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

Self-assembly of differently charged trimesic based lithocholic amphiphiles and their assessment on antimicrobial and biostimulant properties

Biosurfactant based biostimulants plays a vital role in agriculture filed by enhancing the soil quality, promote plant growth, and eliminate plant pathogens, and increasing nutrient uptake. This manuscript describes the synthesis of trimesic based lithocholic ester functionalized amphiphiles (TMLCEA) with oppositely charged head groups using thiol-yne click chemistry, which is an effective and simple approach. The trimesic based lithocholic ester functionalized zwitterionic penicillamine (TMLCEPA), cationic cysteamine·HCl (TMLCECy), and anionic thiomalic acid (TMLCETM) exhibited hierarchically self-assembled microstructures from below to above the CMC. In below the CMC, TMLCEPA, TMLCECy, and TMLCETM showed a bundle of petals, flower-like morphology, and grass seed-like patterns respectively. The morphology of self-assembly was studied by FE-SEM, DLS, OPM, contact angle, and zeta potential measurements. Among these amphiphiles, TMLCECy exhibited potential antimicrobial activity at above the CMC. The biostimulant effect of different concentration of TMLCEA treated with maize and green gram seeds were evaluated under in vitro condition, wherein TMLCECy showed improved seed germination and seedling parameters at 750 µL/mL as compared to TMLCEPA, TMLCETM and untreated amphiphiles as control. Molecular docking and molecular dynamic simulations show that TMLCEPA and TMLCETM showed higher binding affinity for dengue methyltransferase protein. The result of the present study opens up new avenues for bile acid-based amphiphiles as bio-based and cost-effective biostimulants for sustainable agriculture.

On-the-fly resolution enhancement in X-ray protein crystallography using electric field

X-ray crystallography has tremendously served structural biology by routinely providing high-resolution 3D structures of macromolecules. The extent of information encoded in the X-ray crystallography is proportional to which resolution the crystals diffract and the structure can be refined to. Therefore, there is a continuous effort to obtain high-quality crystals, especially for those proteins, which are considered difficult to crystallize into high-quality protein crystals of suitable sizes for X-ray crystallography. Efforts in enhancing the resolution in X-ray crystallography have also been made by optimizing crystallization protocols using external stimuli such as an electric field and magnetic field during the crystallization. Here, we present the feasibility of on-the-fly post-crystallization resolution enhancement of the protein crystal diffraction by applying a high-voltage electric field. The electric field between 2 and 11 kV/cm, which was applied after mounting the crystals in the beamline, resulted in the enhancement of the resolution. The crystal diffraction quality improved progressively with the exposure time. Moreover, we also find that upto defined electric field threshold, the protein structure remains largely unperturbed, a conclusion further supported by molecular dynamics simulations.

Protective effect of 2-hydroxyestrone and 2-hydroxyestradiol against chemically induced hepatotoxicity in vitro and in vivo

Ferroptosis is a form of regulated cell death closely associated with glutathione depletion and accumulation of reactive lipid peroxides. In this study, we seek to determine whether 2-hydroxyestrone (2-OH-E1) and 2-hydroxyestradiol (2-OH-E2), 2 major metabolites of endogenous estrone (E1) and 17β-estradiol (E2) formed by cytochrome P450 in the liver, can protect against erastin- and RSL3-induced ferroptosis in hepatoma cells (H-4-II-E and HuH-7) in vitro and acetaminophen-induced mouse liver injury in vivo. We find that 2-OH-E1 and 2-OH-E2 can protect, in a dose-dependent manner, H-4-II-E hepatoma cells against erastin/RSL3-induced ferroptosis. A similar protective effect of 2-OH-E1 and 2-OH-E2 against erastin- and RSL3-induced ferroptosis is also observed in HuH-7 hepatoma cells. These 2 estrogen metabolites can strongly abrogate erastin- and RSL3-induced accumulation of cellular NO, reactive oxygen species (ROS), and lipid-ROS. Mechanistically, 2-OH-E1 and 2-OH-E2 protect cells against chemically induced ferroptosis by binding to cellular protein disulfide isomerase and then inhibiting its catalytic activity and reducing protein disulfide isomerase-mediated activation (dimerization) of inducible nitric oxide synthase, abrogating cellular NO, ROS, and lipid-ROS accumulation. Animal studies show that 2-OH-E1 and 2-OH-E2 also exhibit strong protection against acetaminophen-induced liver injury in mice. Interestingly, although E1 and E2 have a very weak protective effect in cultured hepatoma cells, they exhibit a similarly strong protective effect as 2-OH-E1 and 2-OH-E2 in vivo, suggesting that the metabolic conversion of E1 and E2 to 2-OH-E1 and 2-OH-E2 contributes importantly to their hepatoprotective effect. This study reveals that 2-OH-E1 and 2-OH-E2 are important endogenous factors for protection against chemically induced liver injury in vivo. SIGNIFICANCE STATEMENT: Ferroptosis is an iron-dependent and lipid reactive oxygen species-dependent form of regulated cell death. Recent evidence has shown that protein disulfide isomerase (PDI) is an important mediator of chemically induced ferroptosis and also a new target for ferroptosis protection. This study shows that 2-hydroxyestrone and 2-hydroxyestradiol are 2 inhibitors of PDI that can strongly protect against chemically induced ferroptotic hepatocyte death in vitro and in vivo. This work supports a PDI-mediated, estrogen receptor-independent mechanism of hepatocyte protection by 2-hydroxyestrone and 2-hydroxyestradiol.

Conformation and binding of 12 Microcystin (MC) congeners to PPP1 using molecular dynamics simulations: A potential approach in support of an improved MC risk assessment

Microcystins (MCs) occur frequently during cyanobacterial blooms worldwide, representing a group of currently about 300 known MC congeners, which are structurally highly similar. Human exposure to MCs via contaminated water, food or dietary supplements can lead to severe intoxications with ensuing high morbidity and in some cases mortality. Currently, one MC congener (MC-LR) is almost exclusively considered for risk assessment (RA) by the WHO. Many MC congeners co-occur during bloom events, of which MC-LR is not the most toxic. Indeed, MC congeners differ dramatically in their inherent toxicity, consequently raising question about the reliability of the WHO RA and the derived guidance values. Molecular dynamics (MD) simulation can aid in understanding differences in toxicity, as experimental validation for all known MC congeners is not feasible. Therefore, we present MD simulations of a total of twelve MC congeners, of which eight MC congeners were simulated for the first time. We show that depending on their structure and toxicity class, MCs adapt to different backbone conformations. These backbone conformations are specific to certain MC congeners and can change or shift to other conformations upon binding to PPP1, affecting the stability of the binding. Analysis of the interactions with PPP1 demonstrated that there are frequently occurring patterns for individual MC congeners, and that published PPP interactions could be reproduced. In addition, common but also unique patterns were found for individual MC congeners, suggesting differences in binding behaviour. The MD simulations presented here therefore enhance our understanding of MC congener-specific differences and demonstrated that congener-specific investigations are prerequisite for allowing characterisation of yet untested or even unknown MC congeners, thereby allowing for a novel potential approach in support of an improved RA of microcystins in humans.

In silico exploration and in vitro validation of the filarial thioredoxin reductase inhibitory activity of Scytonemin and its derivatives

Lymphatic filariasis (LF) caused by the vector borne parasitic nematode Wuchereria bancrofti is of major concern of the World Health Organization (WHO). Lack of potential drug candidates worsens the situation. Presently available drugs are promising in killing the microfilaria (mf) but are not effective as adulticidal therapeutics. Previous studies have revealed that routine administration of the available drugs (albendazole, ivermectin and albendazole) sometime is associated with severe adverse effects (SAEs) in co-infection state. Therefore, potential and safe therapeutics are still required. Earlier studies on filarial thioredoxin reductase (TrxR) have shown that successful inhibition of it can lead to apoptotic death of the parasites. TrxR in filarial parasites plays a significant role in disease progression and pathogenesis, hence efficient non-reversible inhibition of TrxR can be a good strategy to treat LF. In this research, inhibitory potential of Scytonemin, a cyanobacterial metabolite on filarial TrxR was evaluated via different in silico methods and validated through in vitro experiments. Parasite death upon exposure to Scytonemin can be correlated with the TrxR inhibiting capacity of the compound. Therefore, this cyanobacterial-derived compound may possibly be used further as novel and safe therapeutic candidate against filarial infection.Communicated by Ramaswamy H. Sarma.

Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBE) is a neurotrophic disease that has spread more rapidly throughout Europe and Asia in the past few years. At the same time, no cure or specific therapy is known to battle the illness apart from vaccination. To find a pharmacologically relevant drug, a computer-aided drug screening was initiated. Such a procedure probes a possible binding of a drug to the RNA Polymerase of TBE. The crystal structure of the receptor, however, includes missing and partially modeled regions, which rendered the structure incomplete and of questionable use for a thorough drug screening procedure. The quality of the receptor model was addressed by studying three putative structures created. We show that the choice of receptor models greatly influences the binding affinity of potential drug molecules and that the binding location could also be significantly impacted. We demonstrate that some drug candidates are unsuitable for one model but show decent results for another. Without any prejudice on the three employed receptor models, the study reveals the imperative need to investigate the receptor structure before drug binding is probed whether experimentally or computationally.

Elucidation of the Binding Interaction between β-Sitosterol and Lysozyme using Molecular Docking, Molecular Dynamics and Surface Plasmon Resonance Analysis

In this study, the binding behavior of β-sitosterol with lysozyme (LZM) was elucidated by surface plasmon resonance (SPR), computational molecular docking and molecular dynamics simulation studies. Chicken egg white lysozyme (CEWLZM) served as a model protein. Tri-N-acetylchitotriose (NAG3) was used in the redocking experiments to generate precise binding location of the protein. β-sitosterol displayed a slightly better binding energy (-6.68±0.04 kcal/mol) compared to NAG3. Further molecular dynamics simulations and MMPBSA analysis revealed that residues Glu35, Gln57-Asn59, Trp62, Ile98, Ala107 and Trp108 contribute to the binding energy. Then, 2.5 mg/mL CEWLZM, 1X PBS buffer (pH 7.4) as running and coupling buffers, 30 μL/min as flow rate were applied for SPR analysis. Serial β-sitosterol injections (20-150 μM) were performed through SPR sensor surface. According to SPR binding study, KD value for β-sitosterol-CEWLZM binding interaction was calculated as 71.34±9.79 μM. The results could provide essential knowledge for nutrition, pharmaceutical science, and oral biology.

Study of Pineapple Bioactive Compounds Targeting Aldose Reductase: A Natural Intervention for Diabetes Mellitus Pathologies

Aldose reductase is a reduced monomeric enzyme that utilizes NADPH as a cofactor to mediate the glucose reduction to sorbitol in the polyol pathway. Overexpression of aldose reductase has been observed to mediate pathologies associated with diabetes mellitus. Inhibition of aldose reductase thus seems promising to deal with these pathologies. Pineapple and its extract have been identified for its anti-diabetic effect due to the presence of effective bioactive agents. In the present study, the major bioactive compounds of pineapple have been studied for their potential to structurally inhibit aldose reductase. The ADMET analysis of lead bioactive compounds including myrcene, palmitic acid, limonene, n-decanal, beta-carophyllene, 1-cyclohexane-1-caboxaldehyde, and α-farnesene showed most of the compounds were non-toxic and have druglike properties with LD50 values of greater than 2000 mg/kg. Molecular docking of these compounds at the substrate binding site of the aldose reductase-NADPH complex disclosed effective binding with binding energy values of - 5.025 to - 8.003 kcal/mol. α-farnesene, known for its antibacterial, antiviral, and anti-inflammatory properties gave the highest binding energy of - 8.003 kcal/mol. The molecular dynamic simulation studies of α-farnesene-aldose reductase-NADPH ternary complex, aldose reductase-NADPH binary complex, and apo-aldose reductase revealed similar RMSD values with respect to time during the simulation trajectory indicating stable interaction of the compound with the enzyme. DFT analysis showed high reactivity of α-farnesene which favours its utilization as a drug for specific target protein. Therefore, this study provides an efficient natural aldose reductase inhibitor α-farnesene that can be further explored for its potential to develop an effective natural drug to treat diabetes.

The effect of double (S238F/W159H) mutations on the structure and dynamics of PET degrading enzyme

Polyethylene terephthalate (PET) is one of the highly produced synthetic polymers worldwide and had acquired attention due to its impact resistance, high clarity, and light weight. PET has become the first choice in making disposable bottles, leading to massive scales of production resulting in very high utilization across various facets of our daily life. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation, thus presenting a serious threat to the ecosystem. Degradation of PET by enzymatic hydrolysis is a promising strategy to depolymerize the PET into its monomers. In recent studies, a plastic-degrading enzyme known as PETase (IsPETase) from the Ideonella sakaiensis has been identified to hydrolyze PET. The wild-type enzyme from Ideonella sp., has been engineered to improve the catalytic activity. While the IsPETase and its variants have been the subject of extensive structural and biochemical studies, the corresponding computational studies to support the improved activity of the mutant enzyme is not fully understood. In this work, we employed all-atom classical molecular dynamics simulations of the wild-type and double mutant IsPETase enzymes to investigate the underlying reason for the improved catalytic activity in the double mutant by means of structure-dynamics-function relationship. Our results show that the engineered mutations reshape the active site structure, volume, and dynamics of the protein loops which is crucial for substrate binding. We also demonstrate that addition of aromatic and hydrogen bond-forming residues near catalytic site improves binding affinity. This work will enable the rational design of mutants for enhanced PET degrading activity.Communicated by Ramaswamy H. Sarma.

Giardia duodenalis flavohemoglobin is a target of 5-nitroheterocycle and benzimidazole compounds acting as enzymatic inhibitors or subversive substrates

Giardia duodenalis causes giardiasis in humans, companion, livestock and wild animals. Control of infection involves drugs as benzimidazoles (e.g., albendazole, ABZ) and 5-nitroheterocyclics [5-NHs: metronidazole (MTZ), furazolidone (FZD), nitazoxanide (NTZ)] as first-line agents. During infection, Giardia is exposed to immune and pro-oxidant host responses involving nitric oxide (NO). In Giardia, NO is detoxified by a flavohemoglobin (gFlHb), a heme-containing enzyme which is absent in mammals. gFlHb has NO dioxygenase and NADH oxidase activities converting NO into nitrate and producing a superoxide anion (O2•-) that causes oxidative stress and parasite death. The modulation of gFlHb activities may provide novel approaches for treatment of giardiasis. We investigated the capacity of selected benzimidazole-2-carbamates (BZCs: ABZ, oxibendazole, nocodazole), non-BZCs (thiabendazole), an ehtylphenylcarbamate (LQM-996) and 5-NHs (MTZ, NTZ, FZD and some derivatives) to bind to recombinant gFlHb at the heme group, modifying NADH consumption activity and/or inducing ROS production. Of these, BZCs and NTZ bind to heme and increased O2•- production (i.e. caused enzyme subversion), whereas MTZ binds to heme but inhibited NADH consumption. LQM-996 decreased NADH consumption and two out of four NTZ derivatives altered NADH oxidase activity. In silico docking and molecular dynamics studies suggested the interaction of distinct drug moieties in ABZ and NTZ with gFlHb sites involved in NADH and NO catalysis. These findings provide new insights on gFlHb as a novel target of BZCs, MTZ and NTZ, and provides a useful platform to assess the compounds binding capacity to gFlHb prior to experimental and clinical trials in giardiasis.

