CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

Fine-tuning property domain weighting factors and the objective function in force-field parameter optimization

Force field (FF) based molecular modeling is an often used method to investigate and study structural and dynamic properties of (bio-)chemical substances and systems. When such a system is modeled or refined, the force-field parameters need to be adjusted. This force-field parameter optimization can be a tedious task and is always a trade-off in terms of errors regarding the targeted properties. To better control the balance of various properties' errors, in this study we introduce weighting factors for the optimization objectives. Different weighting strategies are compared to fine-tune the balance between bulk-phase density and relative conformational energies (RCE), using n-octane as a representative system. Additionally, a non-linear projection of the individual property-specific parts of the optimized loss function is deployed to further improve the balance between them. The results show that the combined error for the reproduction of the properties targeted in this optimization is reduced. Furthermore, the transferability of the force field parameters (FFParams) to chemically similar systems is increased. One interesting outcome is a large variety in the resulting optimized FFParams and corresponding errors, suggesting that the optimization landscape is multi-modal and very dependent on the weighting factor setup. We conclude that adjusting the weighting factors can be a very important feature to lower the overall error in the FF optimization procedure, giving researchers the possibility to fine-tune their FFs.

Decoding virulence and resistance in Klebsiella pneumoniae: Pharmacological insights, immunological dynamics, and in silico therapeutic strategies

Klebsiella pneumoniae (K. pneumoniae) has become a serious global health concern due to its rising virulence and antibiotic resistance. As one of the leading members of ESKAPE pathogens, it plays a major role in a wide range of infections that cause pneumonia, urinary tract infections, and bacteremia, especially in immunocompromised and hospitalized patients. The recent increase in multidrug-resistant (MDR) and hypervirulent (hvKP) strains due to the production of extended-spectrum beta-lactamases (ESBLs) and carbapenemases, has greatly limited therapeutic options that highlights the need for novel approaches to combat the pathogen. This review outlines the virulence mechanisms, profiles of antibiotic resistance, and immune evasion strategies in K. pneumoniae. Also, it points out the role of capsular polysaccharides, lipopolysaccharides, and fimbriae in host colonization and immune evasion. Additionally, the review discusses the emerging therapeutic strategies of vaccine development, computational drug discovery, and the use of artificial intelligence (AI). The progress achieved in reverse vaccinology and structural biology enables the identification of new drug and vaccine targets, whereas AI and machine learning (ML) stand out as powerful candidates for high-throughput screening and drug design. However, challenges with antigenic variability, safety, and the need to collaborate globally still exist. This review focuses on the need for interdisciplinary approaches involving molecular biology and immunology with computational sciences to address K. pneumoniae infections and provide appropriate therapies in the era of antibiotic resistance.

Particulate methane monooxygenase and cytochrome P450-induced reactive oxygen species facilitate 17β-estradiol biodegradation in a methane-fed biofilm

Methane-fed biosystems have shown great potential for degrading various organic micropollutants, yet underlying molecular degradation mechanisms remain largely unexplored. In this study, we uncover the critical role of biogenic reactive oxygen species (ROS) in driving the degradation of 17β-estradiol (E2) within a methane-fed biofilm reactor. Metagenomic analyses confirm that aerobic methanotrophs, specifically Methylococcus and Methylomonas, are responsible for the efficient degradation of E2, achieving a degradation rate of 367.7 ± 8.3 μg/L/d. ROS scavenging in conjunction with enzyme inhibition experiments indicate that particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) could generate hydroxyl radicals (•OH), which are the primary ROS involved in E2 degradation. Molecular dynamics simulations suggest that E2 can enter the active catalytic site of pMMO through electrostatic attraction. Four amino acid residues are found to form stable hydrogen bonds with E2, with a high binding free energy, indicating a high affinity for the substrate. Additionally, density functional theory calculations combined with transformation product analysis reveal that •OH targets carbon atoms on the benzene ring and the hydroxyl group attaches to the cyclopentane ring, primarily through hydrogen abstraction and hydroxylation reactions. This work provides critical insights into the mechanisms of E2 biodegradation in methane-fed systems and highlights the potential for optimizing microbial pathways to enhance the degradation of organic micropollutants from contaminated water.

Interaction, inhibition and disruption of lysozyme fibrillar aggregates by the plant alkaloid berberine

This study investigated the interaction and impact of berberine, a pharmacologically important natural alkaloid, on lysozyme amyloidosis with the aim to develop effective anti-amyloidogenic agents. Interaction between berberine and lysozyme was analyzed using both theoretical and experimental tools to unleash its anti-amyloidogenic potency. The intrinsic fluorescence of lysozyme was quenched by berberine through static mechanism, indicating the presence of single binding site predominantly involving TRP residues. Complexation with berberine caused microenvironmental and conformational changes in lysozyme as shown by synchronous and 3D fluorescence spectroscopic analysis. Molecular docking and dynamic simulation study revealed the probable binding site and pharmacokinetics involved in lysozyme-berberine complexation. Berberine significantly inhibited lysozyme fibrillation which was confirmed by Thioflavin T, Congo red, Nile red and ANS assays. FTIR and circular dichroism studies revealed that berberine reduced β-sheet content of lysozyme fibrillar samples, indicating inhibition of fibril formation. Additionally, berberine can degrade pathogenic mature fibril as well. Amyloid inhibition and defibrillation was visualised by atomic force microscopy.

Molecular interactions of surfactants with other chemicals in chemical flooding processes: A comprehensive review on molecular dynamics simulation studies

Due to the growing demand for fossil fuels and the transition of many oil fields into a high water-cut stage, enhanced oil recovery (EOR) techniques have become more prevalent to meet this rising demand. Among these techniques, chemical flooding stands out as an effective method, supported by numerous experimental and simulation studies. However, the complexity of a chemical slug composition under harsh reservoir conditions makes the physicochemical phenomena involved in a chemical flooding process highly intricate. To comprehensively understand the microscopic mechanisms governing the phase behavior of complex fluid systems underground, molecular dynamics (MD) simulations have been increasingly employed in recent years to investigate the molecular interactions between various chemicals involved in chemical flooding processes. In this work, we have comprehensively reviewed the recent MD studies focusing on the molecular interactions between surfactants and other chemicals in the chemical flooding processes. Based on the molecular interactions within different chemicals, various nanoscale mechanisms have been proposed to shed light on the physicochemical flow in porous media. Additionally, the MD techniques used in these studies have been summarized, and challenges in the application of MD simulations in the field of chemical flooding have been identified for improving the quality of future MD studies.

Targeting the host protein G3BP1 for the discovery of novel antiviral inhibitors against Chikungunya virus

The molecular interactions between Chikungunya virus (CHIKV) non-structural protein 3 (nsP3) and the host GTPase Activating SH3 Domain Binding Protein 1 (G3BP1) are critical for CHIKV replication. The C-terminus hypervariable domain (HVD) of nsP3 protein binds to the nuclear transport factor 2 (NTF2)-like domain of G3BP1 through two tandem FGDF motifs, aiding in the disruption of stress granule (SG) formation. Given G3BP1's role in the antiviral response, it presents an attractive target for antiviral drug development. In this study, seven potential small molecules targeting the FGDF motif binding pocket of G3BP1 were identified using a structure-based virtual screening approach. The binding modes of these molecules were further investigated through molecular docking and simulations. Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) experiments confirmed their binding to purified G3BP1 with micromolar (μM) affinity. The antiviral efficacy of these molecules was assessed using in vitro cell culture-based assays, revealing that L-7, WIN, SB2, NAL, DHD, GSK, and FLU effectively inhibited CHIKV replication with EC50 values of 1.99, 0.40, 5.38, 1.52, 7.39, 3.66, and 0.61 μM, respectively. Additionally, CHIKV-infected cells treated with these compounds exhibited fewer virus-induced SGs compared to untreated controls without affecting SG formation under oxidative stress conditions. These findings indicate that identified inhibitors successfully block G3BP1-nsP3 interactions and suppress CHIKV replication. This is one of the first reports of small antiviral molecules targeting G3BP1, a host protein essential for stress granule formation in the antiviral cellular response and CHIKV replication.

