All-atom Molecular Dynamics Simulations Research Articles

Insights into short chain polyethylene penetration of phospholipid bilayers via atomistic molecular dynamics simulations

The escalation of global plastic production, reaching an annual output of 400 million tons, has significantly intensified concerns regarding plastic waste management. This has been exacerbated by improper recycling and disposal practices, contributing to the impending crisis of plastic pollution. Predictions indicate that by 2025, the environment will bear the burden of over ten billion metric tons of accumulated plastic waste. This situation has led to the concerning release of microplastics and nanoplastics (NPs) into the environment as plastic materials degrade, thereby posing risks to both ecosystems and human health. Nanoparticle interactions with living organisms have garnered significant attention due to their potential to disrupt vital biological processes. Of particular interest are lipid membranes, acting as crucial gatekeepers, underscoring the importance of comprehending the intricate process of NP penetration. Molecular dynamics (MD) simulations serve as a robust tool, offering molecular-level insights into these intricate interactions. In this study, we leverage all-atom MD simulations to delve into the interactions between lipid bilayers and polyethylene (PETH) chains of varying lengths. The investigation spans diverse lipid bilayer compositions—ranging from pure POPC to POPC:DPPC mixtures—revealing how PETH accommodates itself, adopts extended conformations, and influences membrane structure and ordering. Significantly, while longer PETH chains demonstrate limited passive diffusion, their potential to penetrate bilayers over extended timescales emerges as a significant revelation. Overall, this research significantly advances our comprehension of NP-membrane interactions, shedding light on the potential environmental and health implications that lie ahead.

A novel algorithm for the virtual screening of extensive small molecule libraries against ERCC1/XPF protein-protein interaction for the identification of resistance-bypassing potential anticancer molecules.

Cancer cell's innate chemotherapeutic resistance continues to be an obstacle in molecular oncology. This theory is firmly tied to the cancer cells' integral DNA repair mechanisms continuously neutralizing the effects of chemotherapy. Amidst these mechanisms, the nuclear excision repair pathway is crucial in renovating DNA lesions prompted by agents like Cisplatin. The ERCC1/XPF complex stands center-stage as a structure-specific endonuclease in this repair pathway. Targeting the ERCC1/XPF dimerization brings forth a strategy to augment chemotherapy by eschewing the resistance mechanism integral to cancer cells. This study tracks and identifies small anticancer molecules, with ERCC1/XPF inhibiting potential, within extensive small-molecule compound libraries. A novel hybrid virtual screening algorithm, conjoining ligand- and target-based approaches, was developed. All-atom molecular dynamics (MD) simulations were then run on the obtained hit molecules to reveal their structural and dynamic contributions within the binding site. MD simulations were followed by MM/GBSA calculations to qualify the change in binding free energies of the protein/ligand complexes throughout MD simulations. Conducted analyses highlight new potential inhibitors AN-487/40936989 from the SPECS SC library, K219-1359, and K786-1161 from the ChemDiv Representative Set library as showing better predicted activity than previously discovered ERCC1/XPF inhibitor, CHEMBL3617209. The algorithm implemented in this study expands our comprehension of chemotherapeutic resistance and how to overcome it through identifying ERCC1/XPF inhibitors with the aim of enhancing chemotherapeutic impact giving hope for ameliorated cancer treatment outcomes.

Investigation of the MDM2-binding potential of de novo designed peptides using enhanced sampling simulations