Investigating the binding of fluorescent probes to a trypanosomal-tRNA synthetase: A fluorescence spectroscopic and molecular dynamics study

Given the high prevalence of Chagas disease in the Americas, we targeted the unique arginyl-tRNA synthetase of its causative agent Trypanosoma cruzi. Among their many possible uses, naphthalene-derived fluorescent ligands, such as ANS and bis-ANS, may be employed in pharmacokinetic research. Although ANS and bis-ANS have become prominent fluorescent probes for protein characterization, the structural and spectroscopic characteristics of protein-ANS/bis-ANS complexes remain largely unknown. Both fluorescent dyes bind to either the folded or partially folded hydrophobic regions of proteins. Additionally, they serve to identify molten globule-like intermediates. These probes have been used to study the folding problems of protein structures and the mechanisms of protein-protein interactions. ANS and bis-ANS exhibited significant enhancement and blue shift in their emission spectra upon binding to TcArgRS, the primary enzyme responsible for attaching l-arginine to its corresponding tRNA. Through fluorescence spectroscopy and computational studies, we concluded that bis-ANS binds more tightly to TcArgRS and that ATP affects bis-ANS fluorescence signal. Thus, these probes are useful resources for studying the intricate intermolecular relationships between proteins in terms of their structure, function, and mechanism. Our study provides a framework for identifying the hydrophobic regions present in TcArgRS. The utilization of hydrophobic patches on proteins for drug targeting is noteworthy because they can assist in identifying regions on the surface of proteins that are likely to interact with ligands. These patches help identify hotspot residues that play a vital role in determining binding affinity. Drugs are mainly small and hydrophobic in nature, and they target protein surfaces which have complementary properties. In this study, we elucidated the potential of TcArgRS as a target for combating trypanosomal diseases and extending life expectancy.

Design of New Daunorubicin Derivatives with High Cytotoxic Potential

Chemotherapy with anthracycline antibiotics is a common method of treating tumors of various etiologies. To create more highly effective cytostatics based on daunorubicin, we used the method of reductive amination using polyalkoxybenzaldehydes. The obtained derivatives of the anthracycline structure have much greater cytotoxicity compared to daunorubicin due to increased affinity for DNA, the ability to disrupt the cell cycle, and their inhibition of the glycolysis process, which is confirmed by data from extensive biological studies and the results of molecular modeling.

Simulating Ionized States in Realistic Chemical Environments with Algebraic Diagrammatic Construction Theory and Polarizable Embedding

Theoretical simulations of electron detachment processes are vital for understanding chemical redox reactions, semiconductor and electrochemical properties, and high-energy radiation damage. However, accurate calculations of ionized electronic states are very challenging due to their open-shell nature, importance of electron correlation effects, and strong interactions with chemical environment. In this work, we present an efficient approach based on algebraic diagrammatic construction theory with polarizable embedding that allows to accurately simulate ionized electronic states in condensed-phase or biochemical environments (PE-IP-ADC). We showcase the capabilities of PE-IP-ADC by computing the vertical ionization energy (VIE) of thymine molecule solvated in bulk water. Our results show that the second- and third-order PE-IP-ADC methods combined with the basis of set of triple-ζ quality yield a solvent-induced shift in VIE of -0.92 and -0.93 eV, respectively, in an excellent agreement with experimental estimate of -0.9 eV. This work demonstrates the power of PE-IP-ADC approach for simulating charged electronic states in realistic chemical environments and motivates its further development.

Molecular Understanding of Activity Changes of Alcohol Dehydrogenase in Deep Eutectic Solvents

Deep eutectic solvents (DESs) have emerged as promising solvents for biocatalysis. While their impact on enzyme solvation and stabilization has been studied for several enzyme classes, their role in substrate binding is yet to be investigated. Herein, molecular dynamics (MD) simulations of horse-liver alcohol dehydrogenase (HLADH) are performed in choline chloride-ethylene glycol (ChCl-EG) and choline chloride-glycerol (ChCl-Gly) at varying water concentrations. In the DES solutions, the active site was significantly constricted, and its flexibility reduced when compared to the aqueous medium. Importantly, the cavity size follows a similar trend as the catalytic activity of HLADH and as such explains previously observed activity changes. To understand the impact on the binding of the substrate (cyclohexanone), an umbrella sampling (US) setup was established to calculate the free energy changes along the substrate binding tunnel of HLADH. The US combined with replica exchange and NADH in its cofactor pocket provided the best sampling of the entire active site, explaining why the cyclohexanone binding on HLADH is reduced with increasing DES content. As different components in these multicomponent mixtures influence the substrate binding, we additionally applied the US setup to study the ability of the DES components to be present inside the substrate tunnel. The presented approach may become useful to understand enzyme behaviors in DESs and to enable the design of more enzyme-compatible and tunable solvents.

Fluoxetine Alters the Biophysics of DPPC and DPPG Bilayers through Phase-Dependent and Electrostatic Interactions

Lipid membranes can control the permeability of a pharmaceutical drug, whereas the drug can induce changes in the structural and biophysical properties of the membranes. Understanding this interplay of drug-lipid membrane interactions can be of great importance in drug design. Here, we present a molecular dynamics study to provide insights into the interactions between the antidepressant fluoxetine and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) bilayers. It was found that, due to the electrostatic interaction, the headgroup of the zwitterionic DPPC lipid is more stable than that of the negatively charged DPPG lipid, allowing the gel phase to persist even at the elevated temperature. At 25 °C, fluoxetine cannot penetrate into the gel-phase DPPC bilayer, while the electrostatic interaction between positively charged fluoxetine and negatively charged DPPG bilayer retains the drug within the lipid headgroup domain. When the temperature is increased to 45 °C, both neutral and charged forms of fluoxetine can partition into the DPPC and DPPG bilayers spontaneously. Analysis of the biophysical and structural changes in both DPPC and DPPG bilayers in the presence of fluoxetine revealed a phase-dependent effect. The binding of fluoxetine to the lipid bilayers limits the movement and orientation of the drug. These findings shed light on the interactions between a commonly prescribed antidepressant and lipid membranes, and such information can be beneficial to the development of potential therapeutic agents.

Prediction of angiogenesis suppression by myricetin from Aeginetia indica via inhibiting VEGFR2 signaling pathway using computer-aided analysis

Vascular endothelial growth factor receptor-2 (VEGFR2) plays a pivotal role in promoting angiogenesis and contributing to the growth and progression of renal cancer. Hence, the current investigation was undertaken with the aim of identifying safe and potent phytochemicals from Aeginetia indica whole plant extract (AiWE) that can efficiently suppress the overexpression of VEGFR2. HPLC analysis identified and quantified 11 polyphenols in considerable amounts in AiWE. All the compounds showed good binding energies with VEGFR2 in the molecular docking study, except catechin hydrate and rutin hydrate. However, among the polyphenols, myricetin exhibited an almost similar hydrogen bonding pattern with the active site of VEGFR2. The all-atom molecular dynamic simulation revealed that myricetin showed a very stable interaction with the active site of VEGFR2 throughout the simulation. Based on these results, it is suggested that myricetin may inhibit angiogenesis by suppressing the VEGFR2 signaling, thereby impeding the growth and progression of renal cancer.

Deciphering the potential of plant metabolites as insecticides against melon fly (Zeugodacus cucurbitae): Exposing control alternatives to assure food security

In the absence of effective biological or chemical controls, the melon fly poses a significant threat to food security, particularly impacting cucurbit crops in tropical and subtropical regions. Melon fly infestations have resulted in yield losses of 30 %-100 %, depending on the specific cucurbit species and season. Current control methods using synthetic chemicals are challenging due to their environmental and biological impacts. This study identified 59 phytocompounds with potential insecticidal properties against the melon fly, exhibiting minimal environmental impact. Key protein targets-hedgehog protein, spastin protein, and ABC-type heme transporter ABCB6 protein-were selected for binding affinity analysis. Camptothecin demonstrated the highest binding affinities for hedgehog protein (-57.32 kcal/mol) and spastin protein (-50.84 kcal/mol), while jervine had the strongest binding affinity for ABC-type heme transporter ABCB6 protein (-43.92 kcal/mol). The control compound, malathion, showed lower binding affinities across all three proteins. Stability of the top compound-protein complexes was further confirmed through a 100 ns molecular dynamics simulation. In insecticide-likeness evaluations, jervine consistently scored high, with camptothecin also performing well, while neriifolin ranked lower. The leading compounds showed no adverse effects that could diminish their insecticidal potential. These findings indicate that jervine and camptothecin are promising candidates for melon fly management, offering potential to prevent significant crop losses. However, as this study was conducted solely through computational methods, we recommend subsequent in vitro and field trials for the future drug development.

Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions

Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by the time-consuming process of generating the necessary training, validation, and test data for MLP models through QM/MM simulations. Furthermore, the entire process needs to be repeated for each specific enzyme system and reaction. To overcome this bottleneck, it is required that trained MLPs exhibit transferability across different enzyme environments and reacting species, thereby eliminating the need for retraining with each new enzyme variant. In this study, we explore this potential by evaluating the transferability of a pretrained ΔMLP model across different enzyme mutations within the MM environment using the QM/MM-based ML architecture developed by Pan, X. J. Chem. Theory Comput. 2021, 17(9), 5745-5758. The study includes scenarios such as single point substitutions, a homologous enzyme from different species, and even a transition to an aqueous environment, where the last two systems have MM environment that is substantially different from that used in MLP training. The results show that the ΔMLP model effectively captures and predicts the effects of enzyme mutations on electrostatic interactions, producing reliable free energy profiles of enzyme-catalyzed reactions without the need for retraining. The study also identified notable limitations in transferability, particularly when transitioning from enzyme to water-rich MM environments. Overall, this study demonstrates the robustness of the Pan et al.'s QM/MM-based ML architecture for application to diverse enzyme systems, as well as the need for further research and the development of more sophisticated MLP models and training methods.

Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD

Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics (MD) simulations are utilized to estimate binding poses and binding free energies of small-molecule drugs to proteins, quantitative prediction of the binding thermodynamics of PE-based drugs presents a significant obstacle in computer-aided drug design. This is due to the sluggish dynamics of PEs caused by their size and strong charge-charge correlations. In this paper, we introduce advanced sampling methods based on a force-spectroscopy setup and theoretical modeling to overcome this barrier. We exemplify our method with explicit solvent all-atom MD simulations of the interactions between anionic PEs that show antiviral properties, namely heparin and linear polyglycerol sulfate (LPGS), and the SARS-CoV-2 spike protein receptor binding domain (RBD). Our prediction for the binding free-energy of LPGS to the wild-type RBD matches experimentally measured dissociation constants within thermal energy, k B T, and correctly reproduces the experimental PE-length dependence. We find that LPGS binds to the Delta-variant RBD with an additional free-energy gain of 2.4 k B T, compared to the wild-type RBD, due to the additional presence of two mutated cationic residues contributing to the electrostatic energy gain. We show that the LPGS-RBD binding is solvent dominated and enthalpy driven, though with a large entropy-enthalpy compensation. Our method is applicable to general polymer adsorption phenomena and predicts precise binding free energies and reconfigurational friction as needed for drug and drug-delivery design.

Investigating the Inhibitory Effects of Paliperidone on RAGEs: Docking, DFT, MD Simulations, MMPBSA, MTT, Apoptosis, and Immunoblotting Studies

Chronic diseases such as diabetes and cancer are the leading causes of mortality worldwide. Receptors for Advanced Glycation End products (RAGEs) are ubiquitous factors that catalyse Advanced Glycation End products (AGEs), proteins, and lipids that become glycated from sugar ingestion. RAGEs are cell surface receptor proteins and play a broad role in mediating the effects of AGEs on cells, contributing to modifying biological macromolecules like proteins and lipids, which can cause Reactive Oxygen Species (ROS) generation, inflammation, and cancer. We targeted RAGE inhibition analysis and screening of United States Food and Drug Administration (FDA) libraries through molecular docking studies that identified the four most suitable FDA compounds: Zytiga, Paliperidone, Targretin, and Irinotecan. We compared them with the control substrate, Carboxymethyllysine, which showed good binding interaction through hydrogen bonding, hydrophobic interactions, and π-stacking at active site residues of the target protein. Following a 100 ns simulation run, the docked complex revealed that the Root Mean Square Deviation (RMSD) values of two drugs, Irinotecan (1.3 ± 0.2 nm) and Paliperidone (1.2 ± 0.3 nm), were relatively stable. Subsequently, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) determined that the Paliperidone molecule had a high negative energy of -13.49 kcal/mol, and the Absorption, Distribution, Metabolism, and Excretion (ADME) properties were in control for use in the mentioned cases. We extended this with many in vitro studies, including an immunoblotting assay, which revealed that RAGEs with High Mobility Group Box 1 (HMGB1) showed higher expression, while RAGEs with Paliperidone showed lower expressions. Furthermore, cell proliferation assay and Apoptosis assay (Annexin-V/PI staining) results revealed that Paliperidone was an effective anti-glycation and anti-apoptotic drug-however, more extensive in vivo studies are needed before its use.

Exploring the impact of deleterious missense nonsynonymous single nucleotide polymorphisms in the DRD4 gene using computational approaches

Dopamine receptor D4 (DRD4) plays a vital role in regulating various physiological functions, including attention, impulse control, and sleep, as well as being associated with various neurological diseases, including attention deficit hyperactivity disorder, novelty seeking, and so on. However, a comprehensive analysis of harmful nonsynonymous single nucleotide polymorphisms (nsSNPs) of the DRD4 gene and their effects remains unexplored. The aim of this study is to uncover novel damaging missense nsSNPs and their structural and functional effects on the DRD4 receptor. From the dbSNP database, we found 677 nsSNPs, and then we analyzed their functional consequences, disease associations, and effects on protein stability with fifteen in silico tools. Five variants, including L65ICL1P (rs1459150721), V1163.33D (rs761875546), I1293.46S (rs751467198), I1564.46T (rs757732258), and F2015.47S (rs199609858), were identified as the most deleterious mutations that were also present in the conserved region and showed lower interactions with neighboring residues. To comprehensively understand their impact, we docked agonist dopamine and antagonist nemonapride at the binding site of the receptor, followed by 200 ns molecular dynamics simulations. We identified the V116D and I129S mutations as the most damaging, followed by F201S in the dopamine-bound states. Both the V116D and I129S variants demonstrated significantly high RMSD, Rg, and SASA, and low thermodynamic stability. The F201S-dopamine complex exhibited lower compactness and higher motions, along with a significant loss of hydrogen bonds and active site interactions. By contrast, while interacting with nemonapride, the impact of the I156T and L65P mutations was highly deleterious; both showed lower stability, higher flexibility, and higher motions. Additionally, nemonapride significantly lost interactions with the active site, notably in the I156T variant. We also found the V116D-nemonapride complex as structurally damaging; however, the interaction patterns of nemonapride were less altered in the MMPBSA analysis. Overall, this study revealed five novel deleterious variants along with a comprehensive understanding of their effect in the presence of an agonist and antagonist, which could be helpful for understanding disease susceptibility, precision medicine, and developing potential drugs.

Exploring effector protein dynamics and natural fungicidal potential in rice blast pathogen Magnaporthe oryzae

Rice blast, caused by Magnaporthe oryzae, is one of the most destructive fungal diseases in rice, resulting in major economic losses worldwide. Genetic and genomic studies have identified key genes and proteins, such as AvrPik variants and MAX proteins, that are crucial for the pathogen's virulence. These effector proteins interact with specific alleles of the Pik gene family on rice chromosome 11, modulating the host's immune response. In this study, we investigated 35 plant-derived metabolites known for their antifungal properties as potential fungicides against M. oryzae. Using molecular docking, we identified Hecogenin and Cucurbitacin E as strong binders to MAX40 and APIKL2A proteins, which are essential for the fungus's immune evasion and pathogenicity. Molecular dynamics simulations further confirmed that these compounds form stable, strong interactions with the target proteins, validating their potential as therapeutic agents. Additionally, the compounds were evaluated based on Lipinski's rule of five and toxicity predictions, indicating their suitability for agricultural use. These results suggest that Hecogenin and Cucurbitacin E could serve as promising lead candidates in the development of novel fungicides for rice blast, offering new strategies for crop protection and sustainable agricultural practices.

