-strain responses at a strain rate of 1.5 × 108 s-1 show that incorporating 2% graphene nanofiller remarkably enhances the yield strength. Conversely, increasing the graphene content to 5-10% led to a reduction in yield stress, which is primarily attributed to the disruption of hydrogen bond networks and destabilization of non-covalent interactions. Further analysis shows that increasing the strain rate led to higher yield stress in the G-PVA composite, while elevated temperatures caused its yield stress to decrease. Additionally, the glass transition temperature of the PVA composite rises with the graphene content and strongly correlates with the polymer chain mobility. The proposed theoretical approach may serve as a quantitative framework for elucidating the crucial role of interfacial interaction between polymers and nanomaterials in modulating the conformational, thermodynamic, and macroscopic properties of the hybrid materials.

Unique Formation of a Gauche Conformer in the Crystalline State of 1-Butyl-2,3-dimethylimidazolium Tetrafluoroborate at High Pressures

This study is focused on pressure-induced Raman spectral changes in the ionic liquid (IL) 1-butyl-2,3-dimethylimidazolium tetrafluoroborate ([C4dmim][BF4]) at ∼8 GPa. The sample comprises a methylated C2-H group in the imidazolium cation. As a counterpart of [C4dmim][BF4], a sample with an unmethylated C2-H group in the imidazolium cation, i.e., 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim][BF4]), was compared with [C4dmim][BF4]. Visual observations and Raman spectral changes show crystallization of [C4dmim][BF4] at ∼1.3 GPa. However, the unmethylated [C4mim][BF4] sample exhibited a pressure-induced glass formation similar to that of most ILs reported in the literature. Therefore, only C2-H-methylation leads to the opposite results for [C4dmim][BF4] and [C4mim][BF4]. The results of this study also highlight that a gauche conformer forms in the crystalline state of [C4dmim][BF4] upon applying pressure. This is unexpected, because trans conformers are typically the major conformers when most imidazolium-based ILs crystallize at high pressures. We analyze this unexpected behavior in terms of the local structural changes in the [C4dmim] cation using molecular dynamics calculations.

Characterizing Protein Solvent Accessible Surface Area in Solution by Dual Polarity Native Mass Spectrometry

Native mass spectrometry (nMS) is rapidly emerging as a pivotal technique for exploring protein conformations and protein-ligand interactions. Pioneering research has demonstrated that the charge state distribution (CSD) of proteins in native mass spectra can be indicative of their solvent accessible surface area (SASA). Moreover, beyond SASA, it is postulated that the abundance of acidic and basic amino acids on the protein surface may also impact the CSD. Specifically, basic amino acids tend to acquire positive charges during electrospray ionization (ESI), whereas acidic amino acids are prone to adopting negative charges. Consequently, this study investigates the CSDs of globular proteins in both positive and negative ion modes to provide a comprehensive characterization of protein SASA. Experiments were conducted under both native ESI and native nano-ESI conditions. By harnessing the average charges observed across dual polarity nMS data, we achieved significantly enhanced log linear correlations between protein SASA and its CSDs. The coefficient of determination (R2) improved from 0.9866 to 0.9888 under ESI conditions and from 0.9677 to 0.9902 under nano-ESI conditions when compared to models utilizing only positive ion mode data. These findings suggest that the SASA of globular proteins can be effectively characterized through the CSDs derived from dual polarity nMS analysis.

Alendronate repositioning as potential anti-parasitic agent targeting Trichinella spiralis inorganic pyrophosphatase, in vitro supported molecular docking and molecular dynamics simulation study

