Stable Hydrogen Bonds Research Articles

Interplay of Tetrel, Hydrogen, and Halogen Bonds in F3GeOCl and HCN Complexes: A Comprehensive Theoretical Study of Dimers, Trimers, and Tetramers.

This study investigates the nature and interplay of noncovalent interactions (NCIs)─tetrel bonds (TB), hydrogen bonds (HB), and halogen bonds (XB)─in molecular assemblies formed between trifluorogermyl hypochlorite (F3GeOCl) and hydrogen cyanide (HCN). Using a combination of high-level computational methods, we explored the geometric, energetic, and electronic properties of dimers, trimers, and tetramers formed in different molar ratios of interacting reagents. Various analyses reveal a significant cooperativity between TB and HB, which mutually reinforce each other, while XB interactions are diminished in the presence of TB and HB. Energy decomposition analysis (EDA) through SAPT and sobEDAw methods identified electrostatic and orbital interactions as key contributors to the stabilization of TB and HB, while dispersion plays a prominent role in XB. A perfect linear correlation was found between interaction energy and charge density at bond critical points (BCPs), underscoring the predictive value of these metrics. These findings shed light on the cooperative nature of NCIs and provide a framework for designing molecular systems in supramolecular chemistry and crystal engineering.

Molecular Dynamics Simulation of Clay Mineral–Water Interfaces: Temperature-Dependent Structural, Dynamical, and Mechanical Properties

Water interacting with clay minerals—such as kaolinite, montmorillonite, and pyrophyllite—fundamentally governs their geotechnical and environmental functions, thereby influencing parameters such as retention, transport, and stability. Understanding the effects of temperature on water behavior within clay mineral interlayers is critical for predicting the performance of clay–water systems under dynamic environmental conditions. This study performed molecular dynamics simulations to investigate the structural, dynamical, and mechanical properties of interlayer water in three representative clay minerals over a temperature range of 298.15–363.15 K. Our analyses focused on mean squared displacement (MSD), density profiles, hydrogen bond dynamics, and stress distributions, thereby revealing the interaction between water structuring and thermal fluctuations. Results indicated distinct temperature-dependent changes in water diffusion and hydrogen bond stability, with montmorillonite consistently exhibiting enhanced water retention and steadier hydrogen bonding networks across the studied temperature spectrum. Density profiles highlighted pronounced confinement effects at lower temperatures that gradually diminish with increasing thermal energy. Concurrently, the stress distributions revealed the mechanical responses of clay–water interfaces, highlighting the interplay between thermal motion of water molecules and their interactions with the clay surfaces. These findings offer valuable insights into how temperature regulates water behavior in clay mineral interlayers and provide a foundation for advancing predictive modeling and the design of engineered systems in water-rich, thermally variable environments.

REDOX POTENTIAL STUDIES BASED ON SCAN-RATE ANALYSIS OF THE DIFFUSIONAL CONTROL AND DFT CALCULATIONS OF THE SCHIFF BASE [(E)-4-AMINO-3-((3,5-DI-tert-BUTYL-2- HYDROXYBENZYLIDENE)AMINO) BENZOIC ACID

Schiff bases are diverse organic compounds with an azomethine structure (–C=N–), holding potential in both chemistry and biology. They serve as catalysts, stabilizers, and exhibit various biological activities. The molecular structure of Schiff bases influences their biological properties, including antimicrobial effects. Redox-active compounds with more negative potentials tend to be more effective against microbes. In one of our recent studies, we explored the antimicrobial properties of two Schiff bases derivatives, SB-1 ((E)-4-amino-3-((3,5-di-tert-butyl-2-hydroxybenzylidene)amino) and SB-2 ((E)-2-((4-nitrobenzilidene)amino)aniline). SB-1 showed antibacterial activity against certain Gram-positive bacteria, while SB-2 did not. The difference in their cyclic voltametric profiles, especially SB-1’s more negative reduction potential, prompted us to carry out further characterizations, including scan-rate studies, solvent analysis, and computational calculations. We found that SB-1, which presents a stable intramolecular hydrogen bond, undergoes irreversible oxidation, likely at the –NH2 group, and a quasi-reversible reduction via an intramolecular reductive coupling of the (–C=N–) azomethine group, supported by orbital theoretical calculations. This research sheds light on the potential applications of Schiff bases in antimicrobial contexts, guided by their redox properties and structure.