Subtle Structural Modifications Spanning from EP4 Antagonism to EP2/EP4 Dual Antagonism: A Novel Class of Thienocyclic-Based Derivatives

The development of dual prostaglandin E2 receptors 2/4 (EP2/EP4) antagonists represents an attractive strategy for cancer immunotherapy. Herein, a series of 4,7-dihydro-5H-thieno[2,3-c]pyran derivatives with potent EP2/EP4 dual antagonism were discovered by fine-tuned structural modifications. The biphenyl side chain was found to be the key pharmacophore for the transition from EP4 antagonism to EP2/EP4 dual antagonism. The introduction of large sterically hindered segments posed challenges on obtaining EP2 potency, while having minimal impact on EP4 potency. Molecular dynamics simulations verified that the EP2 pocket is relatively narrow compared to EP4, and the key residues surrounding the EP2 pocket impose spatial restrictions on the entry of antagonists. Representative compound 29 (CZY-1068) significantly reduced PGE2-induced expression of immunosuppression-related genes in macrophages. Notably, compound 29 elicited robust antitumor efficacy in the syngeneic MC38 tumor model. Taken together, this study provides a proof-of-concept for obtaining novel potent dual EP2/EP4 antagonists based on rational structural modifications.

Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation

Phospholipid based vesicles called liposomes are commonly used as packaging in advanced drug delivery applications. Stimuli-responsive liposomes have been designed to release their contents under certain conditions, for example through heating or illumination. However, in the case of photosensitive liposomes based on azo-PC, namely phosphatidylcholine lipids with azobenzene incorporated into one of the two lipid tails, the release mechanism is not known. Here we show, using fully-atomistic molecular dynamics simulations of pure azo-PC bilayers, that drug permeation through the bilayer is driven by a light-induced gel-to-liquid lipid phase transition that softens the membrane bending rigidity by an order of magnitude, increases the area per lipid, and decreases the membrane thickness. Furthermore, using phenol as a model drug, we quantified its translocation free energy and its ability to cross the bilayer as a result of a chemical potential gradient induced through a double-bilayer simulation unit cell. The molecular level structural and dynamic information obtained in this study should be of help in designing new azo-PC based liposomes.

Structure Characterization of a Disordered Peptide Using In-Droplet Hydrogen/Deuterium Exchange Mass Spectrometry and Molecular Dynamics

In-droplet hydrogen/deuterium exchange (HDX)-mass spectrometry (MS) experiments have been conducted for peptides of highly varied conformational type. A new model is presented that combines the use of protection factors (PF) from molecular dynamics (MD) simulations with intrinsic HDX rates (k int) to obtain a structure-to-reactivity calibration curve. Using the model, the relationship of peptide structural flexibility and HDX reactivity for different peptides is elucidated. Additionally, the model is used to describe the degree of conformational flexibility and structural bias for the disease-relevant Nt17 peptide; although highly flexible, intrinsically primed for facile conversion to α-helical conformation upon binding with molecular partners imparts significant in-droplet HDX protection for this peptide. In the future, a scale may be developed whereby HDX reactivity is predictive of the degree of structural flexibility and bias (propensity to form 2° structural elements such as α-helix, β-sheet, and β-turn) for intrinsically disordered regions (IDRs). Such structural resolution may ultimately be used for high-throughput screening of IDR structural transformation(s) upon binding of ligands such as drug candidates.

Balancing enthalpy and entropy in inhibitor binding to the prostate-specific membrane antigen (PSMA)

Understanding the molecular mechanism of inhibitor binding to prostate-specific membrane antigen (PSMA) is of fundamental importance for designing targeted drugs for prostate cancer. Here we designed a series of PSMA-targeting inhibitors with distinct molecular structures, which were synthesized and characterized using both experimental and computational approaches. Microsecond molecular dynamics simulations revealed the structural and thermodynamic details of PSMA-inhibitor interactions. Our findings emphasize the pivotal role of the inhibitor's P1 region in modulating binding affinity and selectivity and shed light on the binding-induced conformational shifts of two key loops (the entrance lid and the interface loop). Binding energy calculations demonstrate the enthalpy-entropy balance in the thermodynamic driving force of different inhibitors. The binding of inhibitors in monomeric form is entropy-driven, in which the solvation entropy from the binding-induced water restraints plays a key role, while the binding of inhibitors in dimeric form is enthalpy-driven, due to the promiscuous PSMA-inhibitor interactions. These insights into the molecular driving force of protein-ligand binding offer valuable guidance for rational drug design.

Evaluating the potential of Kalanchoe pinnata, Piper amalago amalago, and other botanicals as economical insecticidal synergists against Anopheles gambiae

BACKGROUND

Synergists reduce insecticide metabolism in mosquitoes by competing with insecticides for the active sites of metabolic enzymes, such as cytochrome P450s (CYPs). This increases the availability of the insecticide at its specific target site. The combination of both insecticides and synergists increases the toxicity of the mixture. Given the demonstrated resistance to the classical insecticides in numerous Anopheles spp., the use of synergists is becoming increasingly pertinent. Tropical plants synthesize diverse phytochemicals, presenting a repository of potential synergists.

METHODS

Extracts prepared from medicinal plants found in Jamaica were screened against recombinant Anopheles gambiae CYP6M2 and CYP6P3, and Anopheles funestus CYP6P9a, CYPs associated with anopheline resistance to pyrethroids and several other insecticide classes. The toxicity of these extracts alone or as synergists, was evaluated using bottle bioassays with the insecticide permethrin. RNA sequencing and in silico modelling were used to determine the mode of action of the extracts.

RESULTS

Aqueous extracts of Piper amalago var. amalago inhibited CYP6P9a, CYP6M2, and CYP6P3 with IC50s of 2.61 ± 0.17, 4.3 ± 0.42, and 5.84 ± 0.42 μg/ml, respectively, while extracts of Kalanchoe pinnata, inhibited CYP6M2 with an IC50 of 3.52 ± 0.68 μg/ml. Ethanol extracts of P. amalago var. amalago and K. pinnata displayed dose-dependent insecticidal activity against An. gambiae, with LD50s of 368.42 and 282.37 ng/mosquito, respectively. Additionally, An. gambiae pretreated with K. pinnata (dose: 1.43 μg/mosquito) demonstrated increased susceptibility (83.19 ± 6.14%) to permethrin in a bottle bioassay at 30 min compared to the permethrin only treatment (0% mortality). RNA sequencing demonstrated gene modulation for CYP genes in anopheline mosquitoes exposed to 715 ng of ethanolic plant extract at 24 h. In silico modelling showed good binding affinity between CYPs and the plants' secondary metabolites.

CONCLUSION

This study demonstrates that extracts from P. amalago var. amalago and K. pinnata, with inhibitory properties, IC50 < 6.95 μg/ml, against recombinant anopheline CYPs may be developed as natural synergists against anopheline mosquitoes. Novel synergists can help to overcome metabolic resistance to insecticides, which is increasingly reported in malaria vectors.

Study of the pH effects on water-oil-illite interfaces by molecular dynamics

Illite mineral is present in shale rocks, and its wettability behavior is significant for the oil and gas industry. In this work, the pH effects on the affinity between the (001) and (010) crystallographic planes of illite K2(Si7Al)(Al3Mg)O20(OH)4 and direct and inverse emulsions were studied using molecular dynamics simulations. To develop the simulations, an atomistic model of illite was constructed following Löwenstein's rule. The oily phase was modeled using heptane, toluene, and mixtures of heptane/heptanoic acid, heptane/heptanoate, heptane/hexylamine and heptane/hexylammonium. For the heptane/heptanoate and heptane/hexylammonium mixtures, Na+ and Cl- ions were used to neutralize the excess electrical charge of the droplets, respectively. The affinity of the mineral surface to the oil models was estimated by the contact angle for systems where it was possible. However, for systems where the droplets did not adhere to the mineral, a methodology based on the height of the droplet on the surface was proposed. The results showed that, in general, for the inverse emulsions, water exhibited a high affinity for both illite surfaces, with its contact angle remaining below 45° regardless of pH. However, the heptane/heptanoic acid inverse emulsions on the edge surface were an exception to this behavior. Specifically, the contact angles calculated for the water droplets revealed mixed wettability due to hydrogen bonds between the carboxylic functional groups (pH ≪ 4.4) and the surface silanols and aluminols. Oil droplets suspended in water, on the other hand, did not adhere to the illite surfaces, and contact angles were not measurable. Nevertheless, the heptane/heptanoic acid droplets (pH ≪ 4.4) showed heights of approximately 2 Å and 4 Å above the basal and edge surfaces, respectively. This behavior was attributed to the hydrogen bonds formed between the carboxylic functional groups and the water molecules located on the mineral surfaces. Finally, the heptane/heptanoate (pH ≫ 4.4) and heptane/hexylammonium (pH ≪ 10.64) droplets were localized at distances greater than 8 Å from the surface, presumably due to a charge repulsion between the mineral surface and the surface of the droplets.

