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

Unveiling an indole derivative YM818 as a novel tyrosinase inhibitor with anti-melanogenic and anti-melanin transfer effects

Indole and its derivatives, heterocyclic compounds with broad therapeutic potential, have seen limited study in melanogenesis. Here, our virtual screening identified 15 indole derivatives that potentially interacted with tyrosinase (TYR), a key enzyme in melanogenesis. Nine of the 15 indole derivatives tested significantly decreased tyrosinase activity, and 3-hydroxy-5-bromo-(3-indolyl)-2‑carbonyl indole (designated as YM818) exhibited highest inhibitory rate at 74.28 % with IC50 of 0.372 mmol/L. Surface plasmon resonance and fluorescence quenching assays demonstrated the direct interaction between YM818 and TYR with KD value 94.84 ± 45.27 μmol/L. YM818 treatment reduced cellular melanin content to 35.8 %. Furthermore, YM818 treatment enhanced AKT protein phosphorylation, leading to the downregulation of melanogenesis-related proteins, including MITF, TYR and TRP1. In vivo zebrafish studies confirmed the inhibitory effects of YM818 on melanogenesis. Additionally, YM818 disrupted melanin transfer by suppressing the expression of protease-activated receptor-2 (PAR-2) gene, a G protein-coupled receptor that plays a crucial role in mediating cellular responses to serine proteases, including keratinocyte phagocytosis and melanin transfer. YM818 also exhibited robust antioxidant activity, with 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging IC50 values comparable to vitamin C and significantly reducing intracellular ROS levels in a dose-dependent manner. Taken together, these findings highlight YM818 as a promising anti-melanogenic agent, offering valuable insights into the development of novel anti-melanin drugs and tyrosinase inhibitors.

Inhibitory potential of furanocoumarins against cyclin dependent kinase 4 using integrated docking, molecular dynamics and ONIOM methods

Cyclin Dependent Kinase 4 (CDK4) is vital in the process of cell-cycle and serves as a G1 phase checkpoint in cell division. Selective antagonists of CDK4 which are in use as clinical chemotherapeutics cause various side-effects in patients. Furanocoumarins induce anti-cancerous effects in a range of human tumours. Therefore, targeting these compounds against CDK4 is anticipated to enhance therapeutic effectiveness. This work intended to explore the CDK4 inhibitory potential of 50 furanocoumarin molecules, using a comprehensive approach that integrates the processes of docking, drug-likeness, pharmacokinetic analysis, molecular dynamics simulations and ONIOM (Our own N-layered Integrated molecular Orbital and Molecular mechanics) methods. The top five best docked compounds obtained from docking studies were screened for subsequent analysis. The molecules displayed good pharmacokinetic properties and no toxicity. Epoxybergamottin, dihydroxybergamottin and notopterol were found to inhabit the ATP-binding zone of CDK4 with substantial stability and negative binding free energy forming hydrogen bonds with key catalytic residues of the protein. Notopterol exhibiting the highest binding energy was subjected to ONIOM calculations wherein the hydrogen bonding interactions were retained with significant negative interaction energy. Hence, through these series of computerised methods, notopterol was screened as a potent CDK4 inhibitor and can act as a starting point in successive processes of drug design.

Molecular basis of neurosteroid and anticonvulsant regulation of TRPM3

Transient receptor potential channel subfamily M member 3 (TRPM3) is a Ca2+-permeable cation channel activated by the neurosteroid pregnenolone sulfate (PregS) or heat, serving as a nociceptor in the peripheral sensory system. Recent discoveries of autosomal dominant neurodevelopmental disorders caused by gain-of-function mutations in TRPM3 highlight its role in the central nervous system. Notably, the TRPM3 inhibitor primidone, an anticonvulsant, has proven effective in treating patients with TRPM3-linked neurological disorders and in mouse models of thermal nociception. However, our understanding of neurosteroids, inhibitors and disease mutations on TRPM3 is limited. Here we present cryogenic electron microscopy structures of the mouse TRPM3 in complex with cholesteryl hemisuccinate, primidone and PregS with the synthetic agonist CIM 0216. Our studies identify the binding sites for the neurosteroid, synthetic agonist and inhibitor and offer insights into their effects and disease mutations on TRPM3 gating, aiding future drug development.

In silico cooling rate dependent crystallization and glass transition in n-alkanes

n-Alkanes (CnH2n+2) are linear chain compounds spanning length-scales from small molecules to polymers. Intermediate length alkanes (say, n = 10-20) have attracted much interest as organic phase change materials (PCM) for storing energy as latent heat. The cooling rate (γ) determines both the latent heat and temperature of crystallization. While slow cooling of the liquid leads to the crystalline state, rapid cooling leads to a glassy state (glass transition temperature Tg). Albeit scant theoretical investigations concerning the vitrification processes, the role of molecular conformations therein remains completely unexplored. Our work presents an all-atom molecular dynamics study of (a) cooling intermediate length alkanes (n = 12 and 16) at seven different rates, and (b) rapidly cooling 14 n-alkanes (4 ≤ n ≤ 50) for determining Tg(n). We find that for linear molecules the end-to-end distance (Ree) is of special relevance: the crystal is composed solely of fully stretched molecules (maximal Ree). Hence one may define the "degree of crystallization" as the area under the maximal Ree peak in the Ree distribution. Other peaks in the distribution represent conformations that existed in the supercooled liquid just before vitrification. A peak for the shortest, hairpin rotamer appears only for n ≥ n0 = 18, and is also manifested in the minimum of Rg/Ree(n) for liquid n-alkanes. The dependence of Tg on n is represented as two intersecting Ueberreiter and Kanig equations, intersecting near n0 = 18. Extrapolation gives the asymptotic n → ∞ limit of Tg, T∞g = 250 K, which is probably its most accurate estimate obtained theoretically todate.

Multimodal evaluation of lipoxygenase-targeting NSAIDs using integrated in vitro, SAR, in silico, cytotoxicity towards MCF-7 cell line, DNA docking and MD simulation approaches

Lipoxygenase (LOX) and cyclooxygenase (COX) pathways generate biologically active mediators implicated in inflammatory disorders and several classes of cancer. Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit the COX pathway by inhibiting the COX-1 and COX-2 enzymes. We reported earlier that several NSAIDs, including naproxen, aspirin and acetaminophen, inhibited lipoxygenase (LOX) enzyme at sub-micromolar concentrations. In continuation, the present work demonstrates the anti-LOX activity of nine more NSAIDs supported by in vitro, in silico, MD simulation and breast cancer cell line studies. All tested drugs displayed potent to excellent inhibitory profiles with IC50 values <24.93 ± 0.64 μM. Aceclofenac (IC50 0.85 ± 0.06 μM) was the most active drug, followed by indomethacin (IC50 1.13 ± 0.07 μM), meloxicam (IC50 1.94 ± 0.07 μM) and ketorolac (IC50 9.26 ± 0.82 μM). Celecoxib (IC50 15.81 ± 0.71 μM), lornoxicam (IC50 16.54 ± 0.28 μM) and nimesulide (IC50 19.87 ± 0.85 μM) showed excellent inhibitory profiles. Flurbiprofen (IC50 21.73 ± 0.93 μM) and etoricoxib (IC50 24.93 ± 0.64 μM) moderately inhibited the target enzyme. SAR studies revealed that active molecules decorated with the carboxylate group afforded strong binding interactions as observed by in vitro assays and structural features. Other drugs, including enol derivatives and celecoxib, also showcased enhanced binding interactions. However, the cytotoxic effects of NSAIDs against the MCF-7 breast cancer cell line did not disclose significant anticancer activity. Molecular docking studies against human 5-LOX offered the best binding affinities for aceclofenac (-13.54 kcal/mol), accompanied by conventional hydrogen bonding and hydrophobic interactions as supported by the in vitro results. Docking studies with DNA dodecamer established minor groove binding with their possible role in DNA replication and gene expression. Density functional theory (DFT) and ESP studies, MD simulations and MMPBSA free energy calculations further reiterated the stability of ligand-receptor complexes. Overall, these findings highlight the potential of targeted NSAIDs as dual COX/LOX inhibitors with broader therapeutic relevance in inflammatory disorders.