Molecular dynamics study of monomeric chorismate mutase shows large reduction in conformational diversity of loops upon binding of the transition state analog

In this in silico study, we investigated the structure and dynamics of the molten globule enzyme, monomeric chorismate mutase, which catalyzes the conversion of chorismate to prephenate despite its molten globule state. The primary aim was to understand how the enzyme stabilizes the transition state of the reaction while maintaining its molten globule characteristics. Using the transition state analog (TSA) from the NMR structure (PDB code 2GTV), molecular dynamics simulations revealed multiple hydrogen bonds between three of the enzyme's helices and the TSA. Specific residues that formed stable hydrogen bonds with the TSA were identified as potential mutation targets. Furthermore, the binding of the TSA significantly reduced the entropy of the enzyme and led to the rigidification of the backbone dihedrals across all helices. The flexibility of the loop connecting helices 1 and 2, was also analyzed, showing reduced conformational diversity upon TSA binding. Structural differences between the apo and TSA-bound forms were noted, with helices 3 and 4 exhibiting altered helicity, including a kink in helix 3 and unravelling in helix 4. Despite its molten globule nature, monomeric chorismate mutase can stabilize the TSA through hydrogen bonds involving charged residues, which are essential for maintaining the helix bundle structure. This study highlights the importance of local structural dynamics and entropy changes in enzyme catalysis, offering insights into how molten globule states can support efficient enzymatic activity.

Comprehensive analysis of Syzygium cumini L. pomace extract as an α-amylase inhibitor: In vitro inhibition, kinetics, and computational studies

Type 2 diabetes mellitus (T2DM) is a widespread metabolic disorder characterized by impaired regulation of blood glucose levels. Jamun (Syzygium cumini L.) fruits and seeds have been traditionally used in Ayurveda to manage diabetes. While fruit and seed extracts have been extensively studied for their anti-α-amylase properties, pomace, a byproduct of juice extraction, remains under explored. This study investigated the α-amylase inhibitory potential of jamun pomace (JP) extract by using in vitro and in silico methods. Enzyme inhibition assays revealed an half-maximal inhibitory concentration (IC₅₀) value of 85.68 ± 5.22 μg/mL for the JP extract, comparable to acarbose (64.28 ± 7.15 μg/mL). The extract exhibited mixed-mode inhibition, whereas acarbose showed competitive mode inhibition. At 10 μg/mL, the Vmax of JP extract was half that of acarbose, demonstrating significant inhibition. GC-MS analysis identified 11 volatile compounds (R1-R11) in the JP extract. Density Functional Theory (DFT) and ADMET analyses confirmed the chemical reactivity of the volatiles, drug-like properties, and low toxicity. Molecular docking revealed a high binding score for R11 (-8.0 kcal/mol), similar to acarbose (-8.2 kcal/mol). Molecular dynamics simulations further demonstrated the stability of α-amylase complexes with R11, R3, and R8, with R11 showing the lowest binding energy (-28.75 ± 6.25 kcal/mol). These findings suggest that R11 and JP extracts hold promise as anti-diabetic agents. Utilizing JP extract as a nutraceutical offers the dual benefit of diabetes management and sustainable waste valorization in jamun juice production.

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.

Inhibition of FLT3-induced signalling in refractory acute myeloid leukaemia

Mutations in FLT3 make this receptor tyrosine kinase overactive. Such mutations found in ∼30 % of the patients who suffer from acute myeloid leukaemia (AML). FLT3 mediates signalling networks that lead to cell proliferation and survival. FLT3 inhibitors are used to treat AML but patients who are treated with them typically become resistant. Such resistance often emerges through secondary mutations which either restore the activity of FLT3 in the presence of drugs or activate a key player in a signalling network such as NRAS. We had developed AML-specific cell lines resistant to two advanced FLT3 inhibitors: gilteritinib and FF-10101. Resistance in these cell lines proceeds though different mechanisms. In this study, we followed on the efficacy of five FLT3 inhibitors (gilteritinib, FF-10101 and three promising inhibitors that are being developed), two pan-PI3K inhibitors (one of which also inhibits mTOR) and two c-KIT inhibitors in order to examine the significance of different signalling cascades in FLT3+-AML. In addition, we used molecular modelling and quantum chemistry calculations to explain why specific FLT3 mutations affect some inhibitors more than others. Two novel FLT3 inhibitors were found to be only weakly affected by resistance mutations against gilteritinib and FF-10101. The efficacy of most FLT3 inhibitors was only weakly (or not at all) affected by the NRAS/G12C activating mutation. Finally, no non-FLT3 inhibitor has shown sufficient efficacy in the cells, suggesting the central role of FLT3 in FLT3-mutated AML.

Quantifying Cooperativity through Binding Free Energies in Molecular Glue Degraders

Molecular glues represent a novel therapeutic modality facilitating the stabilization of protein-protein interactions (PPIs), thus enabling the targeting of previously "undruggable" proteins. We develop a computational procedure to screen for molecular glues using a pathway-independent free energy calculation method for accurately assessing the cooperativity. We employ a combined ligand and protein free energy perturbation (FEP) method to calculate the cooperative effect of a ligand for ternary binding. We study the cooperative binding mechanisms of molecular glue degraders, specifically cereblon (CRBN) modulators targeting Ikaros family zinc finger 2 (IKZF2), a transcription factor implicated in cancer immunotherapy. We present a comprehensive computational protocol for screening large molecular libraries to identify potent molecular glues. By leveraging cooperative binding principles in ternary complex formation, our approach effectively predicts ligand-induced PPIs and their degradation potential. Benchmarking against experimental data for CRBN-Ikaros complexes, our protocol demonstrates high accuracy in identifying superior molecular glues, highlighting L4 and L5 as top performers. Furthermore, our high-throughput screening identified novel candidates from extensive chemical libraries, validated through advanced FEP+ simulations. This study not only underscores the transformative potential of molecular glues in targeted protein degradation but also sets the stage for their broader application across diverse protein targets, paving the way for innovative therapeutic strategies in drug discovery.

The interactions of Pu22 G-quadruplex, derived from c-MYC promoter sequence, with antitumor acridine derivatives-An NMR/MD combined study

Unsymmetrical bisacridines (UAs) represent a novel class of anticancer agents that exhibit significant antitumor activity against a wide range of cancer cell lines and solid tumors in vivo. UAs consist of two different acridine-based ring systems, which are connected by an aminoalkyl linker. Recent studies have demonstrated that UAs can suppress the c-MYC protooncogene, which is overexpressed in many tumor types. As a proposed molecular basis for this activity, UAs have been suggested to stabilize the G-quadruplex structure formed within the promoter region of c-MYC. In this study, we performed spectroscopic and computational analyses to investigate the stereochemistry of the c-MYC NHE III1 representative G-quadruplex, codenamed Pu22, in complex with two promising bisacridines, C-2045 and C-2053, as well as their monomeric counterparts, C-1311 and C-1748. C-1311 formed a well-defined 1:2 mol/mol DNA:ligand non-covalent adduct, whose solution structure was determined via 2D NMR. In contrast, C-1748 displayed weak and nonspecific interactions with the Pu22 G-quadruplex. Finally, the Pu22:UA complexes were examined using a combination of NMR and molecular modeling approaches, including umbrella sampling simulations. These results provide insights into the interaction mechanisms of UAs with G-quadruplex structures and highlight their potential as therapeutic agents targeting c-MYC.

A designer minimalistic model parallels the phase-separation-mediated assembly and biophysical cues of extracellular matrix

The propensity for controlled liquid-liquid phase separation and subsequent directed phase transition are crucial for the coacervation-mediated assembly of extracellular matrix (ECM). This spatiotemporally controlled ECM assembly can be used to develop coacervate-based polymer assembly strategies to generate biomimetic materials that can emulate the complex structures and biophysical cues of the ECM. Inspired by the tropoelastin structure, here we develop a designer minimalistic model consisting of alternating hydrophobic moieties and covalent crosslinking domains. By increasing the valence and enhancing the interaction strength of the hydrophobic moieties, we can control the degree of the assembly to enhance the propensity for phase separation and thus emulate the extracellular coacervation process of tropoelastin, including droplet formation, coalescence and maturation. The subsequent covalent-bonding-triggered coacervate-hydrogel transition with enhanced assembly order stabilizes the phase-separated structure in the form of a heterogeneous hydrogel, thereby mimicking covalent crosslinking-derived elastin fibrillation. Furthermore, the heterogeneous hydrogel network establishes a biomimetic matrix that can effectively promote the mechanosensing of adherent stem cells.