Trichinellosis represents great public health and economic problems worldwide. Moreover, the development of parasitic resistance against conventional anthelminthic treatment led to the urgent search for new therapeutic strategies, including drug repurposing. Bisphosphonates have been used to inhibit the growth of many parasites and have also emerged as promising candidates for the treatment of cryptosporidiosis and amoebic liver abscess. Alendronate is a second-generation bisphosphonate that is widely used for the treatment and prevention of osteoporosis. Till date, there is not enough data on the effect of this drug on Trichinella spiralis and it is unknown whether the regular use of this drug in osteoporotic patients may alter the course of the infection. ALN showed a significant lethal effect on both adult worms and juveniles, with severe tegumental damage in the form of fissures in the cuticle, widening of the hypodermal gland, and flattening of the cuticular annulation, ending with the appearance of multiple vesicles and large cauliflower masses. Molecular docking outcomes unveiled the potential inhibition of ALN against T. spiralis surface proteins (i.e., Ts-SP, Ts-PPase, Ts-MAPRC2, Ts-TS, Ts-MIF, etc.), with promising results confirmed its ability to defeat T. spiralis via targeting its surface proteins. Moreover, molecular dynamics simulation, through the analysis of RMSD, RMSF, RG, SASA and cluster analysis, proved the prolonged effective inhibition of ALN on T. spiralis inorganic pyrophosphatase, as an essential surface protein required for molting and developmental process of intestinal larval stages. Thus, ALN might be a valuable drug candidate for the treatment of trichinellosis and warrant further investigation in animal models of disease.

Water-directed pinning is key to tau prion formation

Tau forms fibrillar aggregates that are pathological hallmarks of a family of neurodegenerative diseases known as tauopathies. The synthetic replication of disease-specific fibril structures is a critical gap for developing diagnostic and therapeutic tools. This study debuts a strategy of identifying a critical and minimal folding motif in fibrils characteristic of tauopathies and generating seeding-competent fibrils from the isolated tau peptides. The 19-residue jR2R3 peptide (295 to 313) which spans the R2/R3 splice junction of tau, and includes the P301L mutation, is one such peptide that forms prion-competent fibrils. This tau fragment contains the hydrophobic VQIVYK hexapeptide that is part of the core of all known pathological tau fibril structures and an intramolecular counterstrand that stabilizes the strand-loop-strand (SLS) motif observed in 4R tauopathy fibrils. This study shows that P301L exhibits a duality of effects: it lowers the barrier for the peptide to adopt aggregation-prone conformations and enhances the local structuring of water around the mutation site to facilitate site-directed pinning and dewetting around sites 300-301 to achieve in-register stacking of tau to cross β-sheets. We solved a 3 Å cryo-EM structure of jR2R3-P301L fibrils in which each protofilament layer contains two jR2R3-P301L copies, of which one adopts a SLS fold found in 4R tauopathies and the other wraps around the SLS fold to stabilize it, reminiscent of the three- and fourfold structures observed in 4R tauopathies. These jR2R3-P301L fibrils are competent to template full-length 4R tau in a prion-like manner.

Catechins anti-diabetic actions are mediated via multiple receptors, a mechanism deduced via molecular docking and dynamic simulations

Diabetes mellitus is a growing burden that affects a large proportion of the population worldwide, with long-term complications that cause a devastating effect on the function of various organs. The currently available treatments lack optimum therapeutic goals, increasing the need for new drug discovery. Catechins are natural flavonoids that demonstrate anti-diabetic effects; however, catechin's mechanism of action remains unclear. This study was aimed to unleash the molecular mechanism behind the catechin's effect on blood glucose levels. For that, we explored the capability of some catechins to bind and interact with glucagon-like peptide-1 receptor-1, pancreatic ATP-sensitive potassium channel, dipeptidyl peptidase-4, and sodium-glucose transporter-2, which is essential for euglycemia, using molecular docking screening and dynamic simulations. The results showed that all the tested catechins are potential sodium-glucose transporter-2 inhibitors, a mechanism revealed for the first time, and glucagon-like peptide-1 receptor-1 agonists with various affinities to these receptors. Moreover, among these compounds, (-)-Epigallocatechin 3-O-gallate, (-)-Gallocatechin 3-O-gallate demonstrated the ability to act as an ATP-sensitive potassium channel inhibitor, and dipeptidyl peptidase-4 inhibitor in addition to the previously mentioned mechanisms. The discovery introduces (-)-gallocatechin 3-O-gallate and (-)-Epigallocatechin 3-O-gallate as a hot subject for research, as the compounds require further optimization to initiate further pre-clinical and clinical studies.