Structural insights into terminal arabinosylation of mycobacterial cell wall arabinan

The global challenge of tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is compounded by the emergence of drug-resistant strains. A critical factor in Mtb's pathogenicity is its intricate cell envelope, which acts as a formidable barrier against immune defences and pharmacological interventions. Central to this envelope are arabinogalactan (AG) and lipoarabinomannan (LAM), two complex polysaccharides containing arabinan domains essential for maintaining cell wall structure and function. The arabinofuranosyltransferase AftB plays a pivotal role in the biosynthesis of these arabinan domains by catalyzing the addition of β-(1 → 2)-linked terminal arabinofuranose residues. Here, we present the cryo-EM structures of Mycobacterium chubuense AftB in both its apo form and bound to a donor substrate analog, resolved at 2.9 Å and 3.4 Å resolution, respectively. These structures reveal that AftB has a GT-C fold, with a transmembrane (TM) domain comprised of eleven TM helices and a periplasmic cap domain. AftB has a distinctive irregular, tube-shaped cavity that connects two proposed substrate binding sites. Through an integrated approach combining structural analysis, biochemical assays, and molecular dynamics simulations, we delineate the molecular basis of AftB's reaction mechanism and propose a model for its catalytic function.

Cholesterol allosteric modulation of the oxytocin receptor

G-protein coupled receptors are critical components in cellular signaling, mediating various physiological responses to external stimuli. Here, we investigate the intricate relationship between cholesterol and the oxytocin receptor (OXTR), focusing on the binding mechanisms and the allosteric cross talk of bound cholesterol to the orthosteric ligand binding pocket. Utilizing molecular docking and molecular dynamics simulations, we identify cholesterol binding sites both on the agonist-bound and antagonist-bound state, which show differing distributions and residence times of the cholesterol molecules. Importantly, both methods converge on several key sites, demonstrating strong predictive overlap. Notably, one such site, and several sites detected by our molecular dynamics approach, also coincide with electron density observed in an experimental cryo-EM map, providing orthogonal validation for computational predictions. Allosteric network analysis uncovers the distinct pathways through which cholesterol may affect ligand-mediated receptor signaling, highlighting the significance of one site on the extracellular leaflet between TM4 and TM5, and two sites on the intracellular leaflet between TM2, TM3, and TM4 and between TM4 and TM5 in transmitting allosteric signals to the orthosteric pocket. These findings provide insights into the impact of cholesterol on OXTR function, emphasizing specific binding sites and signaling paths for further experimental exploration.

Deciphering the Regulatory Potential of Antioxidant and Electron-Shuttling Bioactive Compounds in Oolong Tea

OT has gained attention for its high polyphenol content and therapeutic potential. To elucidate this further, this study investigated the electron-shuttling bioactive compounds of OT and evaluated their effect on dysregulated breast cancer (BC) genes. OT extracts were obtained via solvent extraction (SE) and supercritical fluid extraction (SFE), followed by in vitro assays. Phytochemical analysis revealed that ethanol-extracted OT (OTL-E) had the highest polyphenol, flavonoid, and tannin contents, correlating with strong antioxidant activity, while water-extracted OT (OTL-W) exhibited greater bioelectricity-stimulating properties in microbial fuel cells (MFC), confirmed by cyclic voltammetry (CV). Based on phytochemical analyses, SE displayed a better extraction technique for isolating OT bioactive compounds compared to SFE. In silico approaches through network pharmacology, molecular docking and dynamics simulations revealed that polyphenols with ortho- or para-dihydroxyl groups targeted dysregulated BC proteins involved in kinase signaling, apoptosis, and hormone receptor pathways. Luteolin exhibited the highest binding affinities to MAPK1 and PIK3CA with free energy (ΔG) of -9.1 and -8.4 kcal/mol, respectively. Trajectory-based analyses confirmed enthalpy-favored ligand-induced conformational changes to these oncoproteins, altering their function in BC development. These findings suggest the potential of OT as a bioelectricity-stimulating and chemopreventive agent, warranting further in vitro and in vivo validation.

Computational approach for the evaluation of sesquiterpene lactone as a modulator of cannabinoid receptor type 2 for neurodegenerative disease prophylactics

Neurodegenerative diseases represent a major global health challenge, with cannabinoid receptor type 2 (CB2) emerging as a promising therapeutic target for its role in inflammation modulation and neuroprotection. Sesquiterpene lactone is a class of natural compounds with diverse molecular structures and known biological activities. This study aimed to explore sesquiterpene lactones for their potential as CB2 modulators using computational approaches such as molecular docking, molecular dynamics simulations (MDS), and ADMET predictions, to identify the promising candidates for neurodegenerative disease prophylactics. Out of 85 sesquiterpene lactones evaluated, podachaenin (PubChem CID: 15,828,229) exhibited the highest binding affinity to CB2 (- 12.242 kcal/mol), outperforming that of the native ligand (- 12.168 kcal/mol) and reference drugs apomorphine (- 9.482 kcal/mol), dantrolene (- 8.861 kcal/mol), and galantamine (- 9.689 kcal/mol). Hydrogen bonds as well as alkyl, Pi-alkyl, and van der Waal's interactions were present in the CB2-podachaenin complex providing structural intactness. MDS of 500 ns evaluated the stability of the protein-ligand complex and receptor structure in apo form through geometrical parameters: root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessible surface area, and hydrogen bond length. Additionally, the binding free energy change calculation supplemented the initial inferences in terms of thermodynamic stability with a value of - 40.92 ± 4.56 kcal/mol. ADMET profiling also indicated favorable pharmacokinetic and pharmacodynamic properties, similar to that of the reference drugs. The preliminary results identified podachaenin as a possible CB2 modulator for treating neurodegenerative diseases and could be a hit compound in neuro-drug design. Further in vivo and in vitro studies are suggested to validate it as a hit candidate.

Self-Assembled Multilayered Concentric Supraparticle Architecture

Supraparticles (SPs) with unique properties are emerging as versatile platforms for applications in catalysis, photonics, and medicine. However, the synthesis of novel SPs with complex internal structures remains a challenge. Self-Assembled Multilayered Supraparticles (SAMS) presented here are composed of concentric lamellar spherical structures made from metallic nanoparticles, formed from a synergistic three-way interaction phenomenon between gold nanoparticles, lipidoid, and gelatin, exhibiting interlayer spacing of 3.5  ± 0.2 nm within a self-limited 156.8  ± 56.6 nm diameter. The formation is critically influenced by both physical (including nanoparticle size, lipidoid chain length) and chemical factors (including elemental composition, nanoparticle cap, and organic material), which collectively modulate the surface chemistry and hydrophobicity, affecting interparticle interactions. SAMS can efficiently deliver labile payloads such as siRNA, achieving dose-dependent silencing in vivo, while also showing potential for complex payloads such as mRNA. This work not only advances the field of SP design by introducing a new structure and interaction phenomenon but also demonstrates its potential in nanomedicine.

Atomistic Modeling of Cross-Linking in Epoxy-Amine Resins: An Open-Source Protocol

Atomistic modeling has become an extensively used method for studying thermosetting polymers, particularly in the analysis and development of high-performance composite materials. Despite extensive research on the topic, a widely accepted, standardized, flexible, and open-source approach for simulating the cross-linking process from precursor molecules has yet to be established. This study proposes, tests, and validates a Molecular Dynamics (MD) protocol to simulate the cross-linking process of epoxy resins. We developed an in-house code based on Python and LAMMPS, enabling the generation of epoxy resin structures with high degrees of cross-linking. In our work, the epoxy network is dynamically formed within the MD simulations, modeling the chemical bonding process with constraints based on the distance between the reactive sites. To validate our model against experimental data from the literature, we then computed the density, thermal conductivity, and elastic response. The results show that the produced structures align well with experimental evidence, validating our method and confirming its feasibility for further analyses and in silico experiments. Beyond the case study presented in this work, focusing on bisphenol A diglycidyl ether (DGEBA) epoxy resin and diethylenetriamine (DETA) as curing agents in a 5:2 ratio, our approach can be easily adapted to investigate different epoxy resins.