Exploring the Effect of Hydrocarbon Cross-Linkers on the Structure and Binding of Stapled p53 Peptides

Short-length peptides are used as therapeutics due to their high target specificity and low toxicity; for example, peptides are designed for targeting the interaction between oncogenic protein p53 and E3 ubiquitin ligase MDM2. These peptide therapeutics form a class of successful inhibitors. To design such peptide-based inhibitors, stapling is one of the methods in which amino acid side chains are stitched together to get conformationally rigid peptides, ensuring effective binding to their partners. In the current work, we use computer simulations to investigate p53 peptides stapled with hydrocarbon chains of different lengths and positions of attachment to the peptide. We subsequently analyze their binding efficiency with MDM2. The introduction of stapling agents restricts the conformational dynamics of peptides, resulting in higher persistence of helicity. The efficiency of the stapling agents has also been verified imposing these stapled peptides to adverse conditions viz. thermal and chemical denaturation. In addition, the conformational exploration of peptides has been investigated using temperature replica exchange molecular dynamics (T-REMD) simulations. From both the unbiased and T-REMD simulations, p53 with a long hydrocarbon cross-linker shows a more conformationally rigid structure having high helicity compared to other stapled peptides. The rigidity gained due to cross-linking reduces the entropy of the peptide in the free state and thereby facilitates the complexation process. From the binding studies, we have shown that the peptide having multiple short staples has a larger enthalpy change during binding, resulting from its orientation and interactions with residues in the binding interface. On the other hand, a peptide with a single long stapling agent shows less entropic penalty than other systems. Our study suggests a plausible rationale for the relation between the length and the position of attachment of cross-linkers to peptides and their binding affinity for target partners.

Unraveling the Molecular Architecture of Mosquito D1-Like Dopamine Receptors: Insights Into Ligand Binding and Structural Dynamics for Insecticide Development

Vector-borne diseases pose a severe threat to human life, contributing significantly to global mortality. Understanding the structure-function relationship of the vector proteins is pivotal for effective insecticide development due to their involvement in drug resistance and disease transmission. This study reports the structural and dynamic features of D1-like dopamine receptors (DARs) in disease-causing mosquito species, such as Aedes aegypti , Culex quinquefasciatus , Anopheles gambiae , and Anopheles stephensi. Through molecular modeling and simulations, we describe the common structural fold of mosquito DARs within the G-protein-coupled receptor family, highlighting the importance of an orthosteric and enlarged binding pocket. The orthosteric binding pocket, resembling a cage-like structure, is situated ~15 Å deep within the protein, with two serine residues forming the roof and an aspartate residue, along with two conserved water molecules (W1 and W2), forming the floor. The side walls are composed of two phenylalanine residues on one side and a valine residue on the other. The antagonist binding site, an enlarged binding pocket (EBP) near the entrance cavity, can accommodate ligands of varying sizes. The binding energy of dopamine is observed to be ~2-3 kcal/mol higher than that of the antagonist molecules amitriptyline, asenapine, and flupenthixol in mosquito DARs. These antagonist molecules bind to EBP, which obstructs dopamine movement toward the active site, thereby inhibiting signal transduction. Our findings elucidate the molecular architecture of the binding pockets and the versatility of DARs in accommodating diverse ligands, providing a foundational framework for future drug and insecticide development.

Chemically induced partial unfolding of the multifunctional apurinic/apyrimidinic endonuclease 1

Apurinic/apyrimidinic endonuclease I (APE1) acts as both an endonuclease and a redox factor to ensure cell survival. The two activities require different conformations of APE1. As an endonuclease, APE1 is fully folded. As a redox factor, APE1 must be partially unfolded to expose the buried residue Cys65, which reduces transcription factors including AP-1, NF-κB, and HIF-1α and thereby enables them to bind DNA. To determine a molecular basis for partial unfolding associated with APE1's redox activity, we characterized specific interactions of a known redox inhibitor APX3330 with APE1 through waterLOGSY and 1H-15N HSQC NMR approaches using ethanol and acetonitrile as co-solvents. We find that APX3330 binds to the endonuclease active site in both co-solvents and to a distant small pocket in acetonitrile. Prolonged exposure of APE1 with APX3330 in acetonitrile resulted in a time-dependent loss of 1H-15N HSQC chemical shifts (~35%), consistent with partial unfolding. Regions that are partially unfolded include adjacent N- and C-terminal beta strands within one of the two sheets comprising the core, which converge within the small binding pocket defined by the CSPs. Removal of APX3330 via dialysis resulted in a slow reappearance of the 1H-15N HSQC chemical shifts suggesting that the effect of APX3330 is reversible. APX3330 significantly decreases the melting temperature of APE1 but has no effect on endonuclease activity using a standard assay in either co-solvent. Our results provide insights on reversible partial unfolding of APE1 relevant for its redox function as well as the mechanism of redox inhibition by APX3330.

Identifying and quantifying membrane interactions of the protein human cis-prenyltransferase

Prenyl chains come in multiple sizes, fulfilling unique and essential functions across all domains of life. Prenyl chains are synthesized by prenyltransferase proteins. Despite their structural similarity, prenyltransferases exhibit substantial functional diversity to create lipophilic products of varying lengths. Human cis-prenyltransferase (h-cisPT) is a tetrameric enzyme responsible for the synthesis of long prenyl chains, consisting of 20-prenyl-unit products that are essential to specific posttranslational modifications such as N-glycosylation upon downstream processing. These long products are hypothesized to transfer from h-cisPT to the ER membrane, but the mechanism of this transfer is not known. We use molecular dynamics simulations to identify a consistent membrane binding pose for h-cisPT. By quantifying protein-membrane contacts, we identify the aromatic amino acid residues in the conserved catalytic domain as critical to membrane binding. Determining relative protein-membrane binding free energies through free energy perturbation highlights the importance of these residues for membrane association, as mutations lower membrane affinity by as much as 27 kcal/mol. These results are validated using FRET to demonstrate decreased catalytic activity and membrane binding in response to mutation. Together, our results suggest a possible mechanism for prenyl substrate transfer, where key aromatic residues facilitate h-cisPT binding to the ER membrane in an orientation that holds the substrate-containing active site near the membrane surface. Molecular dynamics simulations of the mutant exhibiting lower FRET show greater orientational variability relative to wild type. This evidence for a specific orientation of h-cisPT provides a structural basis for isoprenoid association to the membrane during synthesis and prior to its release.

Repurposing dual-C-prenylated flavonoids as potent allosteric inhibitors of PTP1B: Integrated phytochemical, enzymological, and in silico evidence

Protein-tyrosine phosphatase 1B (PTP1B) is a master negative regulator of insulin and leptin signaling, yet clinically useful inhibitors remain elusive. Guided by a repurposing strategy, we investigated Tephrosia villosa as a natural source of PTP1B modulators. Chromatographic fractionation of the aerial parts afforded nine flavonoids and related phenolics, whose structures were elucidated by spectroscopic tools. Enzymatic screening revealed that the diprenylated isoflavonoids 6,8-diprenylgenistein and 6,8-diprenylnaringenin inhibit recombinant PTP1B with sub-micromolar potency (IC₅₀ ≈ 1 μM) and non-competitive kinetics, outperforming the reference inhibitor ursolic acid six-fold. Molecular docking and 200 ns molecular dynamics simulations located both ligands in the hydrophobic α3/α7 allosteric pocket, where dual C-prenyl chains engage an aromatic clamp formed by Phe196 and Phe280; MM/PBSA binding energies (≈ -30 kcal mol-1) and a single deep free-energy basin corroborate tight, entropy-driven binding that locks the WPD loop open. Free energy landscape analysis funnels these trajectories into a single deep basin, confirming that ligand binding rigidifies the WPD-loop in an open, catalytically inactive conformation. ADMET predictions show high oral absorption, no Lipinski violations and minimal cardiotoxic or hepatotoxic risk, positioning 6,8-diprenylgenistein as a promising lead scaffold. This integrated phytochemical, biochemical and computational study uncovers T. villosa as a rich source of allosteric PTP1B inhibitors and highlights diprenylated flavonoids as tractable starting points for antidiabetic and anti-obesity drug development.

The odorant (R)-(-)-carvone promotes glucose-stimulated insulin secretion via the olfactory receptor Olfr1259 in pancreatic β-TC6 cells

Olfactory receptors (ORs) make up the largest subfamily of G protein-coupled receptors that are expressed in olfactory sensory neurons in the nasal cavity and recognize an enormous number of odorants from the external environment. These receptors, however, have also been found in many other tissues including pancreas, liver, and adipose tissue, in which they seem to play important but different roles. Yet, the exact functions of ORs in these extra-nasal tissues are not well understood. Here, we report that (R)-(-)-carvone and a few other odorants were able to evoke calcium responses in mouse pancreatic β-TC6 cells. Furthermore, (R)-(-)-carvone potentiated cytoplasmic cAMP accumulation and glucose-stimulated insulin secretion (GSIS). More importantly, GPCR signaling pathway components adenylyl cyclase, phospholipase C, and inositol triphosphate receptor were involved in (R)-(-)-carvone-induced signal transduction. By reanalyzing the available β-TC6 cells' RNAseq dataset, we identified several candidate ORs for (R)-(-)-carvone. Further analyses with molecular docking and molecular dynamics simulations indicated that (R)-(-)-carvone bound to the odorant-binding pocket of the olfactory receptor Olfr1259 while knockdown of Olfr1259 expression in β-TC6 cells with siRNA significantly reduced the stimulatory effects of (R)-(-)-carvone on cytoplasmic Ca2+ and cAMP levels, and insulin secretion. Together, these results indicated that Olfr1259 is the receptor for (R)-(-)-carvone in β-TC6 cells. Therefore, our study highlighted the important roles of (R)-(-)-carvone and its receptor Olfr1259 in initiating calcium signaling, inducing intracellular cAMP accumulation, and enhancing GSIS in pancreatic β cells, demonstrating that Olfr1259 may be a new therapeutic target for regulating glucose metabolism and for treating diabetes.