Rational computational design and development of an immunogenic multiepitope vaccine incorporating transmembrane proteins of Fusobacterium necrophorum

Fusobacterium necrophorum is a Gram-negative, anaerobic pathogen responsible for Lemierre's syndrome, bovine foot rot, and other necrotizing infections. The rise in antimicrobial resistance and the absence of effective vaccines underscore the need for alternative therapeutic strategies. This study employs computational biology to design a multi-epitope vaccine targeting transmembrane proteins of F. necrophorum to elicit strong immune responses. The selected proteins were evaluated for toxicity, allergenicity, and antigenicity, followed by epitope prediction and screening. B and T cell epitopes were linked using immunogenic linkers, forming a vaccine construct with a VaxiJen score of 0.7293 and a solubility score of 8.30 in E. coli. Structural validation using TrRosetta and Ramachandran plots confirmed 97.4% of residues in favored regions, indicating high stability. Population coverage analysis indicated over 99% global applicability, further enhancing its potential impact. Docking studies revealed strong interactions with immune receptors TLR7 and TLR8. TLR7 formed 12 hydrogen bonds, while TLR8(A) formed 9, and TLR8(B) exhibited the highest interaction, forming 13 hydrogen bonds with the vaccine construct. Molecular dynamics simulations confirmed structural stability and receptor engagement. The RMSD stabilized around 4-5 Å, indicating structural stability of the Vaccine-TLR8(B) complex. The Radius of Gyration remained around 36 Å, showing slight compaction over time, while RMSF peaked at 8-9 Å in flexible regions, with lower fluctuations (1.5-2.5 Å) in stable core regions. Principal component analysis (PCA) identified elastic regions critical for biological activity, and the stable energy levels (-5000 kJ/mol) further confirmed the reliability of the binding. Moreover, the vaccine exhibited high expression levels in E. coli, as demonstrated using SnapGene software with the pET-29a( +) vector. The vaccine demonstrated strong binding affinities with immune receptors and predicted activation of both humoral and cellular immune responses, including increased IgM, IgG, and cytokine levels. However, experimental validation is necessary to confirm safety and efficacy, and challenges in vaccine manufacturing and variable immune responses across populations must also be addressed.

Molecular cloning, overexpression, characterization, and mechanism explanation of an esterase RasEst3 for ester synthesis under aqueous phase

Fatty acid esters are widely used in fragrance compounds, solvents, lubricants, and biofuels. Enzymatic synthesis of these esters in aqueous phase is an environmentally friendly approach. In this study, an esterase RasEst3 from Rasamsonia emersonii was identified for fatty acid ester synthesis through sequence alignment. The gene encoding RasEst3 was heterologously expressed in Escherichia coli BL21(DE3), and its enzymatic properties were analyzed. The enzyme exhibited optimal activity at pH 3.5 and 30 °C, with a preference for medium-chain substrates. Structurally, RasEst3 contains a lid domain and a catalytic domain, with a catalytic triad composed of Ser146-His227-Asp214. The smaller pocket spatial site resistance and the hydrophobicity of the substrate channel facilitate effective substrate binding to the active center. Site-directed mutagenesis and molecular dynamics simulations revealed that the oxygen anion holes formed by Gly69 and Thr70, along with the π-bond stacking formed by Tyr112 and Tyr145, play crucial roles in catalysis. After removing a loop region from RasEst3, its ethyl octanoate synthesis activity increased by 253.22 % compared to the wild-type enzyme. This study not only clarifies the structure-function relationship of RasEst3 but also provides valuable insights for developing novel biocatalysts in green chemistry.