The Binding of Brazilin from C. sappan to the Full-Length SARS-CoV-2 Spike Proteins

The emergence of coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a global issue since 2019. The prominent characteristic of SARS-CoV-2 is the presence of the spike (S) protein protruding from the virus particle envelope. The S protein is a major drug and vaccine target because it initiates the key step in infection. Medicinal herbs are a potential treatment option to enhance immunity to fight viral infections. Caesalpinia sappan L. has been reported to display promising anti-viral activities. Specifically, brazilin (BRA), a major bioactive compound in C. sappan, was reported to play a role in inhibiting viral infection. Thus, the ability of BRA as a COVID-19 treatment was tested. The S protein was used as the BRA target of this work. Understanding the binding mechanism of BRA to the S protein is crucial for future utilisation of C. sappan as a COVID-19 treatment or other coronavirus-caused pandemics. Here, we performed molecular docking of BRA onto the S protein receptor binding domain (RBD) and multimerisation (MM) pockets. Molecular dynamics (MD) simulations were conducted to study the stability of binding to glycosylated and non-glycosylated S protein constructs. BRA can bind to the Receptor-binding motif (RBM) on an RBD surface stably; however, it is too large to fit into the MM pocket, resulting in dissociation. Nonetheless, BRA is bound by residues near the S1/S2 interface. We found that glycosylation has no effect on BRA binding, as the proposed binding site is far from any glycans. Our results thus indicate that C. sappan may act as a promising preventive and therapeutic alternative for COVID-19 treatment.

Single-particle adsorption of ultra-small gold nanoparticles at the biomembrane phase boundary

Nanomaterials are revolutionizing biomedical research by enabling the development of novel therapies, with applications ranging from drug delivery and diagnostics to the modulation of specific biological processes. Current research focuses on tasks such as enhancing cellular uptake of materials while preserving their functionality. However, the mechanisms governing interactions between nanomaterials and biological systems-particularly cellular membranes-remain challenging to elucidate due to the complex, dynamic nature of the lipid bilayer environment. This complexity arises from factors such as coexisting lipid domains (conserved regions of lipids) or lipid rafts, as well as cellular behaviors that induce state changes. The heterogeneous membrane landscape may offer unique adsorption properties and other functional effects, making it crucial to understand these interactions for greater biological control in nanotherapeutics. In this work, we systematically expose a phase-separated phospholipid-supported lipid bilayer (SLB)-specifically, a fluid-gel DOPC:DPPC bilayer-to low concentrations of citrate-capped 5 nm gold nanoparticles (AuNPs) to observe the adsorption process of individual AuNPs at the molecular scale. Using atomic force microscopy (AFM), we experimentally detect the adsorption of some AuNPs at the phase boundary. Complementary molecular dynamics (MD) simulations further elucidate the mechanism of single AuNP adsorption at lipid phase boundaries. Our findings indicate that the AuNP preferentially incorporates into the fluid-phase DOPC lipids while maintaining partial association with the gel-phase DPPC lipids due to diffusion effects. During adsorption, the AuNP disrupts lipid organization by increasing lateral lipid mixing across the phase boundary. This disruption to lipid molecular ordering is further evident upon AuNP incorporation into the bilayer. The ability to modulate the spatial organization and structure of lipid molecules has significant implications for therapeutics that leverage lipid diffusion pathways for alternative drug delivery mechanisms or to induce specific lipid behaviors.

ART-SM: Boosting Fragment-Based Backmapping by Machine Learning

In sequential multiscale molecular dynamics simulations, which advantageously combine the increased sampling and dynamics at coarse-grained resolution with the higher accuracy of atomistic simulations, the resolution is altered over time. While coarse-graining is straightforward once the mapping between atomistic and coarse-grained resolution is defined, reintroducing the atomistic details is still a nontrivial process called backmapping. Here, we present ART-SM, a fragment-based backmapping framework that learns from atomistic simulation data to seamlessly switch from coarse-grained to atomistic resolution. ART-SM requires minimal user input and goes beyond state-of-the-art fragment-based approaches by selecting from multiple conformations per fragment via machine learning to simultaneously reflect the coarse-grained structure and the Boltzmann distribution. Additionally, we introduce a novel refinement step to connect individual fragments by optimizing specific bonds, angles, and dihedral angles in the backmapping process. We demonstrate that our algorithm accurately restores the atomistic bond length, angle, and dihedral angle distributions for various small and linear molecules from Martini coarse-grained beads and that the resulting high-resolution structures are representative of the input coarse-grained conformations. Moreover, the reconstruction of the TIP3P water model is fast and robust, and we demonstrate that ART-SM can be applied to larger linear molecules as well. To illustrate the efficiency of the local and autoregressive approach of ART-SM, we simulated a large realistic system containing the surfactants TAPB and SDS in solution using the Martini3 force field. The self-assembled micelles of various shapes were backmapped with ART-SM after training on only short atomistic simulations of a single water-solvated SDS or TAPB molecule. Together, these results indicate the potential for the method to be extended to more complex molecules such as lipids, proteins, macromolecules, and materials in the future.

Systematic Investigation of CYP3A4 Using Side-by-Side Comparisons of Apo, Active Site, and Allosteric-Bound States

Cytochrome P450 (CYP) 3A4 (CYP3A4) is a complex enzyme that metabolizes diverse substrates. It contains a large binding site accommodating diverse ligands, binding to active or allosteric sites. CYP3A4 does not always follow Michaelis-Menten kinetics. While Km reflects substrate affinity, it does not necessarily determine the enzyme's activity, though it is often considered indicative of substrate binding characteristics. The mechanism may be highly sophisticated and driven by multiple factors. This suggests that the ligand binding affinity alone may not explain the differential behavior of the enzyme conformational stability. Here, we analyzed sequence conserveness of 57 CYPs, followed by a detailed molecular dynamics simulation study (9 μs) on CYP3A4. We studied three CYP3A4 enzyme states (apo-state, active-site, and allosteric-site ligand-bound states) collected from the same experimental setup to reduce the systematic error. We found that the enzyme conformational stability followed a consistent trend of allosteric > active > apo states, which was inconsistent with the enzyme-ligand (active/allosteric) binding affinity and the ligand conformational stability. However, the heme group showed a significant protein affinity and stability pattern directly related to the enzyme stability, suggesting that the active/allosteric binding may work by influencing the heme-CYP3A4 binding affinity, and the allosteric ligand appeared to form the most stable enzyme state of the three studied states.

Bacopa monnieri phytochemicals as promising BACE1 inhibitors for Alzheimer's disease therapy

Alzheimer's disease (AD) remains a formidable challenge, necessitating the discovery of effective therapeutic agents targeting β-site amyloid precursor protein cleaving enzyme 1 (BACE1). This study investigates the inhibitory potential of phytochemicals derived from Bacopa monnieri, a plant renowned for its cognitive-enhancing properties, in comparison to established synthetic inhibitors such as Atabecestat, Lanabecestat, and Verubecestat. Utilizing molecular docking and advanced computational simulations, we demonstrate that Bacopaside I exhibits superior binding affinity and a unique interaction profile with BACE1, suggesting a more nuanced inhibitory mechanism. Our findings highlight the promising role of Bacopa monnieri phytochemicals as viable alternatives to synthetic drugs, emphasizing their potential to overcome limitations faced in clinical settings. Furthermore, the development of the SIMANA ( https://simana.streamlit.app/ ) platform enhances the visualization and analysis of protein-ligand interactions, facilitating a deeper understanding of the dynamics involved. This research not only underscores the therapeutic promise of natural compounds in AD treatment but also advocates for a paradigm shift towards integrating traditional medicinal knowledge into contemporary drug discovery efforts.

Small-Molecule FICD Inhibitors Suppress Endogenous and Pathologic FICD-Mediated Protein AMPylation

The AMP transferase, FICD, is an emerging drug target fine-tuning stress signaling in the endoplasmic reticulum (ER). FICD is a bifunctional enzyme, catalyzing both AMP addition (AMPylation) and removal (deAMPylation) from the ER-resident chaperone BiP/GRP78. Despite increasing evidence linking excessive BiP/GRP78 AMPylation to human diseases, small molecules that inhibit pathogenic FICD variants are lacking. Using an in vitro high-throughput screen, we identify two small-molecule FICD inhibitors, C22 and C73. Both molecules significantly inhibit FICD-mediated BiP/GRP78 AMPylation in intact cells while only weakly inhibiting BiP/GRP78 deAMPylation. C22 and C73 also inhibit pathogenic FICD variants and improve proinsulin processing in β cells. Our study identifies and validates FICD inhibitors, highlighting a novel therapeutic avenue against pathologic protein AMPylation.