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation.

Gaussia Luciferase (GLuc) is a renowned reporter protein that can catalyze the oxidation of coelenterazine (CTZ) and emit a bright light signal. GLuc comprises two consecutive repeats that form the enzyme body and a central putative catalytic cavity. However, deleting the C-terminal repeat only limited reduces the activity (over 30% residual luminescence intensity detectable), despite being a key part of the cavity. How does the remaining GLuc (tGLuc) catalyze CTZ? To address this question, we built a structural model of tGLuc by removing the C-terminal repeat from the resolved structure of intact GLuc, and verified that the cavity-forming component in GLuc remains stable and provides an open-mouth cavity in tGLuc during 500 ns MD simulations in water. Docking simulation and a followed umbrella sampling analysis further revealed that the cavity on tGLuc has a high affinity for CTZ, with a binding energy of up to -114 kJ/mol. Moreover, R76, a validated activity-critical amino acid residue, resides in the cavity and forms a stable hydrogen bond with CTZ. Then, we constructed a cluster model to examine the CTZ oxidation pathway in the cavity using Density Functional Theory (DFT) calculations. The result showed that the pathway consists of four elementary reactions, with the highest Gibbs energy barrier being 65.4 kJ/mol. Both intramolecular electron transfer and the convergence of S1/S0 potential energy surfaces occurred in the last elementary reaction, which was regarded as the reported Chemically-Initiated-Electron-Exchange-Luminescence (CIEEL) reaction. Geometry and wavefunction analysis on the pathway indicated that R76 plays a vital role in CTZ oxidation, which first anchors the environmental oxygen molecule and induces it to form a singlet biradical state, facilitating its attack on CTZ. Subsequently, R76 and the adjacent Q88, positioned near R76 through the tGLuc refolding process, stabilize the transition states and facilitate the emergence of radical electrons on CTZ at the onset of the CIEEL reaction, which contributes to the subsequent intramolecular electron transfer and the production of excited amide product. This study provides a comprehensive explanation of tGLuc's catalytic mechanism. However, it is important to note that these findings are specific to tGLuc and may not extend to other CTZ-based luciferases, particularly those lacking arginine in their catalytic cavities, which likely operate via distinct mechanisms.

Integration of InVitro and In Silico Results From Chemical and Biological Assays of Rheum turkestanicum and Calendula officinalis Flower Extracts.

In this study, we conducted a thorough analysis of Rheum turkestanicum (RT) and Calendula officinalis flowers (COF) extracts with varying polarities using LC-MS chemical profiling and biological tests (antioxidant, antimicrobial, enzyme inhibition, and cytotoxic effects). The highest level of total phenolic content in the ethanol extract of RT with 75.82 mg GAE/g, followed by the infusions of RT (65.00 mg GAE/g) and COF (40.99 mg GAE/g). A total of 20 bioactive compounds were identified and quantified. The ethanol extract of COF was rich in terms of 5-O-caffeoylquinic acid (2780.56 μg/g), isorhamnetin-O-rutinoside (1653.59 μg/g), and rutin (1356.97 μg/g). However, RF extracts were rich in catechin gallate (21.66-80.01 μg/g) and 5-O-caffeoylquinic acid. Except for metal chelating ability, the ethanol extract of RT exhibited the strongest ability (DPPH: 171.5 mg TE/g; ABTS: 387.35 mg TE/g; CUPRAC: 449.80 mg TE/g; FRAP: 195.60 mg TE/g; and PBD: 1.52 mmol TE/g). In the enzyme inhibition tests, the tested ethanol extracts for both species were more active than the infusion. The highest values for tyrosinase were recorded as 72.47 mg KAE/g (in RT extracts) and 71.74 mg KAE/g (in COF extracts). Furthermore, all extracts underwent assessment for their antibacterial and antifungal properties, targeting both Gram-positive and Gram-negative bacteria, as well as clinical yeast and fungal microorganisms. In silico studies yielded valuable insights into the potential therapeutic applications of the bioactive compounds identified in COF and RT extracts. Stable interactions were observed between key compounds, such as isorhamnetin 3-O-glucoside and 3-O-caffeoylquinic acid, with crucial target proteins (AChE, BChE, and MurE). These compounds formed stable hydrogen bonds with minimal root mean square deviation (RMSD) fluctuations, particularly in the isorhamnetin 3-O-glucoside-Staphylococcus aureus MurE and 3-O-caffeoylquinic acid-MurE of S. aureus complexes. These findings further underscore the potential of these compounds as promising candidates for therapeutic development.