Evaluation of synaptotagmin-1 action models by all-atom molecular dynamics simulations

Neurotransmitter release is triggered in microseconds by the two C2 domains of the Ca2+ sensor synaptotagmin-1 and by SNARE complexes, which form four-helix bundles that bridge the vesicle and plasma membranes. The synaptotagmin-1 C2B domain binds to the SNARE complex via a 'primary interface', but the mechanism that couples Ca2+-sensing to membrane fusion is unknown. Widespread models postulate that the synaptotagmin-1 Ca2+-binding loops accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers or helping bridge the membranes, but these models do not seem compatible with SNARE binding through the primary interface, which orients the Ca2+-binding loops away from the fusion site. To test these models, we performed molecular dynamics simulations of SNARE complexes bridging a vesicle and a flat bilayer, including the synaptotagmin-1 C2 domains in various configurations. Our data do not support the notion that insertion of the synaptotagmin-1 Ca2+-binding loops causes substantial membrane curvature or major perturbations of the lipid bilayers that could facilitate membrane fusion. We observed membrane bridging by the synaptotagmin-1 C2 domains, but such bridging or the presence of the C2 domains near the site of fusion hindered the action of the SNAREs in bringing the membranes together. These results argue against models predicting that synaptotagmin-1 triggers neurotransmitter release by inducing membrane curvature, perturbing bilayers or bridging membranes. Instead, our data support the hypothesis that binding via the primary interface keeps the synaptotagmin-1 C2 domains away from the site of fusion, orienting them such that they trigger release through a remote action.

Substitutions at rheostat position 52 of LacI have long-range effects on the LacI conformational landscape

In proteins, amino acid changes at "rheostat" positions exhibit functional changes that vary with the substitution chosen: some substitutions enhance function, some are like wild-type, some are partially detrimental, while others abolish function. One way that substitutions might exert their complex effects is by altering protein conformational landscapes. To test this, we studied five substitutions of V52 in E. coli LacI, an experimentally-known rheostat position. For each variant, we mapped the accessible conformational landscapes by performing molecular dynamics simulations at ambient conditions and under three perturbations: increased pressure, binding to allosteric ligand "ONPF", and ONPF plus pressure. The simulated DNA binding domain landscapes were compared to published experimentally-measured parameters, and the results suggest that complex combinations of dynamic parameters and/or additional simulations in the presence of DNA are needed to predict DNA binding specificity. For the variants regulatory domains all landscapes displayed boundaries similar to wild-type, but changes within the boundaries were unique. Of these, V52A/ONPF was striking: The regulatory domains for ONPF-bound, wild-type LacI are in an "Open" conformation and, experimentally, ONPF enhances DNA binding. Four variants responded to ONPF like wild-type, but ONPF binding to V52A shifted these domains to a "Closed" conformation that is associated with diminished DNA binding for wild-type LacI. This finding predicted that ONPF's allosteric regulation of V52A would change from "anti-inducer" to "inducer", which we experimentally validated in vivo and in vitro. This supports the hypothesis that substituting rheostat positions can alter function by altering the relative populations on protein conformational landscapes.

Exploring the modulation of phosphorylation and SUMOylation-dependent NPR1 conformational switching on immune regulators TGA3 and WRKY70 through molecular simulation

NPR1 (Nonexpressor pathogenesis-related genes 1) is regulated by multisite phosphorylation and SUMOylation, serving as a master switch for effector-triggered plant immunity through a transcriptional activator (TGA3) and repressor (WRKY70) are experimentally well studied. However, the conformational relationship between the various phosphorylation, un-phosphorylation states, and SUMOylation's role in the functional switch remains unclear. Using deep learning-based molecular modeling, docking, and multi-nanosecond simulations (totaling 2 μs) with end-state free energy calculations, we unveil how different phosphorylation states impact the dynamic stability of NPR1's four phospho-serine residues (Ser11, Ser15, Ser55, & Ser59) and binding of the TGA3-WRKY70 over SUMOylation. Results from our simulations show that the salicylic-acid induced P-Ser11/15NPR1-SUMO3 stabilizes helices and the flexible activation loop (α22Lys423 - α1Arg50 & L35Asp467-Arg51α51, and Gly27L3), thereby switching association with TGA3. The inter-helix salt-bridge formed (L10Arg99-Glu323α9 and α14Glu280-Pro264L6) between the phosphorylated NPR1-SUMO3-TGA3 engage in tight control of conformational regulation were disengaged in the unphosphorylated system. The P-Ser55/59NPR1-SUMO3-WRKY70 reorients itself and forms an electrostatic and hydrogen bond with Lys145α7 - L2Asp26, L6Arg99 - Leu293L18 and Lys262L15 - Glu241L15, α13Val239 (α310), & L17Leu267 keeps complex stable and quiescent compare to unphosphorylated NPR1-WRKY70. Subsequently, the essential dynamic and secondary structural analysis reveals that the phosphorylation inhibits the α516 (long helix) formation and reduces the communication space between the 460α25-βturn3-α30-L42590 (NPR1) and 90L9-L10107 (SUMO3), making the binding more suitable for TGA3 (260βturn-L6270) and WRKY70 (230L15-L16265) via activation loop. These findings, which reveal the atomic and structural details of the NPR1's post-translational modification, will illuminate future investigations into enhancing plant immunity.