Kinetic implications of IP6 anion binding on the molecular switch of HIV-1 capsid assembly

HIV-1 capsid (CA) proteins self-assemble into a fullerene-shaped CA, enabling cellular transport and nuclear entry of the viral genome. A structural switch comprising the Thr-Val-Gly- Gly (TVGG) motif either assumes a disordered coil or a 310 helix conformation to regulate hexamer or pentamer assembly, respectively. The cellular polyanion inositol hexakisphosphate (IP6) binds to a positively charged pore of CA capsomers rich in arginine and lysine residues mediated by electrostatic interactions. Both IP6 binding and TVGG coil-to-helix transition are essential for pentamer formation. However, the connection between IP6 binding and TVGG conformational switch remains unclear. Using extensive atomistic simulations, we show that IP6 imparts structural order at the central ring, which results in multiple kinetically controlled events leading to the coil-to-helix conformational change of the TVGG motif. IP6 facilitates the helix-to-coil transition by allowing the formation of intermediate conformations. Our results suggest a key kinetic role of IP6 in HIV-1 pentamer formation.

Structural dynamics of olfactory receptors: implications for odorant binding and activation mechanisms

Olfaction, an ancient and intricate process, profoundly shapes human innate responses yet remains relatively understudied compared to other sensory modalities. Olfactory receptors (ORs), members of the G protein-coupled receptor (GPCR) family, play a pivotal role in detecting and discriminating a vast array of odorants. This comprehensive study explores the functional roles of five diverse ORs: OR1A1, OR2W1, OR11A1, OR51E1 and OR51E2, through detailed investigations into the differences between their apo and odorant-bound forms. By examining key residues and mutations, the possible molecular mechanisms that underlie the modulation of binding landscapes and the consequent alterations in OR stability were elucidated. The findings revealed dynamic conformational changes in ORs upon odorant binding, characterized by hinging motions and tilting of transmembrane helices. Using residue interaction network analyses, critical residues involved in mediating interactions between ORs and odorants were uncovered, shedding light on the molecular determinants of olfactory perception. By examining changes in binding pocket volume and per-residue energy decomposition, the dynamic nature of OR activation and the influence of mutations on receptor stability and functionality was observed.

Discovery and Characterization of Novel Receptor-Interacting Protein Kinase 1 Inhibitors Using Deep Learning and Virtual Screening

Receptor-interacting protein kinase 1 (RIPK1) serves as a critical mediator of cell necroptosis and represents a promising therapeutic target for various human neurodegenerative diseases and inflammatory diseases. Nonetheless, the RIPK1 inhibitors currently reported are inadequate for clinical research due to suboptimal inhibitory activities or lack of selectivity. Consequently, there is a need for the discovery of novel RIPK1 kinase inhibitors. In this study, we integrated a deep learning model, specifically the fingerprint graph attention network (FP-GAT), with molecular docking-based virtual screening to identify potential RIPK1 inhibitors from a library comprising 13 million compounds. Out of 43 compounds procured, two compounds (designated as 24 and 41) demonstrated enzyme inhibition activity exceeding 50% at a concentration of 10 μM against RIPK1. The half-maximal inhibitory concentrations (IC50) for compounds 24 and 41 were determined to be 2.01 and 2.95 μM, respectively. Furthermore, these compounds exhibited protective effects in an HT-29 cell model of TSZ-induced necroptosis, with half-maximal effective concentrations (EC50) of 6.77 μM for compound 24 and 68.70 μM for compound 41. Finally, molecular dynamics simulations and binding free energy calculations were conducted to elucidate the molecular mechanism of compounds 24 and 41 binding to RIPK1. The results show that Met92, Met95, Ala155, and Asp156 are key residues for novel RIPK1 inhibitors. In summary, this work discovered two hit compounds targeting RIPK1, which can be further structurally modified to become promising lead compounds.

Impact of Ruxolitinib Interactions on JAK2 JH1 Domain Dynamics

Janus kinase 2 (JAK2) is an important intracellular mediator of cytokine signaling. Mutations in the JAK2 gene are associated with myeloproliferative neoplasms (MPNs) such as polycythemia vera (PV) and essential thrombocythemia (ET), while aberrant JAK2 activity is also associated with a number of immune diseases. The acquired somatic mutation JAK2 V617F (95% of cases of PV and in 55-60% of cases of ET), which constitutively activates the JAK2, is the most common molecular event in MPN. The development of specific JAK2 inhibitors is therefore of considerable clinical importance. Ruxolitinib is a JAK inhibitor recently approved by the FDA/EMA and effective in relieving symptoms in patients with MPN. Ruxolitinib binds to the JAK2 last domain, namely JH1; its action on the dynamics of the domain is still only partially known. Using Molecular Dynamics simulations, we have analyzed the JH1 domain in four different states as follows: (i) alone, (ii) with one phosphorylation, (iii) adding Ruxolitinib, and (iv) with five phosphorylations and Ruxolitinib. The ligand induces a dynamic behavior similar to the inactive form of JH1, with a less flexible state than the phosphorylated active form of JH1. This study highlights the inhibitory effect of Ruxolitinib on the JH1 domain, demonstrating the importance of dynamics in regulating JH1 activation.

Active Site Plasticity of the Bacterial Sliding Clamp

The rise of antibiotic resistance poses a severe global threat, specifically due to the emergence of multiresistant bacteria (ESKAPE pathogens), which are responsible for countless deaths globally. Consequently, the development of novel antibiotics is in dire need. Targeting proteins essential to DNA replication is a promising pathway, making the β-sliding clamp (β-SC) an attractive target. Currently, there are no antibiotics on the market that target the β-SC. However, numerous compounds are being investigated to create an antibiotic with high potency against a broad range of bacterial species. Interestingly, most proposed compounds do not bind to the entire active site, which may reduce their potential as high-potency inhibitors. This is due to the active site residue Met at position 362, adopting a "closed" conformation, preventing inhibitors access into Subsite II of the active site. This study explored the effect of key residues on the plasticity of the β-SC active site using molecular dynamics and metadynamics simulations under different physiological states. Our results show that the Met gate exhibits flexibility and both open and closed states are thermodynamically and kinetically accessible.

Effects of naphthoquinone scaffold-derived compounds on head and neck squamous cell carcinoma based on network pharmacology and molecular docking

OBJECTIVES

This study aimed to analyze the effects of naphthoquinone scaffold-derived compounds on head and neck squamous cell carcinoma (HNSCC) using network pharmacology and molecular docking.

METHODS

We screened candidate compounds from the ASINEX database and evaluated their drug likeness and toxicity. They identified 80 compounds with naphthalenone structures, focusing on 1,4-naphthoquinone and 1,2-naphthoquinone scaffolds. The possible targets of these compounds were predicted using databases like SwissTargetPrediction and Similarity Ensemble Approach Database (SEA).

RESULTS

The common targets between the compounds and HNSCC were identified, yielding 65 overlapping targets. A protein-protein interaction (PPI) network was constructed, and 20 hub genes were identified based on centrality metrics. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these compounds' protective effects against HNSCC are associated with cancer-related pathways, such as those in cancer and proteoglycans in cancer. Molecular docking was performed to evaluate the binding affinity between the compounds and hub genes. The results showed that the compounds had strong binding affinities with key targets like MET and TYK2, with binding energies < -5 kcal/mol.

CONCLUSIONS

The study suggests that naphthoquinone derivatives could serve as novel chemotherapy agents for HNSCC, warranting further research for clinical application.

MGAT1-Guided complex N-Glycans on CD73 regulate immune evasion in triple-negative breast cancer

Despite the widespread application of immunotherapy, treating immune-cold tumors remains a significant challenge in cancer therapy. Using multiomic spatial analyses and experimental validation, we identify MGAT1, a glycosyltransferase, as a pivotal factor governing tumor immune response. Overexpression of MGAT1 leads to immune evasion due to aberrant elevation of CD73 membrane translocation, which suppresses CD8+ T cell function, especially in immune-cold triple-negative breast cancer (TNBC). Mechanistically, addition of N-acetylglucosamine to CD73 by MGAT1 enables the CD73 dimerization necessary for CD73 loading onto VAMP3, ensuring membrane fusion. We further show that THBS1 is an upstream etiological factor orchestrating the MGAT1-CD73-VAMP3-adenosine axis in suppressing CD8+ T cell antitumor activity. Spatial transcriptomic profiling reveals spatially resolved features of interacting malignant and immune cells pertaining to expression levels of MGAT1 and CD73. In preclinical models of TNBC, W-GTF01, an inhibitor specifically blocked the MGAT1-catalyzed CD73 glycosylation, sensitizing refractory tumors to anti-PD-L1 therapy via restoring capacity to elicit a CD8+ IFNγ-producing T cell response. Collectively, our findings uncover a strategy for targeting the immunosuppressive molecule CD73 by inhibiting MGAT1.