Molecular Insights into Structural Dynamics and Binding Interactions of Selected Inhibitors Targeting SARS-CoV-2 Main Protease.

The SARS-CoV-2 main protease (Mpro, also known as 3CLpro) is a key target for antiviral therapy due to its critical role in viral replication and maturation. This study investigated the inhibitory effects of Bofutrelvir, Nirmatrelvir, and Selinexor on 3CLpro through molecular docking, molecular dynamics (MD) simulations, and free energy calculations. Nirmatrelvir exhibited the strongest binding affinity across docking tools (AutoDock Vina: -8.3 kcal/mol; DiffDock: -7.75 kcal/mol; DynamicBound: 7.59 to 7.89 kcal/mol), outperforming Selinexor and Bofutrelvir. Triplicate 300 ns MD simulations revealed that the Nirmatrelvir-3CLpro complex displayed high conformational stability, reduced root mean square deviation (RMSD), and a modest decrease in solvent-accessible surface area (SASA), indicating enhanced structural rigidity. Gibbs free energy analysis highlighted greater flexibility in unbound 3CLpro, stabilized by Nirmatrelvir binding, supported by stable hydrogen bonds. MolProphet prediction tools, targeting the Cys145 residue, confirmed that Nirmatrelvir exhibited the strongest binding, forming multiple hydrophobic, hydrogen, and π-stacking interactions with key residues, and had the lowest predicted IC50/EC50 (9.18 × 10-8 mol/L), indicating its superior potency. Bofutrelvir and Selinexor showed weaker interactions and higher IC50/EC50 values. MM/PBSA analysis calculated a binding free energy of -100.664 ± 0.691 kJ/mol for the Nirmatrelvir-3CLpro complex, further supporting its stability and binding potency. These results underscore Nirmatrelvir's potential as a promising therapeutic agent for SARS-CoV-2 and provide novel insights into dynamic stabilizing interactions through AI-based docking and long-term MD simulations.

Probing the Conformational Ensemble of the Amyloid Beta 16-22 Fragment with Parallel-Bias Metadynamics.

Aβ(16-22) is a segment of the Alzheimer's-related β-amyloid peptide that plays a crucial role in its aggregation. This study applies well-tempered parallel-bias metadynamics to investigate the impact of several denaturants and osmolytes on the conformational ensembles of both termini-capped and uncapped Aβ(16-22) monomers. Comparison of the different sets of collective variables in the metadynamics bias shows that using the set of backbone torsional angles results in better and faster convergence of simulations than employing more general structural characteristics of the short peptide. The equilibrium conformational ensembles of the peptides are characterized in pure water and in the presence of TMAO, urea, guanidinium chloride, and trifluoroethanol. In particular, trifluoroethanol and TMAO are found to increase the population of compact peptide conformations, whereas urea and guanidinium chloride favor extended structures. The analysis of the free energy surfaces in the presence of various substances with a comparison of the behavior of the capped and uncapped peptide forms reveals the role of different types of intrapeptide interactions such as salt bridges, hydrophobic contacts, and hydrogen bonds in stabilization of the compact or extended structures. As compounds reducing the abundance of the compact states of Aβ(16-22) and other disordered peptides are likely to suppress their amyloid fibril formation, simulations in the systems with this short peptide may be useful for the virtual screening of such compounds.

Elucidating the mechanisms of a herbal compound fumarine and its modulation on the estrogen receptor 1

Stroke-related numbness and weakness (SRNW) are resultant disabilities following a stroke episode and may present with muscle weakness, numbness, tightness, spasticity, and pain in up to 85% of patients. Huangqi Guizhi Wuwu Decoction (HGWD) has been widely investigated to manage the sensorimotor deficiencies at the herb and formula level. However, detailed molecular mechanisms of its constituents are presently lacking. This project employed computational molecular modelling and docking methods to identify candidate compounds of HGWD which may serve as effective modulators of target proteins involved in SRNW. Estrogen Receptor 1 was identified as a promising target for HGWD compounds, while the herbal compound fumarine, a constituent of Jujubae Fructus, was predicted to exhibit high binding affinity and favourable ligand-receptor interactions with ESR1. There is currently a lack of scientific evidence for specific atomic-level interactions between ESR1 and this compound. Therefore, molecular docking and molecular dynamics simulations were used to elucidate the interaction mechanisms of fumarine with ESR1; and the molecular-level structural and functional consequences of ligand binding. Ligand-receptor contact analysis and free energy decomposition calculations identified Glu419 and Leu38 as stable hydrogen bond partners, while favourable contributions to the binding free energy include in Met421 (−10.74 kJ/mol) and Leu525 (−10.02 kJ/mol). This work provides the basis for further studies on discovering lead compounds which modulate the activity of ESR1.