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.

Exploration of the potential therapeutic effects and targets of Coriandrum sativum on non-erosive esophagitis based on bioinformatics and molecular dynamics simulation

Gastroesophageal reflux disease (GERD) is one of the most frequently diagnosed gastrointestinal disorders, adversely affecting quality of life. Coriandrum sativum has been shown to effectively promote gastrointestinal motility, alleviate gastric discomfort, and positively impact esophageal health, but its mechanism of action remains unclear. This study utilized the TCMSP database to retrieve the components of coriander and the GEO database to identify NERD-related genes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning were employed to identify candidate genes, followed by Protein-Protein Interaction (PPI) network analysis and external dataset validation to identify key candidate genes. These genes were further validated through Gene Set Enrichment Analysis (GSEA) and subcellular localization. Finally, molecular docking and molecular dynamics (MD) simulations identified Ammidin, campest-5-en-3beta-ol, Isofucosterol and beta-sitosterol as the key components in Coriandrum sativum for improving NERD. Future research should prioritize experimental validation of these compounds and further investigate potential resistance mechanisms to enhance their therapeutic efficacy and practical applications.

Quantifying the Cooperativity of Backbone Hydrogen Bonding

The hydrogen bonds (H-bonds) between backbone amide and carbonyl groups are fundamental to the stability, structure, and dynamics of proteins. A key feature of such hydrogen bonding interactions is that multiple H-bonds can enhance each other when aligned, as such in theα $$ \alpha $$ -helix orβ $$ \beta $$ -sheet secondary structures. To better understand this cooperative effect, we propose a new physical quantity to evaluate the cooperativity of intermolecular interactions. Using H-bond aligned N-methylacetamide molecules as the model system, we assess the cooperativity of protein backbone hydrogen bonds using quantum chemistry (QM) calculations at the MP2/aug-cc-pVTZ level, revealing cooperative energies ranging from 2 to 4.3 kcal/mol. A set of protein force fields was benchmarked against QM results. While the additive force field failed to reproduce cooperativity, polarizable force fields, including the Drude and AMOEBA protein force fields, have been found to reproduce the trend of QM results, albeit with smaller magnitude. This work demonstrates the theoretical utility of the proposed formula for quantifying cooperativity and its relevance in force field parameterization. Incorporating cooperative energy into polarizable models presents a pathway to achieving more accurate simulations of biomolecular systems.

Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans

Non-covalent interactions (NCI) dominate the properties of condensed phase systems. Towards a detailed understanding of NCI, quantum mechanical (QM) methods allow for accurate estimates of interaction energies and geometries, allowing for the contributions of different types of NCI to condensed phase properties to be understood. In addition, such information can be used for the optimization of empirical force fields, including the specific contribution of electrostatic versus van der Waals interactions. However, to date, the relative orientation of monomers defining molecular interactions of dimers is often based on full geometry optimizations of all degrees of freedom or extracted from known experimental structures of biological molecules. In such cases, the spatial relationship of the monomers often leads to multiple atoms in each monomer making significant contributions to the interactions occurring in the dimer, confounding understanding of the contributions of specific atoms or functional groups. To overcome this, a workflow is presented that allows for systematic control of the interaction orientation between monomers to be performed through the use of molecular interaction rules (MIR) in an extendable tool that can be applied to a broad range of chemical space. Using the "MIR workflow" allows a user to perform automation of the determination of well-defined monomer interaction orientations in dimers using Z-matrices, allowing for potential energy scans (PES) to be performed on combinatorial pairs of the monomers. In addition, compiled monomer and dimer geometries and PES data are stored in an extendable database. Illustration of the utility of the workflow is performed based on a collection of 89 monomers encompassing a variety of functional group classes from which 10,616 interaction dimers can be automatically generated. PES between all dimers were calculated at the QM HF/6-31G*, MP2/6-31G*, and ωb97x-d3/6-31G* model chemistries. In addition, analysis of the benzene dimer in three interaction orientations, a hydrogen bond interaction between azetidinone and N-methylacetamide, and the interaction of pyridine with acetone in the Burgi-Dunitz orientation are presented including results with the aug-cc-pVDZ basis set. Results show the impact of different QM model chemistries on minimum interaction energies and distances over a large ensemble of intermolecular interactions with emphasis on the contributions of dispersion.

Advanced modeling of salt-inducible kinase (SIK) inhibitors incorporating protein flexibility through molecular dynamics and cross-docking

Salt-inducible kinases (SIK1, SIK2, and SIK3) regulate metabolism and immune responses, making them promising targets for inflammatory and autoimmune diseases. Understanding inhibitor selectivity among isoforms is crucial for therapeutic development. In this study, 44 compounds were investigated as SIK inhibitors using molecular modeling. A flexible treatment of the kinases via molecular dynamics (MD) simulations captured binding site conformational changes, followed by molecular docking to generate protein kinase (PK)-ligand complex models. Ligand orientations were validated against crystallographic data using LigRMSD and interaction fingerprints (IFPs). A genetic algorithm was applied to select conformations that maximize correlation between docking energies and biological activities, yielding R² values of 0.821, 0.646, and 0.620 for SIK1, SIK2, and SIK3, respectively. Our results highlight the importance of protein flexibility in achieving accurate correlations between docking energies and experimental pIC50 values, enhancing inhibitor selectivity predictions.

Quantum Coulombic Interactions Mediate Free Radical Control in Radical SAM Viperin/RSAD2

There are thousands of radical S-adenosylmethionine (rSAM) enzymes capable of catalyzing over 80 distinct reactions, yet their use in biotechnological applications is limited, primarily due to a lack of understanding of how these enzymes control highly reactive radical intermediates. Here, we show that little-known quantum Coulombic interactions are, in part, responsible for free radical control in rSAM enzyme Viperin/RSAD2, one of the few radical SAM enzymes expressed in humans. Using molecular dynamics and high-level extensive multistate broken-symmetry quantum mechanical/molecular mechanics calculations (QM/MM), we elucidated both the mechanism and radical control in catalysis, identifying a key step characterized by the formation of an unusual metastable deprotonated ribose radical intermediate. This intermediate is thermodynamically stabilized by spin-charge exchange-correlation interactions─a quantum Coulombic effect. The magnitude of this stabilization is such that the radical displays acidity two to six pKa units lower than that of closed-shell ribose. Given the omnipresence of charges in biological systems, these interactions potentially represent a universal mechanism for stabilizing and controlling highly reactive radical intermediates across radical enzymes, opening new avenues for enzymatic engineering and biotechnological applications.

A direct computational assessment of vinculin-actin unbinding kinetics reveals catch-bonding behavior

Vinculin forms a catch bond with the cytoskeletal polymer actin, displaying an increased bond lifetime upon force application. Notably, this behavior depends on the direction of the applied force, which has significant implications for cellular mechanotransduction. In this work, we present a comprehensive molecular dynamics simulation study, employing enhanced sampling techniques to investigate the thermodynamic, kinetic, and mechanistic aspects of this phenomenon at physiologically relevant forces. We dissect a catch bond mechanism in which force shifts vinculin between either a weakly or strongly bound state. Our results demonstrate that models for these states have unbinding times consistent with those from single-molecule studies, and suggest that both have some intrinsic catch-bonding behavior. We provide atomistic insight into this behavior, and show how a directional pulling force can promote the strong or weak state. Crucially, our strategy can be extended to measure the difficult-to-capture effects of small mechanical forces on biomolecular systems in general, and those involved in mechanotransduction more specifically.