Protonation Effects in Protein-Ligand Complexes - A Case Study of Endothiapepsin and Pepstatin A with Computational and Experimental Methods

Protonation states serve as an essential molecular recognition motif for biological processes. Their correct consideration is key to successful drug design campaigns, since chemoinformatic tools usually deal with default protonation states of ligands and proteins and miss atypical protonation states. The protonation pattern for the Endothiapepsin/PepstatinA (EP/pepA) complex is investigated using different dry lab and wet lab techniques. ITC experiments revealed an uptake of more than one mole of protons upon pepA binding to EP. Since these experiments were performed at physiological conditions (and not at pH=4.6 at which a large variety of crystal structures is available), a novel crystal structure at pH=7.6 was determined. This crystal structure showed that only modest structural changes occur upon increasing the pH value. This lead to computational studies Poisson-Boltzmann calculations and constant pH MD simulation to reveal the exact location of the protonation event. Both computational studies could reveal a significant pKa shift resulting in non-default protonation state and that the catalytic dyad is responsible for the uptake of protons. This study shows that assessing protonation states for two separate systems (protein and ligand) might result in the incorrect assignment of protonation states and hence incorrect calculation of binding energy.

Understanding the structural basis of ALS mutations associated with resistance to sulfonylurea in wheat

Developing herbicide-tolerant wheat varieties is highly desirable for effective weed management and improved crop yield. The enzyme acetolactate synthase (ALS) is the target enzyme for the sulfonylurea class of herbicides. The structural analysis of mutable sites in ALS is crucial for the generation of herbicide-resistant crops. Previous studies indicated that mutant lines of Triticum aestivum ALS (TaALS) with amino acid substitutions at P174, G631, and G632 residues provided resistance to sulfonylurea herbicide, nicosulfuron. The present study aimed to provide structural insights into mutable residues causing sulfonylurea herbicide resistance to TaALS enzyme through in-silico molecular docking and simulation approaches. The molecular docking analysis suggested a single point mutation at TaALS-P174S, its double mutant conformations (TaALS-G632S/P174S and TaALS-G631D/G632S) and associated triple mutant conformation (TaALS-G631D/G632S/P174S) to have the lowest binding affinity with nicosulfuron than the wild-type conformation of TaALS. Furthermore, the molecular dynamic simulation study confirms the weakest and more stable binding of the triple mutant conformation with nicosulfuron. Our computational study identifies a triple mutant conformation (TaALS-G631D/G632S/P174S) to be more effective in developing sulfonylurea herbicide-resistant wheat crops.

Enhanced sampling simulations to explore himalayan phytochemicals as potential phosphodiesterase-1 inhibitor for neurological disorders

The rising incidence of neurological and neuropsychiatric disorders underscores the urgent need for innovative and evidence based treatment strategies. Phosphodiesterase-1 (PDE1) is a dual-substrate (cAMP/cGMP) phosphodiesterase expressed in the central nervous system and peripheral areas, which modulates cyclic nucleotide signaling cascades. Inhibiting PDE1 enhances cAMP/cGMP levels, promoting neuronal plasticity and neuroprotection, making it a promising therapeutic strategy for neurological disorders. The pursuit of targeting this enzyme for treating neurological and neuropsychiatric disorders has faced obstacles due to the absence of potent, selective, and brain-penetrating inhibitors. This study aimed to identify potent PDE1 inhibitors by leveraging a diverse collection of bioactive molecules derived from Himalayan flora through computational screening methods. The four most promising hit molecules were chosen for further investigation and subjected to Molecular Dynamics (MD) simulations, binding free energy calculations, along with standard molecules. It was found that the hit molecules stigmast-7, corilagin and emblicanin-A had formed the most stable complexes, and also, the least binding free energy was observed for stigmast-7 among the hit molecules. Additionally, the pulling simulations indicated that stigmast-7 and corilagin were the most robust binders, and required the highest force to dissociate from the binding cavity completely. The umbrella sampling simulations also revealed the lowest binding free energy for corilagin and stigmast-7. The insights gained from this study provide a foundation for future research into PDE1-targeted therapies, highlighting the potential of Himalayan bioactive compounds in developing novel therapeutic interventions.

Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor

A diverse set of modulators, including stimulants and anesthetics, regulates ion channel function in our nervous system. However, structures of ligand-bound complexes can be difficult to capture by experimental methods, particularly when binding is dynamic. Here, we used computational methods and electrophysiology to identify a possible bound state of a modulatory stimulant derivative in a cryptic vestibular pocket of a mammalian serotonin-3 receptor. We first applied a molecular dynamics simulation-based goal-oriented adaptive sampling method to identify possible open-pocket conformations, followed by Boltzmann docking that combines traditional docking with Markov state modeling. Clustering and analysis of stability and accessibility of docked poses supported a preferred binding site; we further validated this site by mutagenesis and electrophysiology, suggesting a mechanism of potentiation by stabilizing intersubunit contacts. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, psychiatric, and gastrointestinal diseases, characterizing relatively unexplored modulatory sites such as these could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.

Unveiling polyphenol-protein interactions: a comprehensive computational analysis

Our study investigates polyphenol-protein interactions, analyzing their structural diversity and dynamic behavior. Analysis of the entire Protein Data Bank reveals diverse polyphenolic structures, engaging in various noncovalent interactions with proteins. Interactions observed across crystal structures among diverse polyphenolic classes reveal similarities, underscoring consistent patterns across a spectrum of structural motifs. On the other hand, molecular dynamics (MD) simulations of polyphenol-protein complexes unveil dynamic binding patterns, highlighting the influx of water molecules into the binding site and underscoring limitations of static crystal structures. Water-mediated interactions emerge as crucial in polyphenol-protein binding, leading to variable binding patterns observed in MD simulations. Comparison of high- and low-resolution crystal structures as starting points for MD simulations demonstrates their robustness, exhibiting consistent dynamics regardless of the quality of the initial structural data. Additionally, the impact of glycosylation on polyphenol binding is explored, revealing its role in modulating interactions with proteins. In contrast to synthetic drugs, polyphenol binding seems to exhibit heightened flexibility, driven by dynamic water-mediated interactions, which may also facilitate their promiscuous binding. Comprehensive dynamic studies are, therefore essential to understand polyphenol-protein recognition mechanisms. Overall, our study provides novel insights into polyphenol-protein interactions, informing future research for harnessing polyphenolic therapeutic potential through rational drug design.Scientific contribution: In this study, we present an analysis of (natural) polyphenol-protein binding conformations, leveraging the entirety of the Protein Data Bank structural data on polyphenols, while extending the binding conformation sampling through molecular dynamics simulations. For the first time, we introduce experimentally supported large-scale systematization of polyphenol binding patterns. Moreover, our insight into the significance of explicit water molecules and hydrogen-bond bridging rationalizes the polyphenol promiscuity paradigm, advocating for a deeper understanding of polyphenol recognition mechanisms crucial for informed natural compound-based drug design.

Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike

The spike protein is essential to the SARS-CoV-2 virus life cycle, facilitating virus entry and mediating viral-host membrane fusion. The spike contains a fatty acid (FA) binding site between every two neighbouring receptor-binding domains. This site is coupled to key regions in the protein, but the impact of glycans on these allosteric effects has not been investigated. Using dynamical nonequilibrium molecular dynamics (D-NEMD) simulations, we explore the allosteric effects of the FA site in the fully glycosylated spike of the SARS-CoV-2 ancestral variant. Our results identify the allosteric networks connecting the FA site to functionally important regions in the protein, including the receptor-binding motif, an antigenic supersite in the N-terminal domain, the fusion peptide region, and another allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected link between different allosteric sites. Comparison of the FA site connections from D-NEMD in the glycosylated and non-glycosylated spike revealed that glycans do not qualitatively change the internal allosteric pathways but can facilitate the transmission of the structural changes within and between subunits.