Unveiling the mechanisms of mixed surfactant synergy in passivating lignin-cellulase interactions during lignocellulosic saccharification

Surfactants can synergistically enhance the enzymatic hydrolysis of lignocellulosic biomass, achieving higher sugar yields at lower enzyme loading. However, the exact mechanism by which mixed surfactants passivate lignin-cellulase interactions is not fully understood. This study found that the combination of ternary non-ionic and cationic surfactants (Tween 60, Triton X-114, and CTAB) significantly reduced the non-productive adsorption of lignin, with decreases of 35.4 %−55.4 % in equilibrium adsorption (We, 23.2 mg/g) compared to the single surfactant and the control. Meanwhile, mixed surfactants disrupted the entropy-enthalpy co-driven process for non-productive cellulase adsorption while promoting the desorption process. Non-ionic surfactants mainly contributed to reducing the hydrophobic interactions between lignin and cellulases. Positively charged CTAB enabled nonionic surfactants to form stronger H-bonds with lignin by electrophilic modification, and Triton X-114 increased van der Waals forces. Although surfactant-modified lignin exhibited lower hydrophobicity, zeta potential, and a more stable hydrogen bond network, the inhibitory effects of lignin-cellulase interactions by mixed surfactants were susceptible to lignin properties. According to the structure–activity relationship analysis (R2 > 0.80), the main influencing factors included particle size, aliphatic/phenolic OH group contents, contact angle, and zeta potential of lignin. The study on the synergistic passivation of lignin-cellulase interactions by multi-component surfactant systems provides some theoretical insights for selecting and customarily designing effective additives for efficient enzymatic hydrolysis in lignocellulosic biorefineries.

On the similar spectral manifestations of protonic and hydridic hydrogen bonds despite their different origin

Previously studied complexes with protonic and hydridic hydrogen bonds exhibit significant similarities. The present study provides a detailed investigation of the structure, stabilization, electronic properties, and spectral characteristics of protonic and hydridic hydrogen bonds using low-temperature infrared (IR) spectroscopy and computational methods. Complexes of pentafluorobenzene with ammonia (C₆F₅H⋯NH₃) and triethylgermane with trifluoroiodomethane (Et₃GeH⋯ICF₃) were analyzed using both experimental and computational tools. Additionally, 30 complexes with protonic hydrogen bonds and 30 complexes with hydridic hydrogen bonds were studied computationally. Our findings reveal that, despite the opposite atomic charges on the hydrogens in these hydrogen bonds, and consequently the opposite directions of electron transfer in protonic and hydridic hydrogen bonds, their spectral manifestations - specifically, the red shifts in the X–H stretching frequency and the increase in intensity - are remarkably similar. The study also discusses the limitations of the current IUPAC definition of hydrogen bonding in covering both types of H-bonds and suggests a way to overcome these limitations.

Identification and anticoagulant mechanisms of novel factor XIa inhibitory peptides by virtual screening of a in silico generated deep-sea peptide database

The objective of this study was to identify novel anticoagulant peptides from the deep-sea using multiple in silico methods, and to investigate their inhibitory activity and molecular mechanisms. A deep-sea peptide database was firstly constructed by performing virtual proteolysis on protein sequences from animals inhabiting deep-sea hydrothermal vents and cold seeps. Candidate anticoagulant peptides were identified through molecular docking and binding free energy screening against FXIa as the target. Two novel anticoagulant peptides, PRNIF (IC50 = 0.67 mM) and GNDRCL (IC50 = 1.52 mM), were identified, and their anticoagulant activities were verified in vitro. PRNIF was demonstrated to be a noncompetitive inhibitor of FXIa, and caused significant prolongation of thrombin time (TT) and activated partial thromboplastin time (APTT), whereas GNDRCL markedly prolonged the APTT only. Molecular dynamics simulations demonstrated considerable conformational shifts of both anticoagulant peptides when bound to the active sites of FXIa. The lowest energy binding poses of the FXIa-peptide complexes for PRNIF and GNDRCL exhibited comparable numbers of hydrogen bonds and binding free energies. However, occupancy analysis revealed completely distinct stability characteristics of the hydrogen bond interactions. The conserved residue Asp569 in the S1 pocket of FXIa formed strong and stable hydrogen bonds as well as a salt bridge with the arginine residues of PRNIF, which were not observed in the FXIa-GNDRCL complex. To our knowledge, PRNIF represented the first FXIa inhibitory peptide derived from the deep-sea, which may contribute to the development and utilization of deep-sea peptides resources. Two deep-sea peptides may potentially serve as an alternative food-derived ingredient that could be utilized for thrombosis prevention.