Structural Determinants of Buprenorphine Partial Agonism at the μ-Opioid Receptor

The μ-opioid receptor (μOR) is a class A G Protein-Coupled Receptor (GPCR) targeted by natural and synthetic ligands to provide analgesia to patients with pain of various etiologies. Available opioid medications present several unwanted side effects, stressing the need for safer pain therapies. Despite the attractive proposal that biasing μOR signaling toward G protein pathways would lead to fewer side effects, recent studies indicate that low-efficacy opioid drugs, such as buprenorphine, may represent a safer alternative. In the present work, we combine molecular docking, microsecond-time scale molecular dynamics (MD) simulations, and metadynamics to investigate the conformational dynamics of the μOR bound to morphine or buprenorphine. Our objective was to determine structural aspects associated with the unique pharmacological effects caused by the latter, taking morphine as a reference. MD simulations identified a salt bridge with D1493.32 as crucial for stabilizing both ligands into the μOR orthosteric site, with this interaction being weaker in buprenorphine. The morphinan-scaffold of both ligands shared contacts with transmembrane (TM) helix residues of the receptor, including TM3, TM5, TM6, and TM7. Conversely, while morphine showed stronger interactions with a few TM3 residues, additional chemical groups of buprenorphine showed stronger interactions with TM2, extracellular loop 2 (ECL2), and TM7 residues. We also observed distinct TM arrangements induced by these ligands, with buprenorphine causing an extracellular outward movement of TM7 and morphine provoking intracellular inward movements of TM5 and TM7 of the receptor. In addition, we found that buprenorphine tends to explore deeper regions in the μOR orthosteric site, further supported by funnel-metadynamics, resulting in diverse side chain orientations of W2956.48. Metadynamics also unveiled distinct intermediate states for morphine and buprenorphine, with the latter accessing a secondary binding site associated with partial μOR agonists. Our results indicate that the weakened salt bridge of buprenorphine with D1493.32, along with the strong TM7 interaction through its cyclopropyl group, may explain its low efficacy and consequent partial μOR agonism. Furthermore, ECL2 interactions may contribute to explaining the biased agonism of buprenorphine, a common feature shared with other opioid modulators with similar functional effects. Our study sheds light on the complex pharmacology of buprenorphine, identifying structural aspects associated with its partial and biased μOR agonism. These results can provide valuable information for the design of new effective and safer opioid drugs.

Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly

An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nucleocapsid assembly, retaining its structure, or misdirect it into noncapsid-like particles. Previous molecular dynamics (MD) simulations of early capsid-assembly intermediates showed differences in protein conformations for the apo and bound states. Here, we have developed and tested several classification machine learning (ML) models to better distinguish between apo-tetramer intermediates and those bound to accelerating or misdirecting CAMs. Models based on tertiary structural properties of the Cp149 tetramers and their interdimer orientation, as well as models based on direct and inverse contact distances between protein residues, were tested. All models distinguished the apo states and the two CAM-bound states with high accuracy. Furthermore, tertiary structure models and residue-distance models highlighted different tetramer regions as being important for classification. Both models can be used to better understand structural transitions that govern the assembly of nucleocapsids and to assist in the development of more potent CAMs. Finally, we demonstrate the utility of classification ML methods in comparing MD trajectories and describe our ML approaches, which can be extended to other systems of interest.

Formation of a triple complex of viral capsid protein 1 and two capsid-binding inhibitors explains synergistic interactions observed in combination studies with rhinoviruses

Capsid-binding inhibitors, such as pleconaril and OBR-5-340, which prevent the attachment and/or uncoating of most rhinovirus (RV) types, were considered promising candidates for effective anti-RV drug development. Both inhibitors target viral protein 1 (VP1), but their efficacy, spectrum of anti-RV activity, and binding mechanism are different. We hypothesized that combinations of pleconaril and OBR-5-340 might be a promising approach to improve treatment strategies for RV infections. To validate our hypothesis, we analyzed the anti-RV effects of a 6 × 6 concentration matrix compared to monotherapy in vitro. Antiviral studies included multiple RV types, some of which are sensitive or insensitive to pleconaril and OBR-5-340, to consider the diversity of VP1. Synergy analysis was performed with Loewe additivity, Bliss independence, highest single agent, and zero interaction potency models. The results indicate a significant synergistic effect at certain concentrations. Molecular dynamic simulations investigated the molecular basis of the observed synergy. Intriguingly, VP1, pleconaril and OBR-5-340 can bind simultaneously to form a triple complex with additional stabilizing hydrophobic interactions and hydrogen bonds. Consequently, pleconaril-OBR-5-340 combination surpassed the efficacy of monotherapy and inhibited a broader RV spectrum compared to monotherapy. In conclusion, this study contributes to the development of broader-spectrum anti-RV treatments and provides insights into the mechanism behind. This strategy could also be important for treatment of diseases caused by other enteroviruses. The identified strong synergism warrants further preclinical studies for example with, ex vivo or human viral challenge models to translate this synergy into oral or inhaled/topical use for rhinovirus treatment.

PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop

Molecular dynamics simulations are invaluable tools that provide both a molecular understanding and a means for the rational design of polymers. A key bottleneck in current polymer molecular dynamics simulations is the lack of a comprehensive and generalizable method that streamlines the preparation of simulations for novel polymer architectures and chemistries. Here, we present PolyConstruct, a generalizable computational framework that leverages the GROMACS biomolecular simulation package for force field agnostic atomistic simulations of biocompatible and stimuli-responsive polymers. PolyConstruct contains three workflows, PolyBuild, PolyTop, and PolyConf, for generating chemically accurate topology parameters from monomer parameters and structural coordinates for complex polymer architectures and chemistries. We highlight the utility and robustness of PolyBuild, PolyTop, and PolyConf with examples of linear, branched, star, and dendritic polymers.

Tailoring the Regioselectivity of Lentinula edodes O-Methyltransferases for Precise O-Methylation of Flavonoids

A novel O-methyltransferase, LeOMT4, from Lentinula edodes was identified, expressed, and characterized. Although its catalytic activity was lower than that of the previously reported LeOMT2, LeOMT4 displayed strong regioselectivity for the meta-hydroxy group across different catecholic compounds, producing e.g., ferulic acid with an almost exclusive regioisomeric ratio of 98:2 and homoeriodictyol with a ratio of 82:18 (3'-product:4'-product). Leveraging the high sequence and predicted structural similarity between LeOMT2 and LeOMT4, key sites for the tailoring of LeOMT2 were identified through site-directed mutagenesis. This approach aimed for robust mutants retaining the high specific activity of LeOMT2, while enhancing regioselectivity. A single amino acid substitution, F182Y, enabled a regioisomeric ratio of 91:9 for the production of homoeriodictyol. Notably, another single amino acid substitution, I53M reversed the regioselectivity to 2:98 in favor of hesperetin. This strategy enables the selective production of sought-after pharmacologically active flavonoids (butein) and flavor-active flavonoids (homoeriodictyol, hesperetin, hesperetin dihydrochalcone).

Iodine recombination in xenon solvent: Clusters in the gas to liquid-like state transition

Supercritical fluids (SCFs) have attracted significant attention as solvents for chemical reactions due to their unique properties, such as high diffusivity, low viscosity, and tunable solvation properties. These properties profoundly influence reaction kinetics and are often attributed to the formation of molecular clusters within SCFs. To study the effect of supercritical solvent on chemical reactivity and dynamics of reactions, one needs to understand the dynamics of clusters in supercritical fluid. Extensive experiments on the photodissociation and recombination of iodine in supercritical fluids served as a model system for understanding these effects. Experimental studies have been complemented by theoretical and computational investigations, which mostly employ Monte Carlo or empirical molecular dynamics simulations. However, computational studies using non-reactive force fields and ab initio approaches present challenges in capturing reactive processes at larger scales within supercritical fluids. In this work, we developed the ReaxFF parameters by training against quantum mechanics data. ReaxFF reactive force field based molecular dynamics simulations were performed, studying the dynamics of a xenon solvent and cage effect at different thermodynamic conditions for the iodine recombination reaction. We show that the conditions near the critical point are the optimal conditions to study the cage effect. We show that the average lifetime of xenon clusters ranging between 5 and 11 ps is comparable to iodine geminate recombination. Our simulation results of iodine recombination in xenon solvent demonstrate the higher probability of iodine molecule formation in the presence of xenon clusters. Finally, we show that the supercritical condition exhibits the highest recombination rate for iodine atoms.

Activation fingerprints and allosteric modulation at the free fatty acid receptor 1 (FFAR1) revealed by molecular dynamics simulation

The free fatty acid receptor 1 (FFAR1) is a transmembrane G-protein coupled receptor that mediates the metabolic and insulinotropic effects of endogenous free fatty acids in pancreatic cells while also exerting neuro-regulatory effects in the brain. The complexity of FFAR1 derives from its multiple binding sites and the absence of conventional activation motifs observed in class A GPCRs. This study uses molecular dynamics simulations to investigate the molecular mechanisms that underpin endogenous signaling and allosteric regulation in the FFAR1. We investigated and compared three ligand-bound states and the APO state. The ligand-bound simulations included FFAR1 in complex with γ-linolenic acid, FFAR1 in complex with γ-linolenic acid and TAK875, and a fully activated FFAR1 bundle complexed with docosahexaenoic acid and G-protein. The results highlight distinct protein contact fingerprints and dynamics in the ligand-bound states relative to the APO state. While ligand binding, in the absence of stabilizing G-protein, destabilizes the intracellular domain of the receptor, the second extracellular loop exhibits greater stability and salt bridge contact with the transmembrane domain. Notably, simulations of FFAR1 complexed with γ-linolenic acid, bound at the intracellular domain, revealed stable interactions between γ-linolenic acid and the receptor, as well as similar activation fingerprints when compared to FFAR1 in complex with docosahexaenoic acid and Gq. This suggests an effective allosteric regulation of the receptor following γ-linolenic acid binding to the intracellular domain. Finally, a set of hydrophobic amino acid residues at the intracellular and extracellular domains appears to function as potential rotameric switches, facilitating water-mediated receptor activation.