Structure-Based Optimization of TBK1 Inhibitors

TBK1 is a crucial kinase involved in immunity, inflammation, and autophagy with dysregulation linked to various diseases, making it a potential therapeutic target. In this study, we applied a structure-based lead optimization approach to design potent and selective TBK1 inhibitors. A focused virtual library containing over 5,000 compounds was constructed, sampled, and refined within the kinase binding site, followed by a 10 ns molecular dynamics simulation for each modeled binding complex. Based on MM/PBSA binding free energies and structural clustering, we selected 14 structurally diverse compounds for chemical synthesis and biological assays. This strategy yielded a potent TBK1 inhibitor (IC50 = 775 pM) from an initial hit of 19.57 μM. This inhibitor features a novel scaffold and exhibits excellent enzymatic inhibition. Furthermore, it enhances immune-mediated cytotoxicity without exhibiting cytotoxicity when used as a single agent. These findings provide a foundation for the development of targeted therapies for the treatment of TBK1-associated diseases.

Meta-analysis and review of in silico methods in drug discovery - part 1: technological evolution and trends from big data to chemical space

This review offers an overview of advanced in silico methods crucial for drug discovery, emphasizing their integration with data science, and investigates the effectiveness of data science, machine learning, and artificial intelligence via a thorough meta-analysis of existing technologies. This meta-analysis aims to rank these technologies based on their applications and accessibility of knowledge. Initially, a search strategy yielded 900 papers, which were then refined into two subsets: the top 300 most-cited papers since 2000 and papers selected for systematic review based on high impact. From these, 97 articles were identified for discussion, categorized by their influence on society. The focus remains on the qualitative impact of these disciplines rather than solely on metrics like new drug approvals. Ultimately, the review underscores the role of big data in enhancing our comprehension of drug candidate trajectories from development to commercialization, utilizing information stored in publicly available databases to chemical space. Graphical extrapolation of some keywords (Drug Discovery; Big Data; Database; Metadata) discussed in this article and their evolution (in terms of absolute items that are available) by time.

QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials

Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we validate relative binding free energy (RBFE) accuracy using neural network potentials (NNPs) for the ligands. We utilize a novel NNP model, AceFF 1.0, based on the TensorNet architecture for small molecules that broadens the applicability to diverse drug-like compounds, including all important chemical elements and supporting charged molecules. Using established benchmarks, we show overall improved accuracy and correlation in binding affinity predictions compared with GAFF2 for molecular mechanics and ANI2-x for NNPs. Slightly less accuracy but comparable correlations with OPLS4. We also show that we can run the NNP simulations at 2 fs time step, at least two times larger than previous NNP models, providing significant speed gains. The results show promise for further evolutions of free energy calculations using NNPs while demonstrating its practical use already with the current generation. The code and NNP model are publicly available for research use.

Controlling the Morphology and Orientation of the Helical Self-Assembly of Pyrazine Derivatives by Tuning Hydration Shells

A combination of density functional theory (DFT) and classical molecular dynamics simulations is performed to unveil the guiding force in the self-assembly process of the pyrazine-based biopolymers to helical nanostructures. The highlight of the study shows the decisive role of the solvent-ligand H-bonding and the inter-molecular pi-pi stacking not only ensures the unidirectional packing of the helical structure but also the rotation of left-handed to the right-handed helical structure of the molecule. This transition is supported by the bulk release of the "ordered" water molecules. The extent of this bonding can be tuned by the temperature, concentration, and type of the metal ions. Smaller ions like Na+ and Al3+ destroy the structure, whereas bigger ions like Zn2+, Ni2+, and Au3+ preserve and rotate the structure according to their concentration. The interaction energy between the pyrazine derivatives is found to be high (-9000 kJ mol-1) for right-handed rotation of the helix, which increases further with the addition of D-histidine, forming a superhelical structure (-10300 kJ mol-1). The insights gained from this work can be used to generate nanostructures of desired morphology.

Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis

N49P9.6-FR-LS and PGT121 are promising antibodies with significant therapeutic potential against HIV infection, but they are prone to precipitation at concentrations greater than 12 to 13 mg/mL. This study evaluates the influence of six excipients─arginine, alanine, sucrose, trehalose, methionine, and glutamate─on the biophysical stability of antibodies. We employed a comprehensive approach, combining computational mAb-excipient interaction analysis via the site-identification by ligand competitive saturation (SILCS) method with extensive experimental characterization. Our experimental matrix included viscosity measurements across temperature gradients, particle size distribution, zeta potential, pH value, and solution appearance, alongside a short-term stability product study at 30 °C and 65% relative humidity, with assessments at t0 (initial), t1 (14 days), and t2 (28 days). Results indicated that sucrose, arginine, alanine, and trehalose provided varying degrees of stabilization for both antibodies. Conversely, glutamate destabilized PGT121 but stabilized N49P9.6-FR-LS, while methionine had a negative effect on N49P9.6-FR-LS but a positive one on PGT121. SILCS-Biologics analysis suggested that stabilization by these excipients is linked to their ability to occupy regions involved in self-protein interactions. Debye-Hückel-Henry charge calculations further indicated that neutral excipients like sucrose and trehalose could alter mAb charges by affecting buffer binding, influencing aggregation propensity. These findings offer valuable insights for optimizing antibody formulations, ensuring enhanced product stability and therapeutic efficacy for HIV treatment.

Determining the effect of natural compounds on mutations of pyrazinamidase in multidrug-resistant tuberculosis: Illuminating the dark tunnel

Mycobacterium tuberculosis (MTB), the pathogen responsible for tuberculosis (TB), remains a significant global health concern, especially with the growing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. This study focuses on understanding the molecular basis of pyrazinamide (PZA) resistance, particularly mutations in the pyrazinamidase (Pzase) enzyme, including D8G, H71R, K96T, and S104R. We used computational methods to explore the effects of bioactive compounds on these PZA-resistant mutations. The structures of wild-type (WT) Pzase and its mutant variants were prepared, and molecular docking simulations were carried out using the CDOCKER protocol to assess potential binding interactions. To evaluate the stability of these interactions, we performed 0.5 μs molecular dynamics (MD) simulations followed by MM-PBSA analysis to calculate the binding free energies. Our results showed that garcinone D and neodiospyrin had stronger binding affinities than the reference molecule, pyrazinoic acid (POA), across both WT and mutant forms of Pzase. These compounds demonstrated lower Root Mean Square Deviation (RMSD) and radius of gyration (Rg) values, suggesting more stable binding interactions. Further validation through steered molecular dynamics (SMD) simulations indicated that garcinone D and neodiospyrin required significantly higher pulling forces to dissociate from the binding site compared to POA. Additionally, umbrella sampling simulations revealed more negative binding free energies for these two compounds, reinforcing their strong interaction with Pzase. These findings position garcinone D and neodiospyrin as promising candidates for the development of new treatments for MDR-TB and XDR-TB, offering a potential strategy to combat drug-resistant TB. This study provides valuable insights into the binding mechanisms and stability of these compounds, advancing the search for novel anti-TB therapies.

Multiscale Simulations and Profiling of Human Thymidine Phosphorylase Mutations: Insights into Structural, Dynamics, and Functional Impacts in Mitochondrial Neurogastrointestinal Encephalopathy

Mitochondrial neurogastrointestinal encephalopathy (MNGIE) is a rare metabolic disorder caused by missense mutations in the TYMP gene, leading to the loss of human thymidine phosphorylase (HTP) activity and subsequent mitochondrial dysfunction. Despite its well-characterized biochemical basis, the molecular mechanisms by which MNGIE-associated mutations alter HTP's structural stability, dynamics, and substrate (thymidine) binding remain unclear. In this study, we employ a multiscale computational approach, integrating AlphaFold2-based structural modeling, all-atom and coarse-grained molecular dynamics (MD) simulations, protein-ligand (HTP-thymidine) docking, HTP-thymidine complex simulations, binding free-energy landscape analysis, and systematic mutational profiling to investigate the impact of key MNGIE-associated mutations (R44Q, G145R, G153S, K222S, and E289A) on HTP function. Analyses of our long-duration multiscale simulations (comprising 9 μs coarse-grained, 1.2 μs all-atom apo HTP, and 1.2 μs HTP-thymidine complex MD simulations) and physicochemical properties reveal that while wild-type HTP maintains structural integrity and strong thymidine-binding affinity, MNGIE-associated mutations induce substantial destabilization, increased flexibility, and reduced enzymatic efficiency. Free-energy landscape analysis highlights a shift toward less stable conformational states in mutant HTPs, further supporting their functional impairment. Additionally, the G145R mutation introduces steric hindrance at the active site, preventing thymidine binding and causing off-site interactions. These findings not only provide fundamental insights into the physicochemical and dynamic alterations underlying HTP dysfunction in MNGIE but also establish a computational framework for guiding future experimental studies and the rational design of therapeutic interventions aimed at restoring HTP function.