The tumor suppressor p53 plays a crucial role in cellular responses to various stresses, regulating key processes such as apoptosis, senescence, and DNA repair. Dysfunctional p53, prevalent in approximately 50 % of human cancers, contributes to tumor development and resistance to treatment. This study employed deep learning-based protein design and structure prediction methods to identify novel high-affinity peptide binders (Pep1 and Pep2) targeting MDM2, with the aim of disrupting its interaction with p53. Extensive all-atom molecular dynamics simulations highlighted the stability of the designed peptide in complex with the target, supported by several structural analyses, including RMSD, RMSF, Rg, SASA, PCA, and free energy landscapes. Using the steered molecular dynamics and umbrella sampling simulations, we elucidate the dissociation dynamics of p53, Pep1, and Pep2 from MDM2. Notable differences in interaction profiles were observed, emphasizing the distinct dissociation patterns of each peptide. In conclusion, the results of our umbrella sampling simulations suggest Pep1 as a higher-affinity MDM2 binder compared to p53 and Pep2, positioning it as a potential inhibitor of the MDM2-p53 interaction. Using state-of-the-art protein design tools and advanced MD simulations, this study provides a comprehensive framework for rational in silico design of peptide binders with therapeutic implications in disrupting MDM2-p53 interactions for anticancer interventions.

Molecular Dynamics Insights into the Aggregation Behavior of N-Terminal β-Lactoglobulin Peptides.

β-lactoglobulin (BLG) forms amyloid-like aggregates at high temperatures, low pH, and low ionic strengths. At a pH below 2, BLG undergoes hydrolysis into peptides, with N-terminal peptides 1-33 and 1-52 being prone to fibrillization, forming amyloid-like fibrils. Due to their good mechanical properties, BLG amyloids demonstrate great potential for diverse applications, including biosensors, nanocomposites, and catalysts. Consequently, further studies are essential to comprehensively understand the factors governing the formation of BLG amyloid-like morphologies. In this study, all-atom molecular dynamics simulations were employed to explore the aggregation of N-terminal 1-33 and 1-52 BLG peptides under conditions of pH 2 and at 10 mM NaCl concentration. The simulations revealed that the peptides spontaneously assembled into aggregates of varying sizes. The aggregation process was enabled by the low charge of peptides and the presence of hydrophobic residues within them. As the peptides associated into aggregates, there was a concurrent increase in β-sheet structures and the establishment of hydrogen bonds, enhancing the stability of the aggregates. Notably, on average, 1-33 peptides formed larger aggregates compared to their 1-52 counterparts, while the latter exhibited a slightly higher content of β-sheets and higher cluster orderliness. The applied approach facilitated insights into the early stages of amyloid-like aggregation and molecular-level insight into the formation of β-sheets, which serve as nucleation points for further fibril growth.

All-Atom Photoinduced Charge Transfer Dynamics in Condensed Phase via Multistate Nonlinear-Response Instantaneous Marcus Theory.

Photoinduced charge transfer (CT) in the condensed phase is an essential component in solar energy conversion, but it is challenging to simulate such a process on the all-atom level. The traditional Marcus theory has been utilized for obtaining CT rate constants between pairs of electronic states but cannot account for the nonequilibrium effects due to the initial nuclear preparation. The recently proposed instantaneous Marcus theory (IMT) and its nonlinear-response formulation allow for incorporating the nonequilibrium nuclear relaxation to electronic transition between two states after the photoexcitation from the equilibrium ground state and provide the time-dependent rate coefficient. In this work, we extend the nonlinear-response IMT method for treating photoinduced CT among general multiple electronic states and demonstrate it in the organic photovoltaic carotenoid-porphyrin-fullerene triad dissolved in explicit tetrahydrofuran solvent. All-atom molecular dynamics simulations were employed to obtain the time correlation functions of energy gaps, which were used to generate the IMT-required time-dependent averages and variances of the relevant energy gaps. Our calculations show that the multistate IMT could capture the significant nonequilibrium effects due to the initial nuclear state preparation, and this is corroborated by the substantial differences between the population dynamics predicted by the multistate IMT and the Marcus theory, where the Marcus theory underestimates the population transfer. The population dynamics by multistate IMT is also shown to have a better agreement with the all-atom nonadiabatic mapping dynamics than the Marcus theory does. Because the multistate nonlinear-response IMT is straightforward and cost-effective in implementation and accounts for the nonequilibrium nuclear effects, we believe this method offers a practical strategy for studying charge transfer dynamics in complex condensed-phase systems.

Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein.