G-protein-coupled receptor FZD7 as a therapeutic target in glioblastoma: Multi-cohort validation and identification of Cycloartobiloxanthone as an inhibitor

G-protein-coupled receptors (GPCRs) play a pivotal role in oncogenesis, mediating key signaling pathways that drive tumor progression and therapy resistance. In this study, we employed an integrated computational approach combining comparative transcriptomics and structure-based drug discovery to identify differentially expressed GPCRs in glioblastoma multiforme (GBM). Our multi-cohort analysis, integrating glioblastoma (GBM) patient datasets from diverse populations revealed consistent overexpression of Frizzled-7 (FZD7) across all cohorts. This finding aligns with comparative transcriptomic profiling of GBM tumor grades, further underscoring FZD7's role as a conserved oncogenic driver. Given the absence of FDA-approved therapeutics targeting the FZD7 oncoprotein, we pursued a structure-based drug discovery strategy to identify natural inhibitors. To achieve this, we performed high-throughput virtual screening of 10,000 phytochemicals against FZD7-CRD domain, followed by molecular docking to prioritize candidates based on binding affinity. Molecular dynamics (MD) simulations were subsequently employed to evaluate ligand-binding stability, conformational dynamics, and receptor-ligand interaction patterns. Among the screened compounds, Cycloartobiloxanthone emerged as the most promising candidate, exhibiting high binding affinity, stable interactions, and minimal conformational fluctuations. Binding free energy calculations (MMPBSA = -65.2 ± 3.8 kcal/mol) and free energy landscape (FEL) analysis further validated its strong inhibitory potential. Cycloartobiloxanthone, a bioactive flavonoid with favorable ADMET properties and lipid bilayer delivery, emerged as a prioritized candidate. Its preclinical efficacy in other malignancies (e.g., lung cancer), coupled with a mitochondrial apoptosis mechanism akin to cisplatin, but with enhanced safety as a natural compound, supports its repurposing potential for FZD7-targeted GBM therapy.

How Omecamtiv Modulates Myosin Motion

Myosin VI is a unique reverse-directed motor protein in the myosin family. The D179Y mutation in Myosin VI is associated with deafness in mammals. This mutation destroys the processive motion of myosin and inhibits its functional activity due to an elevated phosphate release rate. The current work explores the way by which this mutation affects the phosphate release rate and changes the action of Myosin VI. Our study involves a wide range of approaches comprising free energy-based simulations, contact map analysis, binding energy investigation, structural inspection, renormalization simulation, multiple sequence alignment, and bioinformatics analysis. It is found that when the evolutionary conserved aspartic acid (D179) of Myosin VI is mutated to tyrosine (Y179), it leads to premature phosphate release from Myosin VI. Most importantly, the drug omecamtiv rescues the processivity of the mutant by slowing down the actin-independent phosphate release from Myosin VI. Thus, we also explore the molecular mechanism behind the premature phosphate release of the D179Y mutant of Myosin VI and the actin-independent slowing down of the phosphate release in the presence of omecamtiv. This phosphate release modulation is related to Myosin VI's processivity as found experimentally. Overall, our proposed model indicates that omecamtiv significantly alters the interaction between the P-loop of Myosin VI and the interfacial residues, which is the driving force behind the slowing down of the phosphate release of the D179Y mutant in the presence of omecamtiv. Finally, our study provides additional support to our proposal that the directionality of myosins is determined by the highest barrier along the cycle and not by any dynamical effect.

Molecular insights into human phosphatidylserine synthase 2 and its regulation of SREBP pathways

Homologous proteins share similar sequences, enabling them to work together in cells to support normal physiological functions. Phosphatidylserine synthases 1 and 2 (PSS1 and PSS2) are homologous enzymes that catalyze the synthesis of phosphatidylserine (PS) from different substrates. PSS2 shows a preference for phosphatidylethanolamine (PE) as its substrate, whereas PSS1 can utilize either PE or phosphatidylcholine. Previous studies showed that inhibiting PSS1 promotes SREBP-2 cleavage. Interestingly, despite their homology, our findings reveal that PSS2 exerts an opposing effect on the cleavage of both SREBP-1 and SREBP-2. We resolved the cryo-electron microscopy (cryo-EM) structure of human PSS2 at 3.3 Å resolution. Structural comparison of the catalytic cavities between PSS1 and PSS2 along with molecular dynamics simulations uncovers the molecular details behind the substrate preference of PSS2 for PE. The lipidomic analysis showed that PSS2 deficiency leads to PE accumulation in the endoplasmic reticulum, which has been shown to inhibit the cleavage of sterol regulatory element-binding proteins (SREBPs) in mice. Thus, our findings reveal the intricate network of intracellular phospholipid metabolism and underscore the distinct regulatory roles of homologous proteins in cellular activities.

Prostate Cancer and Tea: CYP17A1 Inhibition by Phytochemicals from Tea Plant Camellia sinensis L. and Implications for Anti-androgenic Effect

Camellia sinensis L., commonly known as the tea plant, produces derivatives such as green tea, which are among the most extensively consumed beverages worldwide. Green tea is rich in polyphenolic compounds, such as epigallocatechin-3-gallate (EGCG) and gallocatechin gallate. These phytochemicals have drawn particular attention as antioxidants, especially in relation to their potential to reduce the risks for prostate cancer (PC) among other common human diseases. However, the molecular evidence base needs to be strengthened before large-scale controlled clinical trials with C. sinensis L. and/or specific phytochemicals are pursued. We investigated cytochrome P45017A1 (CYP17A1), a key enzyme in androgen biosynthesis, as a molecular target for the green tea phytochemicals. In this study, molecular docking, pharmacokinetic and toxicity evaluations, molecular dynamics (MD) simulations, and post-MD simulation analyses were performed to assess the binding potential of green tea phytochemicals with the CYP17A1 enzyme. A library of 92 green tea-derived phytochemicals, along with the reference inhibitor abiraterone, was docked against the CYP17A1 enzyme. MD simulations validated the stability and enhanced binding affinity of the CYP17A1-EGCG complex compared with the abiraterone complex, as further confirmed by post-MD simulation analyses. Collectively, these findings suggest that EGCG inhibits CYP17A1, potentially reducing androgen biosynthesis and thereby highlighting green tea as a promising natural source for PC therapeutics. Further preclinical and translational studies are warranted to substantiate the clinical applicability of green tea phytochemicals.

In silico discovery of multi-target small molecules and efficient siRNA design to overcome drug resistance in breast cancer via local therapy

In this study, we designed an efficient siRNA for PKMYT1 gene knockdown and evaluated the binding affinity of various natural small molecules to key proteins associated with breast cancer through molecular docking and molecular dynamics (MD) simulations. Subsequently, among these molecules, The small molecule, SCHEMBL7562664, was introduced as a "golden ligand" that showed potent multi-target activity as an antagonist for aromatase, estrogen receptor α, HER2, and PARP10, and as an agonist for MT2 and STING. Next, MD simulations of six protein- golden ligand complexes (PDB IDs: 4QXQ, 5GS4, 5JL6, 5LX6, 6ME6, and 7PCD), performed with GROMACS over 100 ns at 298.15 K, provided valuable information about their structural dynamics. Analysis of the radius of gyration (Rg) revealed that, while five complexes (7PCD, 5GS4, 5LX6, 4QXQ, and 5JL6) maintained compact structures (Rg between 1.7 and 2.3 nm), the 6ME6 complex exhibited a more extended and flexible conformation (average Rg ∼3.4 nm). Complementary RMSD analysis confirmed that most complexes rapidly stabilized with minimal deviations (generally <0.3 nm), whereas the 6ME6 complex showed higher variability, reaching up to 0.67 nm. Furthermore, Binding free energy calculations using MM-GBSA and PBSA methods further supported these findings, with energies ranging from -21.45 ± 2.28 kcal/mol (5LX6) to -39.79 ± 1.34 kcal/mol (6ME6), indicating an optimal balance between intrinsic interactions and desolvation costs in the 6ME6 and 5JL6 systems. Based on DFT results, the golden ligand showed higher stability and lower reactivity compared to control ligands such as aromatase, tamoxifen, and dacomitinib, potentially leading to reduced off-target interactions and a more favorable safety profile. The integration of these data underscores the therapeutic potential of SCHEMBL7562664 as a multi-target agent for breast cancer, with promising pharmacokinetic properties that can be optimized for local treatment by incorporation into a 3D scaffold.