An intramolecular FRET biosensor for the detection of SARS-CoV-2 in biological fluids

The development of a FRET-based sensor for detecting the Spike surface antigen of SARS-CoV-2 in biological fluids is described here, exploiting the fluorescence properties of Green Fluorescent Protein (GFP). Our design strategy combines experimental and molecular modeling and simulations to build a smart modular architecture, allowing for future optimization and versatile applications. The prototype structure incorporates two reporter elements at the N-terminus and C-terminus, with two interaction elements mediating their separation. This design supports two fluorescence measurement methods: direct measurement and the molecular beacon approach. The former detects changes in GFP fluorescence intensity due to interactions with the Spike protein, while the latter involves an organic quencher that restores GFP fluorescence upon Spike protein binding. In silico design of linkers, using molecular dynamics (MD) simulations, ensured optimal flexibility and stability. The AAASSGGGASGAGG linker was selected for its balance between flexibility and stability, while the LEAPAPA linker was chosen for its minimal structural impact on the interaction elements. Fluorophores' behavior was analyzed, showing stable FRET efficiency, essential for reliable detection. Quenching efficiency calculations, based on Förster energy transfer theory, validated the sensor's sensitivity. Further, MD simulations assessed GFP stability, confirming minimal unfolding tendencies, which explains the sensor functioning mechanism. The sensor was successfully produced in E. coli, and functional validation demonstrated its ability to detect the Spike protein, with fluorescence recovery proportional to protein concentration, while the modular computer aided design allowed for sensitivity optimization. The developed biosensor prototype offers a promising tool for rapid and precise viral detection in clinical settings.

Impact of a Terahertz electromagnetic field on the ion permeation of potassium and sodium channels

Ion channels are essential for various physiological processes, and their defects are associated with many diseases. Previous research has revealed that a Terahertz electromagnetic field can alter the channel conductance by affecting the motion of chemical groups of ion channels, and hence regulate the electric signals of neurons. In this study, we conducted molecular dynamics simulations to systematically investigate the effects of terahertz electromagnetic fields on the ion permeation of voltage-gated potassium and sodium channels, particularly focusing on the bound ions in the selectivity filters that have not been extensively studied previously. Our results identified multiple new characteristic frequencies and showed that 1.4, 2.2, or 2.9 THz field increases the ion permeability of Kv1.2, and 2.5 or 48.6 THz field increases the ion permeability of Nav1.5. Such effects are specific to the frequencies and directions of the electric field, which are determined by the intrinsic oscillation motions of the permeating ions in the selectivity filter or certain chemical groups of the ion channels. The amplitude of the THz field positively correlates with the change in ion permeation. This study demonstrates that THz fields can specifically regulate ion channel conductances by multiple mechanisms, which may carry great potential in biomedical applications.

Unraveling the impact of binary vs. ternary alcohol solutions on the conformation and solvation of the SARS-CoV-2 receptor-binding domain

The use of alcohol as hand sanitizer to prevent the spread of contamination of SARS-CoV-2 is known. In this work, a series of atomistic molecular dynamics (MD) simulations were carried out with the receptor-binding-domain (RBD) of SARS-CoV-2 in different aqueous binary and ternary mixtures of concentrated ethanol, n-propanol (n-pr), and iso-propanol (iso-pr) solutions to elucidate the structural alteration of RBD at ambient and elevated temperature and to understand RBD's interactions with the host cellular receptor ACE2. Computation of several structural metrics like RMSD, Rg, and fraction of native contacts along with the construction of a 2D-free energy landscape suggests that among all the water-alcohol(s) solutions, the structural transition of RBD conformation was more pronounced in the water-etoh-iso-pr mixture under ambient conditions which further altered significantly and RBD adopted partially unfolded states at 350 K, as compared to the native form. We observed that the preferential exclusion of different alcohols from the RBD surface regulates the solvation features of RBD and hence the RBD-alcohol hydrogen bonds, which is one of the crucial factors that rupture RBD's structure heterogeneously. From the comparative study, it was inferred that relative to binary mixtures, the ternary solutions rupture the native RBD structure more effectively which was caused by the relative reduction in dynamics in the ternary mixture for the particular pair of hydrogen bonds arising from the hindered rotation of certain alcohol molecules. Our microscopic investigation identified that the specific binding zone was disrupted remarkably, and as a result, the contact distances between the deformed binding zone of RBD and ACE2 were found to increase from the molecular docking study; this could prevent further transmission.

PCDTBT: Force Field Parameterization and Properties by Molecular Dynamics Simulation

Conjugated polymers are indispensable building blocks in a variety of organic electronics applications such as solar cells, light-emitting diodes, and field-effect transistors. Poly[N-9'-heptadecanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT) is a carbazole-benzothiadiazole-based copolymer with a donor-acceptor structure, consisting of electron-donating and electron-withdrawing subunits and featuring a low band gap. In this work, the General Amber Force Field is extended in two ways, specifically for modeling PCDTBT. First, a set of partial atomic charges is derived that mimic a long chain and adequately describe different conformations that may be encountered in a bulk environment. Second, torsional terms are reparametrized for all dihedral angles in the backbone via ab initio computations. Subsequently, a series of large-scale Molecular Dynamics simulations are employed to construct and equilibrate bulk ensembles of three PCDTBT oligomers using different starting conformations of the oligomer chains. Several structural properties are computed, namely mass density, chain stiffness (through persistence length and Kuhn segment length), and glass transition temperature. Our results are in good agreement with available literature data, demonstrating the suitability of the new parametrization.

Design of CoQ10 crops based on evolutionary history

Coenzyme Q (CoQ) is essential for energy production by mitochondrial respiration, and it is a supplement most often used to promote cardiovascular health. Humans make CoQ10, but cereals and some vegetable/fruit crops synthesize CoQ9 with a side chain of nine isoprene units. Engineering CoQ10 production in crops would benefit human health, but this is hindered by the fact that the specific residues of the enzyme Coq1 that control chain length are unknown. Based on an extensive investigation of the distribution of CoQ9 and CoQ10 in land plants and the associated Coq1 sequence variation, we identified key amino acid changes at the base of the Coq1 catalytic pocket that occurred independently in multiple angiosperm lineages and repeatedly drove CoQ9 formation. Guided by this knowledge, we used gene editing to modify the native Coq1 genes of rice and wheat to produce CoQ10, paving the way for developing additional dietary sources of CoQ10.

Optimizing Polyethylene Glycol Coating for Stealth Nanodiamonds

Nanodiamonds (NDs) have emerged as potential candidates for versatile platforms in nanomedicine, offering unique properties that enhance their utility in drug delivery, imaging, and therapeutic applications. To improve their biocompatibility and nanomedical applicability, NDs are coated with organic polymer chains, such as poly(ethylene glycol) (PEG), which are well known to prolong their blood-circulating lifetime by reducing the surface adsorption of serum proteins. Theoretical simulations are useful tools to define, at the atomic level, the optimal parameters that guide the presentation of the coating chains in the biological environment and the interaction of coated NDs with proteins. In this work, we perform atomistic molecular dynamics (MD) simulations of several PEGylated spherical ND models immersed in a realistic physiological medium. In particular, we evaluate the effect of the polymer chain's terminal group, length, grafting density, and the ND core dimension on both the structural properties of the PEG coating and the interaction of the nanoconjugates with the aqueous phase. Moreover, we investigate the role played by the chemical nature of the core material through a comparative analysis with a PEGylated spherical titanium dioxide (TiO2) nanoparticle (NP). Among all the parameters evaluated, we find that the PEG grafting density, the PEG chain length, and the NP core material are key factors in determining the dynamic behavior of PEGylated nanosystems in solution, whereas the PEG terminal group and the ND dimension only play a marginal role. These factors can be strategically adjusted to identify the optimal conditions for enhanced clinical performance. Finally, we prove that the PEG coating prevents the aggregation of two ND particles. We believe that this computational study will provide valuable insights to the experimental community, supporting the rational design of polymer-coated inorganic NPs for more efficient nanomedical applications.

Synergistic reduction in interfacial flexibility of TREM2R47H and ApoE4 may underlie AD pathology

BACKGROUND

The strongest genetic drivers of late-onset Alzheimer's disease (AD) are apolipoprotein E4 (ApoE4) and TREM2R47H. Despite their critical roles, the mechanisms underlying their interactions remain poorly understood.