Hydroxyl and amino co-modified imidazole based ionic liquid functionalized TS-1 molecular sieve for efficient CO2 capture

Herein, an integrative solid adsorbent of [AHOPMIm]Cl with hydroxyl and amino groups functional sites modified TS-1 molecular sieve is designed and fabricated for efficient CO2 adsorption. The optimal [AHOPMIm]Cl/TS-1 exhibits 73% enhancement in CO2 adsorption capacity compared with the TS-1 molecular sieve, even outperforming other state of the art adsorbent systems. The greatly improved CO2 adsorption capacity is mainly attributed to the strong adsorption of amino groups on the ionic liquids surface, which can form low-temperature stable amino ester species. Moreover, it is preserved that the hydroxyl groups on the surface of ionic liquids can form stable hydrogen bonds with oxygen atoms in CO2, and coordinate with amino groups to capture CO2 from different directions based on in situ DRIFTS and DFT. The porous TS-1 molecular sieve provides a structural basis for the uniform dispersion, effective support, and enhanced CO2 adsorption capacity of ionic liquids. A new design concept for constructing ionic liquid-based composite adsorbent with dual functional sites using TS-1 molecular sieve as a carrier is provided, and the avenues for efficient CO2 adsorption are paved.

Exploring the competitive inhibition of α-glucosidase by citrus pectin enzymatic hydrolysate and its mechanism: An integrated experimental and simulation approach

The endo-polygalacturonase D (PgaD) from Aspergillus niger JL15 was recombinantly expressed in Escherichia coli BL21, exhibiting an optimal activity at 55 °C and pH 4.0. Hydrolysis products of citrus pectin by recombinant PgaD included galacturonic acid (GalA), digalacturonic acid (GalA2), trigalacturonic acid (GalA3), and tetragalacturonic acid (GalA4). The hydrolysates exhibited significant antioxidant capacity and dose-dependent competitive inhibition of α-glucosidase. GalA2 and GalA3 acted as competitive inhibitors of α-glucosidase, with inhibition constant of 0.0589 mmol.L−1 and 0.6732 mmol.L−1, respectively. Molecular dynamics (MD) simulations revealed that both GalA2 and GalA3 penetrated the catalytic pocket of α-glucosidase and formed stable hydrogen bonds with key catalytic residues D352 and D215. The binding free energies of GalA2-α-glucosidase and GalA3-α-glucosidase complexes were − 10.3 ± 0.6 kcal·mol−1 and -10.8 ± 0.7 kcal·mol−1, respectively. These findings might offer new ideas for the development of α-glucosidase inhibitors sourced from citrus pectin, as well as enhance utilization of the renewable plant polysaccharide resources.

Integrative computational approach for hyperuricemia treatment: 3D QSAR, molecular docking and dynamics of flavonoid analogues as xanthine oxidase inhibitors

Hyperuricemia is characterized by an excessive accumulation of uric acid in the joints, and this condition remains a therapeutic challenge with limited options and significant side effects associated with conventional pharmacological treatments. This research aims to identify new molecular structures capable of inhibiting uric acid production by targeting key enzymes in purine metabolism. In this study, a comprehensive in silico analysis was conducted to explore the relationship between the chemical structure of flavonoid analogs and their inhibitory capacity on xanthine oxidase (XO). The results revealed that the analogs meet the structural requirements for xanthine oxidase inhibition. A 3D-QSAR model was generated, accurately predicting the biological activity of flavonoids targeting XO and identifying a potential lead compound with a q2 of 0.77 and R2 of 0.98. The CoMFA analysis disclosed how substituents affect XO affinity, with bulky groups enhancing it at positions R2 and R7. These strategies were applied and a new molecule was generated with better binding energy with the XO receptor. Electron-donating or accepting groups, such as phenyl and carbonyl, interact with amino acid residues (T1010 and R880) in XO's active site. Molecular docking analysis highlights different common interaction types in flavonoid-XO binding, emphasizing the importance of hydrogen and CH bonds. Previous studies underscore the significance of these specific residues in flavonoid-XO binding. Molecular dynamics showed that 3(R,S)-3′-Hydroxy-8-methoxyvestitol predominantly interacts through hydrophobic interactions, inducing a conformational change in the binding pocket and stabilizing the complex along with stable hydrogen bonds.