Pharmacophore modeling, 2D-QSAR, molecular docking and ADME studies for the discovery of inhibitors of PBP2a in MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is considered to be a worldwide threat to human health and the global spread of MRSA has been associated with the emergence of different types of infections and resultant selection pressure due to exposure to many antibiotics. In the current era characterized by incessant antibiotic resistance, assessment of multiple molecular targets represents notable therapeutic opportunities in the medical and pharmaceutical industry and can aid in the discovery of novel molecules that inhibit various receptors effectively to replace the current weak antimicrobial agents. Penicillin binding protein 2a (PBP2a) of MRSA is a major determinant of resistance to β-lactam antibiotics. The activity of PBP2a is not inhibited by β-lactam antibiotics, allowing the strain to survive in the presence of β-lactams leading to resistance to β-lactam antibiotics. The study aimed at identifying potential inhibitors of PBP2a receptor of MRSA through ligand-based pharmacophore modeling, 2D-QSAR, molecular docking, ADMET screening as well as molecular dynamic (MD) simulations. The study led to the development of a satisfactory, predictive and significant 2D-QSAR model for predicting anti-MRSA activity of compounds and also led to the identification of two molecules: C21H25N7O4S2 (ChEMBL30602) and C20H17NO6S (ChEMBL304837) with favorable pharmacophore features and ADME properties with potential to bind strongly to PBP2a receptor of MRSA. MD simulation analysis showed that the interactions of C20H17NO6S (ChEMBL304837) with PBP2a over 100 ns was more stable and similar to the interaction of ceftobiprole with PBP2a and may become potential drug candidate against MRSA which has developed a lot of resistance to current antibiotics.

A constant pH molecular dynamics and experimental study on the effect of different pH on the structure of urease from Sporosarcina pasteurii

CONTEXT

Urease is pivotal in microbial-induced calcium carbonate precipitation (MICP), where its catalytic efficiency directly governs calcium carbonate formation. However, practical MICP applications in extreme environments (e.g., acidic mine drainage, industrial waste sites) are hindered by limited understanding of urease behavior under extreme pH conditions. This study combines laboratory experiments and constant pH molecular dynamics (CpHMD) simulations to investigate how pH variations (3-11) affect the structural stability of Sporosarcina pasteurii urease, focusing on its α-subunit (PDB: 4CEU). Experimental validation identified pH 7-8 as optimal for urease activity, aligning with molecular dynamics results showing minimal structural deviations (RMSD) and stable protonation states under neutral to mildly alkaline conditions. Extreme pH (3, 4, 11) disrupted active-site geometry and induced charge fluctuations, impairing catalytic function. CpHMD simulations revealed that the α-subunit retains structural integrity at pH 7-8, suggesting potential reassembly post-environmental stress. This work bridges gaps in enzymatic stability under harsh conditions, offering insights for optimizing MICP in geotechnical and environmental remediation applications.

METHODS

The study combined experimental and computational approaches. Sporosarcina pasteurii urease activity was experimentally assessed across pH 3-11 by monitoring urea hydrolysis-induced conductivity changes. Computational analyses employed GROMACS constant pH with the CHARMM36 force field to perform pH-dependent molecular dynamics simulations. The urease structure was solvated, neutralized, energy-minimized, and subjected to constant pH simulations. Structural stability, active site dynamics, and protonation states of titratable residues were analyzed via RMSD, hydrogen bonds, solvent-accessible surface area (SASA), and Epock 1.0.5. Free energy landscapes and residue interactions were evaluated using principal component analysis (PCA) and λ-dynamics. Experimental data were processed with OriginPro 2024b and Python, linking pH-induced conformational shifts to enzymatic function.

Quantitative Nanometrology of Binary Particle Systems Using Fluorescence Recovery after Photobleaching: Application to Colloidal Silica

We present an application of fluorescence recovery after photobleaching (FRAP) to measure the size of the individual nanoparticles in binary systems. The presence of nanoparticles with varying sizes was successfully demonstrated using a straightforward biexponential model and their sizes were accurately determined. Furthermore, we have demonstrated the benefits of preprocessing the data using a simple machine learning algorithm based on the gradient boosting machine and fitting the resulting curves to a triexponential model. This approach allows the accurate recovery of the sizes of each of the three components in a binary particle system, namely, the 6 nm LUDOX HS40, 11 nm LUDOX AS40, and the free R6G labeling dye. Lastly, it has been demonstrated using molecular dynamics simulations that R6G adsorption to silica nanoparticles (SNPs) is indeed size-dependent, with larger constructs as the preferred target because of their higher charge and smaller curvature. The theoretical and experimental results were therefore consistent with one another.

Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking

EnzyDock is a multistate, multiscale CHARMM-based docking program which enables mechanistic docking, i.e., modeling enzyme reactions by docking multiple reaction states, like substrates, intermediates, transition states, and products to the enzyme, in addition to standard protein-ligand docking. To achieve docking of multiple reaction states with similar poses (i.e., consensus docking), EnzyDock employs consensus pose restraints of the docked ligand states relative to a docking template. In the current work, we present an implementation of a Maximum Common Substructure (MCS)-guided docking strategy using EnzyDock, enabling the automatic detection of similarity among query ligands. Specifically, the MCS multistate approach is employed to efficiently dock ligands along enzyme reaction coordinates, including reactants, intermediates, and products, which allows efficient and robust mechanistic docking. To demonstrate the effectiveness of the MCS strategy in modeling enzymes, it is first applied to two highly complex enzyme reaction cascades catalyzed by the diterpene synthase CotB2 and the Diels-Alderase LepI. In addition, the MCS strategy is applied to dock enzyme inhibitors using cocrystallized inhibitors or substrates to guide the docking in the enzymes dihydrofolate reductase and the SARS-CoV-2 enzyme Mpro. The latter case exemplifies the use of MCS with EnzyDock's covalent docking capabilities and QM/MM scoring option. We show that different protocols of the implemented MCS algorithm are needed to obtain mechanistic consistency (i.e., similar poses) in mechanistic docking or to accurately dock chemically diverse ligands in inhibitor docking. Although the current implementation is specific for EnzyDock, the findings should be general and transferable to additional docking programs.

Subtractive proteomics unravel the potency of D-alanine-D-alanine ligase as the drug target for Burkholderia pseudomallei

Melioidosis, also known as Whitmore's disease, is caused by the deadly pathogen Burkholderia pseudomallei and remains a significant global health concern, particularly in South Asia. The disease is contracted through exposure to contaminated soil, water, air, and food. Infected individuals often present with abscesses in internal organs such as the lungs, spleen, and liver, and in soft tissues, with severe cases leading to septic shock and acute pneumonia. The rising incidence and mortality rates, coupled with B. pseudomallei's ability to form biofilms and develop resistance to antibiotics like cephalosporins, make treatment increasingly challenging. This highlights the urgent need for novel therapeutic approaches. D-Alanine-D-Alanine ligase (Ddl), a crucial enzyme involved in the final stage of bacterial cell wall synthesis, which protects the pathogen from the hostile cellular environment of the host. While many bacteria have two isoforms of this enzyme, B. pseudomallei possesses only the DdlB isoform, presenting a significant vulnerability. Our study represents the first successful attempt to target DdlB through a combination of molecular docking and molecular dynamics simulations. These investigations provide strong evidence that Conivaptan acts as an effective inhibitor of DdlB, offering a novel therapeutic approach for combating melioidosis.

The Impact of Permeation Enhancers on Transcellular Permeation of Small Molecule Drugs

Passive permeation through an epithelial membrane may be enhanced by using a class of amphiphilic molecules known as permeation enhancers (PEs). PEs have been studied in clinical trials and used in coformulations with peptides and small molecule drugs, and yet, an understanding of the permeant-PE interactions leaves much to be desired. This manuscript uses all-atom molecular dynamics (MD) simulations to showcase the effects of sodium caprate (C10) and salcaprozate sodium (SNAC), two commonly applied PEs, on membrane properties and the free energy profiles of five small molecule drugs (mannitol, atenolol, ketoprofen, decanedecaol, mucic acid). Our results show that both C10 and SNAC make the lipid molecules pack more densely, but C10 increases the lipid lateral diffusivity while SNAC decreases it. The change in the lipid order parameter also shows both PEs increasing the order near the lipid heads, possibly due to the dense packing in the membrane. A decrease in the central barrier of the permeation free energy was observed by embedding PEs into a lipid bilayer and SNAC is more efficient in doing so than C10. Neither SNAC nor C10 has a large impact on the diffusion coefficient of the small molecules. The analysis of the MD simulations revealed that PEs make the membrane tail region more hydrophilic by forming hydrogen bonds with small molecule drugs, i.e., decreasing the central barrier of the permeation free energy. While this study was only limited to small molecule drugs, this lays the groundwork for future studies to which the effects of the PEs in the permeation of macromolecules and peptides may be observed.