Allosteric regulation of protein dynamics infers a long-range deliberate propagation of information via micro- and macroscale interactions. The Y220C structural mutant is one of the most frequent cancerous p53 mutants. The mutation is distally located from the DNA-binding site of the p53 DNA-binding domain yet causes changes in DNA recognition. This system presents a unique opportunity to examine the allosteric control of mutated proteins under a drug design paradigm. We focus on the key case study of p53 Y220C mutation restoration by a series of new compounds suggested to have Y220C reactivation properties in comparison to our previous findings on the restorative potential of PK11000, a compound studied extensively for reactivation in vitro and in vivo. Previously, we implemented all-atom molecular dynamics (MD) simulations and our lab's techniques of MD-Sectors and MD-Markov state models on the wild type, the Y220C mutant, and Y220C with PK11000 to characterize the effector's restorative properties in terms of conformational dynamics and hydrogen bonding. In this study, we turn to probing the effects made by docking the battery of a new but less well-tested set of aminobenzothiazole derivative compounds reported by Baud et al., which show promise of Y220C rescue. We find that while complete and precise reconstitution of p53 WT molecular dynamics may not be observed as was the case with PK11000, dispersed local reconstitution of loop dynamics provides evidence of rescuing effects by aminobenzothiazole derivative N,2-dihydroxy-3,5-diiodo-4-(1H-pyrrol-1-yl)benzamide, Effector 22, like what we observed for PK11000. Generalizable insights into the mutation and allosteric reactivation of p53 by various effectors by reconstitution of WT dynamics observed in statistical conformational ensemble analysis and network inference are discussed, considering the development of allosteric drug design rooted in first principles.

Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b

ORF3b is one of the SARS-CoV-2 accessory proteins. Previous experimental study suggested that ORF3b prevents IRF3 translocating to nucleus. However, the biophysical mechanism of ORF3b-IRF3 interaction is elusive. Here, we explored the conformation ensemble of ORF3b using all-atom replica exchange molecular dynamics simulation. Disordered ORF3b has mixed α-helix, β-turn and loop conformers. The potential ORF3b-IRF3 binding modes were searched by docking representative ORF3b conformers with IRF3, and 50 ORF3b-IRF3 complex poses were screened using molecular dynamics simulations ranging from 500 to 1000 ns. We found that ORF3b binds IRF3 predominantly on its CBP binding and phosphorylated pLxIS motifs, with CBP binding site has the highest binding affinity. The ORF3b-IRF3 binding residues are highly conserved in SARS-CoV-2. Our results provided biophysics insights into ORF3b-IRF3 interaction and explained its interferon antagonism mechanism.

Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution

DNAJB6b is a molecular chaperone of the heat shock protein network, shown to play a crucial role in preventing aggregation of several disease-related intrinsically disordered proteins. Using homology modeling and microsecond-long all-atom molecular dynamics (MD) simulations, we show that monomeric DNAJB6b is a transiently interconverting protein cycling between three states: a closed state, an open state (both abundant), and a less abundant extended state. Interestingly, the reported regulatory autoinhibitory anchor between helix V in the G/F1 region and helices II/III of the J-domain, which obstructs the access of Hsp70 to the J-domain remains present in all three states. This possibly suggests a mechanistically intriguing regulation in which DNAJB6b only becomes exposed when loaded with substrates that require Hsp70 processing. Our MD results of DNAJB6b carrying mutations in the G/F1 region that are linked to limb-girdle muscular dystrophy type D1 (LGMDD1) show that this G/F1 region becomes highly dynamic, pointing towards a spontaneous release of the autoinhibitory helix V from helices II/III. This would increase the probability of non-functional Hsp70 interactions to DNAJB6b without substrates. Our cellular data indeed confirm that non-substrate loaded LGMDD1 mutants have aberrant interactions with Hsp70.