Novel bibenzyl compound 8Ae induces apoptosis and inhibits glycolysis by detaching hexokinase 2 from mitochondria in A549 cells

In this paper, we investigated the anticancer effect and the mechanism of our newly synthesized bibenzyl 8Ae against human lung cancer A549 cells. Compound 8Ae could induce apoptosis by inhibiting the glycolysis in A549 cells. Hexokinase 2 (HK2), the first key enzyme in glycolysis process, was significantly down-regulated by 8Ae. Besides, compound 8Ae induced HK2 dissociated from mitochondria to cytosol, which could be induced by inhibiting the phosphorylation of Akt. In addition, 8Ae could induce mitochondrial-mediated apoptosis, and mitochondrial membrane potential (MMP) was decreased. After 8Ae treatment, the Bax/Bcl-2 ratio was increased and cytochrome c (Cyt c) was release from mitochondria to cytosol. Molecular docking indicated that 8Ae have an interaction with HK2 by extending into acitve pockets of the protein to form stable hydrogen bonds. Additionally, 8Ae had significantly improved pharmacokinetic properties through the prediction, comparison, and analysis of the ADMET properties of 8Ae and moscatilin (MST). Taken together, 8Ae might inhibit glycolysis by stimulating the shedding of HK2 from mitochondria and promoting mitochondria-regulated apoptosis to inhibit the proliferation of A549 cells. This article provides a research basis for bibenzyl compounds as new small molecule drugs for lung cancer.

Molecular insights and inhibitory dynamics of flavonoids in targeting Pim-1 kinase for cancer therapy.

Pim-1 kinase, a serine/threonine kinase, is often overexpressed in various cancers, contributing to disease progression and poor prognosis. In this study, we explored the potential of flavonoids as inhibitors of Pim-1 kinase using a combination of molecular docking and steered molecular dynamics (SMD) simulations. Our docking studies revealed two main binding orientations for the flavonoid molecules. The SMD simulations showed that the binding mode with higher pulling forces was linked to stronger inhibitory activity, with a strong positive correlation (R 2 ≈ 0.92) between pulling forces and IC50 values. Quercetin stood out as the most potent inhibitor, showing a pulling force of about 820pN and an IC_(5) 0 of less than 6µM. Further dynamic simulations indicated that quercetin's hydroxyl groups at the C3, C-5 and C-7 positions formed stable hydrogen bonds with key residues GLU-121, Leu-44 and Val-126, respectively enhancing its binding stability and effectiveness. Our results emphasized the critical role of the hydroxyl group at the C-3 position, which plays a pivotal function in effectively anchoring these molecules in the active site of Pim-1 kinase. Principal component analysis (PCA) of Pim-1 kinase's conformational changes revealed that potent inhibitors like quercetin, galangin, and kaempferol significantly restricted the enzyme's flexibility, suggesting potential inhibitory effect. These findings provide insights into the structural interactions between flavonoids and Pim-1 kinase, offering a foundation for future experimental investigations. However, further studies, including in vitro and in vivo validation, are necessary to assess the pharmacological relevance and specificity of flavonoids in cancer therapy.