Retinoids as Alternative Antifungal Agents Against Candida albicans: In Vitro and In Silico Evidence

Candida albicans (C. albicans) is the most common pathogen responsible for a wide spectrum of human infections ranging from superficial mucocutaneous mycoses to systemic life-threatening diseases. Its main virulence factors are the morphological transition between yeast and hyphal forms and the ability to produce biofilm. Novel antifungal strategies are required given the severity of systemic candidiasis, especially in immunocompromised patients, and the lack of effective anti-biofilm treatments. We previously demonstrated that all-trans retinoic acid (ATRA), an active metabolite of vitamin A, exerted an inhibitory effect on Candida growth, yeast-hyphal transition and biofilm formation. Here, we further investigated the possible anti-Candida potential of trifarotene and tazarotene, which are the other two molecules belonging to the retinoid family, compared to ATRA. The results indicate that both drugs were able to suppress Candida growth, germination and biofilm production, although trifarotene was proven to be more effective than tazarotene, showing effectiveness comparable to ATRA. In silico studies suggest that all three retinoids may exert antifungal activity through their molecular interactions with the heat shock protein (Hsp) 90 and 14α-demethylase of C. albicans. Moreover, interactions between retinoids and ergosterol have been observed, suggesting that those compounds have great potential against C. albicans infections.

IP6, PF74 affect HIV-1 capsid stability through modulation of hexamer-hexamer tilt angle preference

The HIV-1 capsid is an irregularly shaped protein complex containing the viral genome and several proteins needed for integration into the host cell genome. Small molecules, such as the drug-like compound PF-3450074 (PF74) and the anionic sugar inositolhexakisphosphate (IP6), are known to impact capsid stability, although the mechanisms through which they do so remain unknown. In this study, we employed atomistic molecular dynamics simulations to study the impact of molecules bound to hexamers at the central pore (IP6) and the FG-binding site (PF74) on the interface between capsid oligomers. We found that the IP6 cofactor stabilizes a pair of neighboring hexamers in their flattest configurations, whereas PF74 introduces a strong preference for intermediate tilt angles. These results suggest that the tilt angle between neighboring hexamers is a primary mechanism for the modulation of capsid stability. In addition, hexamer-pentamer interfaces were highly stable, suggesting that pentamers are likely not the locus of disassembly.

The evolution of the Amber additive protein force field: History, current status, and future

Molecular dynamics simulations are pivotal in elucidating the intricate properties of biological molecules. Nonetheless, the reliability of their outcomes hinges on the precision of the molecular force field utilized. In this perspective, we present a comprehensive review of the developmental trajectory of the Amber additive protein force field, delving into researchers' persistent quest for higher precision force fields and the prevailing challenges. We detail the parameterization process of the Amber protein force fields, emphasizing the specific improvements and retained features in each version compared to their predecessors. Furthermore, we discuss the challenges that current force fields encounter in balancing the interactions of protein-protein, protein-water, and water-water in molecular dynamics simulations, as well as potential solutions to overcome these issues.

Understanding Folding of bFGF and Potential Cellular Protective Mechanisms of Neural Cells

Traumatic brain injury (TBI) is a serious health condition that affects an increasing number of people, especially veterans and athletes. TBI causes serious consequences because of its long-lasting impact on the brain and its alarming frequency of occurrence. Although the brain has some natural protective mechanisms, the processes that trigger them are poorly understood. Fibroblast growth factor (FGF) proteins interact with receptor proteins to protect cells. Gaps in the literature include how basic-FGF (bFGF) is activated by heparin, can heparin-like molecules induce neural protection, and the effect of allosteric binding on bFGF activity. To fill the gap in our understanding, we applied temperature replica exchange to study the influence of heparin binding to bFGF and how mutations in bFGF influence stability. A new favorable binding site was identified by comparing free energies computed from the potential of mean force (PMF). Although the varied sugars studied resulted in different interactions with bFGF compared to heparin, they each produced structural effects similar to those of bFGF that likely facilitate receptor binding and signaling. Our results also demonstrate how point mutations can trigger the same conformational change that is believed to promote favorable interactions with the receptor. A deeper atomic-level understanding of how chemicals are released during TBI is needed to improve the development of new treatments for TBI and could contribute to a better understanding of other diseases.

The Aedes aegypti mosquito evolves two types of prophenoloxidases with diversified functions

Insect phenoloxidase, presented as an inactive precursor prophenoloxidase (PPO) in hemolymph, catalyzes melanin formation, which is involved in wound healing, pathogen killing, reversible oxygen collection during insect respiration, and cuticle and eggshell formation. Mosquitoes possess 9 to 16 PPO members across different genera, a number that is more than that found in other dipteran insects. However, the reasons for the redundancy of these PPOs and whether they have distinct biochemical properties and physiological functions remain unclear. Phylogenetic analysis confirmed that Aedes aegypti PPO6 (Aea-PPO6) is an ortholog to PPOs in other insect species, classified as the classical insect type, while other Aea-PPOs are unique to Diptera, herein referred to as the dipteran type here. We characterized two Aea-PPO members, Aea-PPO6, the classical insect type, and Aea-PPO10, a dipteran type, which exhibit distinct substrate specificities. By resolving Aea-PPO6's crystal structure and creating a chimera protein (Aea-PPO6-cm) with Motif 1 (217GDGPDSVVR225) from Aea-PPO10, we identified the motif that determines PPO substrate specificity. In vivo, loss of Aea-PPO6 led to larval lethality, while Aea-PPO10 was involved in development, pigmentation, and immunity. Our results enhance the understanding of the functional diversification of mosquito PPOs.

Baicalein inhibits PRRSV through direct binding, targeting EGFR, and enhancing immune response

Porcine reproductive and respiratory syndrome virus (PRRSV) presents significant economic challenges to the global pork industry due to its ability to mutate rapidly. The current commercial vaccines have limited effectiveness, and there are strict restrictions on the use of antiviral chemical drugs. Therefore, it is urgent to identify new strategies for preventing and controlling PRRSV infections. Baicalein, a flavonoid derived from Scutellaria baicalensis, has gained attention for its potential antiviral properties. However, there is little information about the effects and mechanisms of baicalein in relation to PRRSV. In this study, a network pharmacology analysis identified seven potential targets of baicalein against PRRSV, with the epidermal growth factor receptor (EGFR) emerging as the core target. The results of molecular docking and dynamics (MD) simulations confirmed that baicalein has a high binding affinity for EGFR, with a measured value of - 7.935 kcal/mol. Additionally, both in vitro (EC50 = 10.20 μg/mL) and in vivo (2.41 mg/kg) experiments were conducted to assess the effectiveness of baicalein against PRRSV. Notably, baicalein was found to inhibit various stages of the PRRSV replication cycle and could directly bind to PRRSV in vitro. Baicalein inhibited the entry of PRRSV by blocking EGFR phosphorylation and the downstream PI3K-AKT signaling pathway. This was confirmed by a decrease in the expression of p-EGFR/EGFR, p-AKT/AKT, PI3K, and SRC following treatment with baicalein. Additionally, baicalein significantly enhanced the immune response in piglets infected with PRRSV. In conclusion, this study suggests that baicalein may be a promising pharmaceutical candidate for preventing and controlling PRRS, offering new insights into the antiviral potential of Chinese herbal medicine.