Multi-approach study on diethylhexyl phthalate and monoethylhexyl phthalate binding to lysozyme: In silico, bioactivity and surface plasmon resonance analyses

Diethylhexyl phthalate (DEHP) and its metabolite monoethylhexyl phthalate (MEHP) are recognized as endocrine disruptors with significant toxicological effects on various human physiological systems. While previous research has explored phthalate-protein interactions, there is a notable gap in studies focusing on the interaction between these endocrine disruptors and lysozyme (LZM), a critical component of the immune system. This study aimed to investigate the interactions of DEHP and MEHP with chicken egg white lysozyme (CEWLZM) using molecular docking, molecular dynamics simulations, bioactivity and surface plasmon resonance (SPR) analyses to evaluate the molecular mechanisms, binding affinity, kinetic properties and bioactivity effects of these interactions. Complementary insights from molecular docking and molecular dynamics simulations indicate that DEHP has a stronger binding affinity for CEWLZM than MEHP. This affinity value was corroborated by an intense hydrophobic and van der Waals interaction network especially maintained by the active residue Leu75 and Asp101-Ala107. Although MEHP did not exhibit a significant effect on enzyme activity in lysozyme bioactivity assay, DEHP inhibited lysozyme with an IC50 value of 453 µM. SPR analysis revealed that DEHP exhibits a significantly stronger binding affinity to CEWLZM compared to MEHP.

Design and optimization of bifunctional peptides for controlled core-shell nanocapsule formation

Nanocapsules with core-shell structures hold significant potential across diverse applications. Biomimetic templating offers a benign approach for synthesizing inorganic nanostructures using biomolecules, leveraging amino acid sequences from natural sources and combinatorial biology in a process known as biomineralization. This study investigates the design and functionality of bifunctional peptides for controlled interfacial biosilicification. Five bifunctional peptides were designed and compared for their surface activity, structural behavior, and biosilicification capability under benign conditions. AM1 and SurSi-G1 demonstrate rapid adsorption, lower interfacial tension, and higher surface activity. In contrast, SurSi and its variants show slower adsorption due to higher molecular charge, resulting in high interfacial tension. Biosilicification assays confirmed that peptide charge strongly influences particle morphology, with SurSi and SurSi-R3 yielding well-dispersed silica nanoparticles, while AM1, SurSi-R2, and SurSi-G1 formed larger aggregates. Low ionic strength and sufficient surface charge enhance electrostatic interaction between positively charged bifunctional peptides and negatively charged hydrolyzed silicic acid, facilitating controlled biosilicification at interface and enabling the precise formation of core-shell nanocapsules. These findings highlight the pivotal role of peptide sequence and charge distribution in determining surface activity and interfacial biosilicification, providing insights for optimizing nanocapsule synthesis.

Design, synthesis, docking, DFT, and MD simulation studies of new piperazine, 1,3,4-oxadiazole, and quinoline conjugates: A search for potent antiepileptic agents

In this study, novel substituted 2-(5-(2-phenylquinolin-4-lyl)-1,3,4-oxadiazol-2-ylthio)-1-(4-phenylpiperazine-1-yl) ethanones (11a-i) were synthesized and assessed for their anticonvulsant potential. The structures of the synthesized compounds were confirmed through FT-IR, 1H NMR, 13C NMR, and mass spectrometry. In vivo, anticonvulsant investigations were performed using the maximal electroshock seizure (MES) and subcutaneous pentylenetetrazol (scPTZ) induced epilepsy animal models. Compounds 11b, 11e, and 11 h demonstrated the most promising action against the induced seizures. To prove that the synthetic derivatives' ability to prevent seizures is not caused by any depression brought on by the use of synthesized derivatives, antidepressant activity has been conducted via a forced swim test (FST). In addition, in silico evaluations comprising ADME predictions, molecular docking, and molecular dynamics simulations on GABAA receptors were also performed to determine the pharmacokinetic profiles, binding mode, orientation, and stability of synthesized compounds at the active sites of the targets. The electronic structure of synthesized compounds was also described by density functional theory (DFT) through various reactivity descriptors such as HOMO, LUMO, electron affinity, ionization potential, chemical potential, and global softness. The results of computational studies reinforced the findings of in vivo screening. In summary, this study introduces a promising class of piperazine-1,3,4-oxadiazole-quinoline hybrids with significant antiepileptic properties, warranting further pharmacological exploration for their potential clinical applications.

3,4-Dihydroxyphenylacetaldehyde synthase evolved an ordered structure to deliver oxygen to pyridoxal 5'-phosphate for cuticle assembly in the mosquito Aedes aegypti

3,4-Dihydroxyphenylacetaldehyde synthase (DHPAAS) catalyzes oxygen-dependent conversion of 3,4-dihydroxyphenylalanine (dopa) to 3,4-dihydroxyphenylacetaldehyde (DHPAA), a likely cross-linking agent precursor of the insect cuticle. In the current study, extensive in vivo experiments in Aedes aegypti show that DHPAAS is essential for abdominal integrity, egg development and cuticle structure formation. Solid-state 13C nuclear magnetic resonance analysis of the Ae. aegypti cuticle molecular structure shows chemical shifts of 115 to 145 ppm, suggesting the presence of catechols derived from DHPAA. The crystal structure of insect DHPAAS was then solved, revealing an active site that is divergent from that of the homologous enzyme dopa decarboxylase. In the DHPAAS crystal structure, stabilization of the flexible 320-350 region accompanies the positioning of the 350-360 loop relatively close to the catalytic Asn192 residue while the conserved active site residue Phe103 adopts an open conformation away from the active center; these distinct features participate in the formation of a specific hydrophobic tunnel which potentially facilitates delivery of oxygen to pyridoxal 5'-phosphate in the conversion of dopa to DHPAA.

A computational perception of BBOX1-IP3R3 interaction uncovers inhibitors for dysregulated calcium signalling in triple negative breast cancer

Triple Negative Breast Cancer (TNBC) is the most aggressive type of breast cancer unveiling negative expression on oestrogen receptors, progesterone receptors, and HER2. The anomalous activation of signalling pathways and specific types of mutations characterize the progression of TNBC. Protein-protein interaction in the tumour microenvironment plays a crucial role in tumour aggressiveness. Disrupting the signalling pathways that promote cell progression, migration, and survival opens up a promising avenue for targeting the aggressive form of TNBC. The present study emphasizes the molecular interaction mechanism driving the aggressive and recalcitrant TNBC between BBOX1-IP3R3. The BBOX1-IP3R3 complex destabilization was accomplished using compounds obtained from various databases through virtual screening, molecular, and essential dynamics. The interaction study revealed that the four hits bound at the interface and facilitated better binding affinity with the highest docking score and optimal binding free energy. In addition, the molecular dynamics simulation, PCA/FEL, and MM/PBSA analysis conclusively evaluate the binding potential of the compounds and unequivocally stabilize specific conformations or deception of the complexes in high-energy states. Thus, the identified compounds lead to the disruption of BBOX1-IP3R3 interaction, which aids in the therapeutic option of TNBC.

The molecular mechanisms of visual chromophore release from cellular retinaldehyde-binding protein

Cellular retinaldehyde-binding protein (CRALBP) is an 11-cis-retinoid binding protein operating within the visual cycle. CRALBP serves as the terminal acceptor of 11-cis-retinaldehyde (11cRAL) produced within the retinal pigment epithelium (RPE) and mediates 11cRAL transport to the RPE apical microvilli. Crystallographic structures of CRALBP revealed that the 11cRAL-binding pocket is sealed off from bulk solvent, indicating a necessity for conformational changes to allow ligand egress. Here, we performed long timescale all-atom molecular dynamics simulations of CRALBP to elucidate the mechanisms of ligand release. CRALBP exhibits slower diffusive behavior in the presence of membranes containing negatively charged phospholipids, which bind to an exposed cationic pocket in CRALBP. Umbrella sampling calculations revealed thermodynamically likely pathways for 11cRAL egress. Our data suggest that the CRALBP-acidic phospholipid interaction facilitates 11cRAL release through allosteric, conformational changes that perturb the binding site, lowering ligand affinity. These findings offer insights into the molecular pathology of CRALBP-associated retinopathy.