Overcoming methicillin resistance by methicillin-resistant Staphylococcus aureus: Computational evaluation of napthyridine and oxadiazoles compounds for potential dual inhibition of PBP-2a and FemA proteins

Abstract The treatment of the various infections caused by Staphylococcus aureus has become challenging due to the evolving resistance against current therapeutics. In this study, the potentials of napthyridine and oxadiazole derivatives to serve as dual inhibitors of penicillin-binding protein 2a (PBP-2a) and FemA protein, which are crucial to resistance to methicillin-based drugs by S. aureus, were evaluated using molecular modeling techniques. Seventy-two compounds were subjected to molecular docking against the proteins, and the hit compounds were subjected to drug-likeness evaluation and in silico pharmacokinetics prediction. The compounds with good safety profiles were subjected to a 250-ns molecular dynamics (MD) simulation and other relevant analyses based on the MD trajectories. Five hit compounds were selected based on their high affinity for the targets as evidenced by their docking scores ranging from −8.6 to −10.1 kcal/mol for PBP-2a and −9.6 to −9.9 kcal/mol for FemA. These compounds also passed Lipinski’s rule of five evaluation with no violation and possessed high human intestinal absorption potential, showcasing their potential as orally administered therapeutic agents. However, three of the compounds were potential mutagens. MD simulation revealed that the final two compounds maintained stable interactions with the target proteins over 250 ns, with minimal deviations and fluctuations. Hydrogen bond stability and energy decomposition analysis further confirmed the strong binding affinity of the hit compounds compared to the control drug, methicillin. Conclusively, the compounds with the CID “135964525” and “44130718” are worthy of further experimental validation in the development of potential inhibitors of PBP-2a and FemA.

Bioinformatics analysis of the antigenic epitopes of L7/L12 protein in the B- and T-cells active against Brucella melitensis.

The objective is to analyse the physicochemical properties, spatial structure and protein-protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine (MEV). The National Center for Biotechnology Information (NCBI) database was searched for the amino acid sequences of L7/L12 from Brucella melitensis. In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties: NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyse the PPIs; and the IEDB, ABCpred, SVMTrip and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 was docked to Toll-like receptor 4 (TLR4), B-cell receptor (BCR), Major histocompatibility complex I-T cell receptor (MHC I-TCR) and MHC II-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 6 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16 %, β-turns for 2.42 %, extended strands for 8.87 % and irregular coils for 18.55 % of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cells, two cytotoxic T lymphocytes and three helper T lymphocyte epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC I-TCR and MHC II-TCR complexes and forms stable hydrogen bonds, respectively. L7/L12, which governs the translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing MEVs.

Virtual Screening of Flavonoids against Plasmodium vivax Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation.

Plasmodium vivax (P. vivax) is one of the highly prevalent human malaria parasites. Due to the presence of extravascular reservoirs, P. vivax is extremely challenging to manage and eradicate. Traditionally, flavonoids have been widely used to combat various diseases. Recently, biflavonoids were discovered to be effective against Plasmodium falciparum. In this study, in silico approaches were utilized to inhibit Duffy binding protein (DBP), responsible for Plasmodium invasion into red blood cells (RBC). The interaction of flavonoid molecules with the Duffy antigen receptor for chemokines (DARC) binding site of DBP was investigated using a molecular docking approach. Furthermore, molecular dynamic simulation studies were carried out to study the stability of top-docked complexes. The results showed the effectiveness of flavonoids, such as daidzein, genistein, kaempferol, and quercetin, in the DBP binding site. These flavonoids were found to bind in the active region of DBP. Furthermore, the stability of these four ligands was maintained throughout the 50 ns simulation, maintaining stable hydrogen bond formation with the active site residues of DBP. The present study suggests that flavonoids might be good candidates and novel agents against DBP-mediated RBC invasion of P. vivax and can be further analyzed in in vitro studies.

Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations.

c-Src is involved in multiple signaling pathways and serves as a critical target in various cancers. Growing evidence suggests that prolonging a drug's residence time (RT) can enhance its efficacy and selectivity. Thus, the development of c-Src antagonists with longer residence time could potentially improve therapeutic outcomes. In this study, we employed molecular dynamics simulations to explore the binding modes and dissociation processes of c-Src with antagonists characterized by either long or short RTs. Our results reveal that the long RT compound DAS-DFGO-I (DFGO) occupies an allosteric site, forming hydrogen bonds with residues E310 and D404 and engaging in hydrophobic interactions with residues such as L322 and V377. These interactions significantly contribute to the long RT of DFGO. However, the hydrogen bonds between the amide group of DFGO and residues E310 and D404 are unstable. Substituting the amide group with a sulfonamide yielded a new compound, DFOGS, which exhibited more stable hydrogen bonds with E310 and D404, thereby increasing its binding stability with c-Src. These results provide theoretical guidance for the rational design of long residence time c-Src inhibitors to improve selectivity and efficacy.