METHODS

We conducted microsecond-long molecular dynamics simulations of TREM2-ApoE complexes, including TREM2R47H, validating our findings through comparison with published experimental data on TREM2-ApoE binding interactions.

RESULTS

Our simulations reveal TREM2WT can sample an "open" CDR2 conformation, challenging the prevailing notion that this conformation is pathogenic. TREM2WT exhibits greater flexibility, accessing diverse CDR2 conformations, while rigidity in TREM2R47H's CDR2 may explain its reduced ligand-binding properties. ApoE2 facilitates dynamic reconfiguration of TREM2-ApoE2 complexes, which is absent with ApoE4. TREM2R47H and ApoE4 mutually rigidify each other, suppressing interfacial flexibility.

DISCUSSION

Our findings suggest mechanisms underlying ApoE2's neuroprotective functions, ApoE4's pathogenicity, and the synergistic effects of ApoE4 and TREM2R47H in AD. TREM2WT's flexibility and reconfiguration with ApoE2 may support microglial activation, while rigidity in TREM2R47H-ApoE4 interactions may drive pathogenic signaling.

HIGHLIGHTS

TREM2WT samples diverse CDR2 conformations, challenging prior assumptions that an "open" CDR2 state is solely pathogenic. ApoE2 promotes dynamic reconfiguration of TREM2-ApoE2 complexes, preserving TREM2WT's flexibility. ApoE4's hinge forms a unique binding pocket that enhances TREM2 binding. The TREM2R47H-ApoE4 complex exhibits mutual rigidity, suppressing CDR2 and hinge flexibility.

Exploring antibiofilm potential of some new imidazole analogs against C. albicans: synthesis, antifungal activity, molecular docking and molecular dynamics studies

A series of 1, 2, 4, 5-tetrasubstituted imidazole derivatives were synthesized and their antibiofilm potential against Candida albicans was evaluated in vitro. Two of the synthesized derivatives 5e (IC50 = 25 µg/mL) and 5m (IC50 = 6 µg/mL),displayed better antifungal and antibiofilm potential than the standard drug Fluconazole (IC50 = 40 µg/mL) against C. albicans. Based on the in vitro results, we escalated the real time polymerase chain reaction (RT-PCR) analysis to gain knowledge of the enzymes expressed in the generation and maintenance of biofilms and the mechanism of biofilm inhibition by the synthesized analogues. We then investigated the possible interactions of the synthesized compounds in inhibiting agglutinin-like proteins, namely Als3, Als4 and Als6 were prominently down-regulated using in-silico molecular docking analysis against the previously available crystal structure of Als3 and constructed structure of Als4 and Als6 using the SWISS-MODEL server. The stability and energy of the agglutinin-like proteins-ligand complexes were evaluated using molecular dynamics simulations (MDS). According to the 100 ns MDS, all the compounds remained stable, formed a maximum of 3, and on average 2 hydrogen bonds, and Gibb's free energy landscape analysis suggested greater affinity of the compounds 5e and 5m toward Als4 protein.

Binding of Selected Ligands to Human Protein Disulfide Isomerase and Microsomal Triglyceride Transfer Protein Complex and the Associated Conformational Changes: A Computational Molecular Modelling Study

Human protein disulfide isomerase (PDI) is a multifunctional protein, and also serves as the β subunit of the human microsomal triglyceride transfer protein (MTP) complex, a lipid transfer machinery. Dysfunction of the MTP complex is associated with certain disease conditions such as abetalipoproteinemia and cardiovascular diseases. It is known that the functions of PDI or the MTP complex can be regulated by the binding of a small-molecule ligand to either of these two proteins. In the present study, the conformational changes of the MTP complex upon the binding of three selected small-molecule ligands (17β-estradiol, lomitapide and a phospholipid) are investigated based on the available biochemical and structural information by using the protein-ligand docking method and molecular dynamics (MD) simulation. The ligand-binding sites, the binding poses and binding strengths, the key binding site residues, and the ligand binding-induced conformational changes in the MTP complex are analyzed based on the MD trajectories. The open-to-closed or closed-to-open transitions of PDI is found to occur in both reduced and oxidized states of PDI and also independent of the presence or absence of small-molecule ligands. It is predicted that lomitapide and 1,2-diacyl-sn-glycero-3-phosphocholine (a phospholipid) can bind inside the lipid-binding pocket in the MTP complex with high affinities, whereas 17β-estradiol interacts with the lipid-binding pocket in addition to its binding to the interface region of the MTP complex. Additionally, lomitapide can bind to the b' domain of PDI as reported earlier for E2. Key residues for the ligand-binding interactions are identified in this study. It will be of interest to further explore whether the binding of small molecules can facilitate the conformational transitions of PDI in the future. The molecular and structural insights gained from the present work are of value for understanding some of the important biological functions of PDI and the MTP complex.

Identification of novel inhibitors for epidermal growth factor receptor tyrosine kinase using absolute binding free-energy simulations

Mutations in the kinase domain of the epidermal growth factor receptor (EGFR), a critical biological macromolecule involved in cell growth and division, can lead to drug resistance in patients undergoing chemotherapy with kinase inhibitors. Notably, the emergence of the C797S mutation poses new challenges for targeted EGFR therapy, highlighting the urgent need for agents effective against this triple mutation (L858R/T790M/C797S, EGFR™). Building on our previous finding that sulfonyl and piperidinyl groups significantly contribute to the EGFR™-inhibitor interactions, we have identified the best-in-class inhibitors containing these groups through functional-group-based screening and formally exact absolute binding free-energy calculations. Our new strategy offers greater flexibility than traditional workflows leaning on relative binding free-energy calculations and accommodates ligands with substantial structural variations. The result shows that the top candidate exhibits a binding affinity of -15.8 kcal/mol towards the EGFR™ mutant, surpassing BLU-945, a state-of-the-art fourth-generation inhibitor with a binding free energy of -12.6 kcal/mol. Subsequent free-energy decomposition indicates that the presented top candidate primarily enhances interactions with the K745, D800 and R841 residues, suggesting its potential to overcome resistance from the C797S mutation. Notably, K745 forms highly favorable hydrogen bonds and cation-π interactions with C6. Targeting lysine has emerged as a promising strategy, especially in cases where the C797S mutation renders traditional covalent inhibitors ineffective. We propose that these novel inhibitors represent promising drug candidates for non-small cell lung cancer treatment and offer new strategies to overcome drug resistance caused by EGFR mutation.

Bioactive structures for inhibitors of Candida auris polymerase enzyme by artificial intelligence

AIMS

Present new bioactive compounds, created by De novo Drug Design and artificial intelligence (AI), as possible inhibitors of C. auris polymerase.

MATERIALS & METHODS

MolAICal's AI module was configured to identify FDA-approved molecular fragments with therapeutic effectiveness against C. auris polymerase, where the model with optimized synthetic accessibility and structural complexity was subjected to docking and molecular dynamics simulations and pharmacokinetic prediction.

RESULTS

Among 1,722 new forms, the Hit-960 compound stood out for its high bioaffinity and stability, with a binding energy of -9.12 kcal/mol and 75% synthetic accessibility.

CONCLUSIONS

Clinical studies are recommended to test its efficacy, contributing to the development of new treatments for C. auris infections.

Linear Antimicrobial Peptide, Containing a Diindolyl Methane Unnatural Amino Acid, Potentiates Gentamicin Against Methicillin-Resistant Staphylococcus aureus

The headway for the management of emerging resistant microbial strains has become a demanding task. Over the years, antimicrobial peptides (AMP), have been recognized and explored for their highly systematized SAR and antibacterial properties. With this background, we have reported a new class of AMPs. These peptides incorporate an unnatural amino acid, with a motivation from cruciferous bioactive phytochemical bisindoles methane derivatives with highly selective antimicrobial action. These peptides may also be considered as linear derivatives of hirsutide isolated from entomopathogenic fungus. The synthesized peptides were tested for their antimicrobial activity against an ESKAPE pathogen panel, where peptide 3 exhibited equipotent MIC and potent synergistic action along with gentamicin against Staphylococcus aureus and Enterococcus clinical isolates. This combination was also able to repotentiate gentamicin against NRS119, a gentamicin-resistant MRSA. Molecular dynamics study and free energy calculations provided insights to membrane disruptive properties of AMP action, which assisted gentamicin pass through the lipid-water interface.

Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections

The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.