Exploring the impact of the stargazin V143L mutation on the dynamics of the AMPA receptor: stargazin complex

Stargazin, a transmembrane AMPAR regulatory protein (TARP), plays a crucial role in facilitating the transport of AMPA receptors to the cell surface, stabilising their localisation at synapses and influencing their gating properties. The primary objective of this study was to investigate the effect of the V143L mutation in stargazin, previously linked to intellectual disability, on the interaction between stargazin and AMPA receptors. To achieve this, we conducted a thorough examination of eight distinct molecular dynamics simulations of AMPA receptor-stargazin complexes, each associated with different conductance levels. Through extensive analysis of complex interface structures and dynamics, we revealed that the stargazin V143L mutation had a more pronounced destabilising effect on complexes with lower conductance levels than on the conductive states of the receptor, suggesting a potential association with impaired synaptic transmission in individuals with this mutation.

Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2

Sphingosine-1-phosphate (S1P) is a signaling lysolipid critical to heart development, immunity, and hearing. Accordingly, mutations in the S1P transporter SPNS2 are associated with reduced white cell count and hearing defects. SPNS2 also exports the S1P-mimicking FTY720-P (Fingolimod) and thereby is central to the pharmacokinetics of this drug when treating multiple sclerosis. Here, we use a combination of cryo-electron microscopy, immunofluorescence, in vitro binding and in vivo S1P export assays, and molecular dynamics simulations to probe SPNS2's substrate binding and transport. These results reveal the transporter's binding mode to its native substrate S1P, the therapeutic FTY720-P, and the reported SPNS2-targeting inhibitor 33p. Further capturing an inward-facing apo state, our structures illuminate the protein's mechanism for exchange between inward-facing and outward-facing conformations. Finally, using these structural, localization, and S1P transport results, we identify how pathogenic mutations ablate the protein's export activity and thereby lead to hearing loss.

Exploring the conformational space of ROS1 kinase domain and the impact of allosteric mutations

Chromosomal rearrangements are common oncogenic events in Non-Small Cell Lung Cancer. An example is the fusion of the ROS1 kinase domain with extracellular receptors. Although the fusion leads to a target that is druggable with multi-kinase inhibitors, several reports indicate the emergence of point mutations leading to drug resistance. Although these mutations are often located in the ATP binding pocket, a subset of them is neighboring the pocket without a direct effect on drug binding. Due to the clinical impact of these allosteric mutations, there is an urge to identify the mechanism of resistance and characterize the pocket for further drug design studies. This study aimed to unravel the resistance mechanism of L1982F and S1986F/Y mutations. The variants were modeled and simulated using classical Molecular Dynamics simulations and accessed for their conformational flexibility. Our results indicate a direct effect of these allosteric mutants in the binding pocket volume with an indication of the G-loop playing a central role.

Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization

The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models. Our MD simulation results show that GTP binding significantly enhances the conformational flexibility of KRAS, and thus promotes its transition to an active conformation with more open switch I and II regions. MSMs analyses show that KRAS in the GTP-bound state can be transitioned to the active state more efficiently during the simulation than in the GDP-bound state. In addition, NRI model calculations showed that GTP binding enhanced residue-residue interactions within the KRAS protein, especially when the long-range interactions were significantly enhanced. Furthermore, the allosteric signaling pathways from the P-loop to switch I and II as well as the key amino acid sites along the pathways were obtained using a graph-based shortest path analysis. Our results can contribute to a deeper understanding of the mechanism of KRAS allosteric activation and provide a foundation for the development of targeted therapeutic drugs to regulate KRAS activity.

Identification of novel cyclin-dependent kinase 4/6 inhibitors from marine natural products

Cyclin-dependent kinases 4 and 6 (CDK4/6) are crucial regulators of cell cycle progression and represent important therapeutic targets in breast cancer. This study employs a comprehensive computational approach to identify novel CDK4/6 inhibitors from marine natural products. We utilized structure-based virtual screening of the CMNPD database and MNP library, followed by rigorous filtering based on drug-likeness criteria, PAINS filter, ADME properties, and toxicity profiles. From an initial hit of 9,497 compounds, 2,344 passed drug-likeness and PAINS filters. Further ADME filtering yielded 50 compounds, of which 25 exhibited non-toxic profiles. These 25 candidates underwent consensus molecular docking using seven distinct algorithms: AutoDockTools 4.2, idock, LeDock, Qvina 2, Smina, AutoDock Vina 1.2.0, PLANTS, and rDock. Based on these results, six top-scoring compounds were selected for comprehensive 500 nanosecond all-atom molecular dynamics simulations to evaluate their structural stability and interactions with CDK4/6. Our analysis revealed that compounds CMNPD11585 and CMNPD2744 demonstrated superior stability in their interactions with CDK4/6, exhibiting lower RMSD and RMSF values, more favorable binding free energies, and persistent hydrogen bonding patterns. These compounds also showed lower Solvent Accessible Surface Area values, indicating better compatibility with the CDK4/6 active site. Subsequent in-vitro studies using MTT assays on MCF-7 breast cancer cells confirmed the cytotoxic effects of these compounds, with CMNPD11585 showing the highest potency, followed by CMNPD2744.

Establishing a General Atomistic Model for the Stratum Corneum Lipid Matrix Based on Experimental Data for Skin Permeation Studies

Understanding the permeation of drugs through the intercellular lipid matrix of the stratum corneum layer of skin is crucial for effective transdermal delivery. Molecular dynamics simulations can provide molecular insights into the permeation process. In this study, we developed a new atomistic model representing the multilamellar arrangement of lipids in the stratum corneum intercellular space for permeation studies. The model was built using ceramides in extended conformation as the backbone along with free fatty acids and cholesterol. The properties of the equilibrated model were in agreement with the neutron scattering data and hydration behavior previously reported in the literature. The permeability of molecules, such as water, benzene and estradiol, and the molecular mechanism of action of permeation enhancers, such as eucalyptol and limonene, were evaluated using the model. The new model can be reliably used for studying the permeation of small molecules and for gaining mechanistic insights into the action of permeation enhancers.

NMR and MD Simulations of Non-Ionic Surfactants

Non-ionic surfactants are an important solvent in the field of green chemistry with tremendous application potential. Understanding their phase properties in bulk or in confined environments is of high commercial value. In recent years, the combination of molecular dynamics (MD) simulations with multinuclear solid-state NMR spectroscopy and calorimetric techniques has evolved into the most powerful tool for their investigation. Showing recent examples from our groups, the present review demonstrates the power and versatility of this approach, which can handle both small model-surfactants like octanol and large technical surfactants like technical polyethylene glycol (PEG) mixtures and reveals otherwise unobtainable knowledge about their phase behavior and the underlying molecular arrangements.

In Silico Structural Insights and Potential Inhibitor Identification Based on the Benzothiazole Core for Targeting Leishmania major Pteridine Reductase 1

Leishmaniasis is reported as the second most common protozoonosis, with the highest prevalence and mortality rate. Among the Leishmania drug targets, Pteridine Reductase 1 of Leishmania major (LmPTR1) proved to be promising because Leishmania is auxotrophic for folates. Thus, this study employed a combination of ligand- and structure-based approaches to screen new benzothiazole compounds as LmPTR1 inhibitor candidates. Initially, a highly predictive quantitative structure-activity relationship (QSAR) model was able to identify the relevant hybrid descriptors, with an accuracy of over 93%. Insights into the mechanism of action indicated Phe113, His241, Leu188, Met183, and Leu226 as key residues. New commercially available compounds were screened using QSAR, docking, and pharmacokinetic properties as filters. Molecular dynamics, non-covalent interactions analysis, and quantum chemical calculation of binding enthalpy demonstrated that the lead compound (ZINC 72229720) forms a stable complex with LmPTR1, indicating it as a new promising LmPTR1 inhibitor.