Structural insights into the selective recognition of RF-amide peptides by neuropeptide FF receptor 2

Neuropeptide FF Receptor 2 (NPFFR2), a G-protein-coupled receptor, plays a role in pain modulation and diet-induced thermogenesis. While NPFFR2 is strongly activated by neuropeptides FF (NPFFs), it shows low activity in response to RF-amide-related peptides (RFRPs), despite the peptides belonging to a shared family. In contrast, NPFFR1, which shares high sequence similarity with NPFFR2, is activated by RFRPs and regulates reproductive hormone balance. The molecular basis for these receptor-specific interactions with their RF-amide peptides remains unclear. Here, we present cryo-electron microscopy structures of NPFFR2 in its active state bound to the agonist RF-amide peptide hNPSF, and in its ligand-free state. Structural analysis reveals that the C-terminal RF-amide moiety engages conserved residues in the transmembrane domain, while the N-terminal segment interacts in a receptor subtype-specific manner. Key selectivity-determining residues in NPFFR2 are also identified. A homology model of NPFFR1 bound to RFRP, supported by mutagenesis studies, further validates this selectivity mechanism. Additionally, structural comparison between the inactive and active states of NPFFR2 suggests a TM3-mediated activation mechanism. These findings provide insights into RF-amide peptide recognition by NPFF receptors.

Improved genetic screening with zygosity detection through multiplex high-resolution melting curve analysis and biochemical characterisation for G6PD deficiency

Accurate diagnosis of glucose-6-phosphate dehydrogenase (G6PD) deficiency is crucial for relapse malaria treatment using 8-aminoquinolines (primaquine and tafenoquine), which can trigger haemolytic anaemia in G6PD-deficient individuals. This is particularly important in regions where the prevalence of G6PD deficiency exceeds 3%-5%, including Southeast Asia and Thailand. While quantitative phenotypic tests can identify women with intermediate activity who may be at risk, they cannot unambiguously identify heterozygous females who require appropriate counselling. This study aimed to develop a genetic test for G6PD deficiency using high-resolution melting curve analysis, which enables zygosity identification of 15 G6PD alleles. In 557 samples collected from four locations in Thailand, the prevalence of G6PD deficiency based on indirect enzyme assay was 6.10%, with 8.08% exhibiting intermediate deficiency. The developed high-resolution melting assays demonstrated excellent performance, achieving 100% sensitivity and specificity in detecting G6PD alleles compared with Sanger sequencing. Genotypic variations were observed across four geographic locations, with the combination of c.1311C>T and c.1365-13T>C being the most common genotype. Compound mutations, notably G6PD Viangchan (c.871G>A, c.1311C>T and c.1365-13T>C), accounted for 15.26% of detected mutations. The high-resolution melting assays also identified the double mutation G6PD Chinese-4 + Canton and G6PD Radlowo, a variant found for the first time in Thailand. Biochemical and structural characterisation revealed that these variants significantly reduced catalytic activity by destabilising protein structure, particularly in the case of the Radlowo mutation. The refinement of these high-resolution melting assays presents a highly accurate and high-throughput platform that can improve patient care by enabling precise diagnosis, supporting genetic counselling and guiding public health efforts to manage G6PD deficiency-especially crucial in malaria-endemic regions where 8-aminoquinoline therapies pose a risk to deficient individuals.