Toward a Generalizable Machine-Learned Potential for Metal-Organic Frameworks

Machine-learned potentials (MLPs) have transformed the field of molecular simulations by scaling "quantum-accurate" potentials to linear time complexity. While they provide more accurate reproduction of physical properties as compared to empirical force fields, it is still computationally costly to generate their training data sets from ab initio calculations. Despite the emergence of foundational or general MLPs for organic molecules and dense materials, it is unexplored if one general MLP can be effectively developed for a wide variety of nanoporous metal-organic frameworks (MOFs) with different chemical moieties and geometric properties. Herein, by leveraging upon data-efficient equivariant MLPs, we demonstrate the possibility of developing a general MLP for nearly 3000 Zn-based MOFs. After curating a training data set comprising augmented MOF structures generated from density functional theory optimization, we validate the reliability of the general MLP in predicting accurate forces and energies when evaluated on a test set with chemically distinct MOF structures. Despite incurring slightly higher errors on structures containing rare chemical moieties, the general MLP can reliably reproduce physical (e.g., vibrational, thermodynamic, and mechanical) properties for a large sample of Zn-based MOFs. Crucially, by developing one MLP for many MOFs, the computational cost of high-throughput screening is potentially reduced by a few orders of magnitude. This enables us to predict quantum-accurate properties for notable Zn-MOFs that were previously uninvestigated via expensive theoretical calculations. To facilitate computational discovery among other families of complex chemical structures, we provide our data set and codes in the public Zenodo repository.

Mutational analysis of an antimalarial drug target, PfATP4

Among new antimalarials discovered over the past decade are multiple chemical scaffolds that target Plasmodium falciparum P-type ATPase (PfATP4). This essential protein is a Na+ pump responsible for the maintenance of Na+ homeostasis. PfATP4 belongs to the type two-dimensional (2D) subfamily of P-type ATPases, for which no structures have been determined. To gain better insight into the structure/function relationship of this validated drug target, we generated a homology model of PfATP4 based on sarco/endoplasmic reticulum Ca2+ ATPase, a P2A-type ATPase, and refined the model using molecular dynamics in its explicit membrane environment. This model predicted several residues in PfATP4 critical for its function, as well as those that impart resistance to various PfATP4 inhibitors. To validate our model, we developed a genetic system involving merodiploid states of PfATP4 in which the endogenous gene was conditionally expressed, and the second allele was mutated to assess its effect on the parasite. Our model predicted residues involved in Na+ coordination as well as the phosphorylation cycle of PfATP4. Phenotypic characterization of these mutants involved assessment of parasite growth, localization of mutated PfATP4, response to treatment with known PfATP4 inhibitors, and evaluation of the downstream consequences of Na+ influx. Our results were consistent with modeled predictions of the essentiality of the critical residues. Additionally, our approach confirmed the phenotypic consequences of resistance-associated mutations as well as a potential structural basis for the fitness cost associated with some mutations. Taken together, our approach provides a means to explore the structure/function relationship of essential genes in haploid organisms.

Understanding the Termination Effect of Ti3C2TX MXene Membrane on Water Structure and Interaction with Alginate Foulants: A Molecular Dynamics Study

The effects of termination functional groups of the Ti3C2Tx MXene membrane on the structural and dynamics properties of nearby water molecules and foulants are investigated through molecular dynamics simulations. The simulation results show that a much denser water layer can be formed at the vicinity of hydroxyl (OH) termination than that near fluorine (F) or oxygen (O) termination. Particular focus is given to the molecular binding properties of β-d-mannuronic acid (M) and α-l-guluronic acid (G) alginate monomers on the MXene membrane surface with different termination groups. Further steered molecular dynamics (SMD) simulations show that M alginate monomers exhibit significant binding with the MXene membrane surface with O termination, due to the strong electrostatic interaction and the van der Waals attraction. In contrast, the binding between the alginate monomers and the MXene membrane surface with OH termination is negligible, as the stable hydration water network prevents them from direct contact. In addition, SMD simulation results show that calcium (Ca2+) ions could significantly enhance the surface fouling between M alginate monomers and the MXene with an O termination through the formation of contact ionic pair (CIP) and solvent-shared ionic pair (SSIP) structures.

Molecular Dynamics Simulation on the Conformational Change of a pH-Switchable Lipid

pH-sensitive lipids are important components of lipid nanoparticles, which enable the targeted delivery and controlled release of drugs. Understanding the mechanism of pH-triggered drug release at the molecular level is important for the rational design of ionizable lipids. Based on a recently reported pH-switchable lipid, named SL2, molecular dynamics (MD) simulations were employed to explore the microscopic mechanism behind the membrane destabilization induced by the conformational change of pH-switchable lipids. The simulated results showed that, at neutral pH, the neutral SL2 lipids assembled with other components (helper lipids and cholesterol) to form a structurally ordered bilayer structure. At this moment, the two hydrocarbon chains of SL2 were closely aligned and inserted in an orderly manner inside of the membrane. With a decrease in pH, the protonation of the pyridinium ring caused a large degree of molecular structural change. The pyridinium ring preferred to form intramolecular H-bonds with the methoxy groups and intermolecular H-bonds with water, resulting in the flip of the pyridinium ring. Meanwhile, due to the structural flip, the two alkane chains showed a more open state, which perturbed the arrangement of molecules within the membrane. The perturbations caused local collapse of the membrane and the formation of water molecule channels, which contributed to the pH-induced drug release. Our results verified the experimentally proposed mechanism at the molecular level and provided more complementary information, which are expected to have deeper insights into the pH-triggered drug release.

Towards New Anti-Inflammatory Agents: Design, Synthesis and Evaluation of Molecules Targeting XIAP-BIR2

The X-chromosome-linked inhibitor of apoptosis protein (XIAP) plays a crucial role in controlling cell survival across multiple regulated cell death pathways and coordinating a range of inflammatory signalling events. The discovery of selective inhibitors for XIAP-BIR2, able to disrupt the direct physical interaction between XIAP and RIPK2, offer promising therapeutic options for NOD2-mediated diseases like Crohn's disease, sarcoidosis, and Blau syndrome. The objective of this study was to design, synthesize, and evaluate small synthetic molecules with binding selectivity to XIAP-BIR2 domain. To achieve this, we applied an interdisciplinary drug design approach and firstly we have synthesized an initial fragment library to achieve a first XIAP inhibition activity. Then using a growing strategy, larger compounds were synthesized and one of them presents a good selectivity for XIAP-BIR2 versus XIAP-BIR3 domain, compound 20 c. The ability of compound 20 c to block the NOD1/2 pathway was confirmed in cell models. These data show that we have synthesized molecules capable of blocking NOD1/2 signalling pathways in cellulo, and ultimately leading to new anti-inflammatory compounds.

Fatty Alcohol Membrane Model for Quantifying and Predicting Amphiphilicity

Amphiphilicity is an important property for drug development and self-assembly. This paper introduces a general approach based on a simple fatty alcohol (dodecanol) membrane model that can be used to quantify the amphiphilicity of small molecules that are in good agreement with experimental surface tension data. By applying the model to a systematic series of compounds, it was possible to elucidate the effect of different motifs on amphiphilicity. The results further indicate that amphiphilicity correlates strongly with water-octanol partition coefficients (logP) for the 29 organic molecules examined in the 0 < logP < 4 range. Importantly, the simulation of the model membrane is an order of magnitude faster than a phospholipid membrane (e.g., 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) simulation and offers a simple atomistic approach for quantifying and predicting amphiphilicity of small drug-like molecules that could be used in quantitative structure-activity relationship studies.

Design and Synthesis of Triazine-Based Hydrogel for Combined Targeted Doxorubicin Delivery and PI3K Inhibition

Melanoma, an aggressive skin cancer originating from melanocytes, presents substantial challenges due to its high metastatic potential and resistance to conventional therapies. Hydrogels, 3D networks of hydrophilic polymers with high water-retention capacities, offer significant promise for controlled drug delivery applications. In this study, we report the synthesis and characterization of hydrogelators based on the triazine molecular scaffold, which self-assemble into fibrous networks conducive to hydrogel formation. Rheological analysis confirmed their hydrogelation properties, while microscopic techniques, including FE-SEM and FEG-TEM, provided insights into their morphological networks. The drug delivery capability of these hydrogelators was evaluated using doxorubicin, a widely employed anticancer agent, demonstrating enhanced biocompatibility and reduced side effects compared to free doxorubicin. Additionally, the hydrogelators exhibited inhibitory activity against phosphoinositide 3-kinase (PI3K), a key enzyme frequently mutated in cancer and also involved in melanoma progression. The dual functionality of this delivery system─controlled drug release and PI3K inhibition─highlights the potential of triazine-based hydrogelators as innovative therapeutic platforms for melanoma treatment.