In silico study on graphene quantum dots modified with various functional groups inhibiting α‑synuclein dimerization

Hypothesis: Graphene quantum dots (GQDs) with various functional groups are hypothesized to inhibit the α-synuclein (αS) dimerization, a crucial step in Parkinson’s disease pathogenesis. The potential of differently functionalized GQDs is systematically explored.Experiments: All-atom replica-exchange molecular dynamics simulations (accumulating to 75.6 μs) in explicit water were performed to study the dimerization of the αS non-amyloid component region and the influence of GQDs modified with various functional groups. Conformation ensemble, binding behavior, and free energy analysis were conducted.Findings: All studied GQDs inhibit β-sheet and backbone hydrogen bond formation in αS dimers, leading to looser oligomeric conformations. Charged GQDs severely impede the growth of extended β-sheets by providing extra contact surface. GQD binding primarily disrupts αS inter-peptide interactions through π-π stacking, CH-π interactions, and for charged GQDs, additionally through salt-bridge and hydrogen bonding interactions. GQD-COO– showed the most optimal inhibitory effect, binding mode, and intensity, which holds promise for the development of nanomedicines targeting amyloid aggregation in neurodegenerative diseases.

Molecular dynamics simulation study of sodium ion structure & dynamics in water in ionic liquids electrolytes using 1-butyl-3-methyl imidazolium tetrafluoroborate and 1-butyl-3-methyl imidazolium hexafluorophosphate

In this paper, we have performed an all-atom molecular dynamics simulation to understand the structure and dynamics of Na+ ions in water mixed Ionic liquids (Water in Ionic liquid). Two ionic liquid (IL) systems consist of (1) 1-butyl-3-methylimidazolium [BMIM] tetrafluoroborate [BF4] and (2) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF6] were considered in this work. We understand various inter-molecular structures and dynamic and thermodynamic behaviours of Na+ ions in the water-mixed IL systems. The water (H2O) mole fractions (x) varied from 0.33 to 0.71. The neat ILs [BMIM][BF4] and [BMIM][PF6] pairwise radial distribution functions show a decrease with an increase in x. The [BMIM][PF6] exhibits a strong coordination structure with Na+ ions across the entire range of x values. The rdf between the pairs of Na+-[PF6] presents a significant interaction compared to Na+ and [BF4]. The Na + ions manifested greater coordination with H2O In H2O-[BMIM][PF6] compared to H2O-[BMIM][BF4]. The self-diffusion coefficient (D) values of Na + ions increase with the rise in x in both ILs. The D values of Na + ions are 10-fold higher in [BMIM][BF4] than [BMIM][PF6]. The ionic conductivity values are higher for [BMIM][BF4]. Overall, this paper unveils molecular-level insights for understanding the behavior of Na+ ions in the water in ionic liquid systems.

Effects of C479W Mutation on the Structure and Function of Band 3 Protein

Band 3, or anion exchanger 1 (AE1), is one of the indispensable transmembrane proteins involved in effective respiratory processes in the human body, mainly responsible for the exchange of bicarbonate and chloride ions on the plasma membrane of red blood cells. However, the effect of related gene mutations on Band 3 ion transport is not fully understood. In this work, we used all-atom molecular dynamics (MD) simulations to systematically investigate the effects of the mutation from cysteine (C) to tryptophan (W) at site 479 in Band 3 on the structure of Band 3 and its interaction with anions. We studied the kinetics of wild-type (WT) and mutant Band 3 interactions with bicarbonate and chloride ions on the microsecond scale. The results showed that the mutation at site 479 affected the stability of Band 3 structure and the distribution of anions, and changed the affinity of anions to different parts of Band 3. These findings provide some insights into the structural and functional effects of gene mutations in Band 3 and contribute to understanding Band 3 anion exchange.

Interaction between Yersinia pestis Ail Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin.

Yersinia pestis, the causative agent of plague, is capable of evading the human immune system response by recruiting the plasma circulating vitronectin proteins, which act as a shield and avoid its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from the Y. pestis outer membrane. By using all-atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents.

The influence of anions in the ionic liquid-water mixtures on the conformational structures of emeraldine base and emeraldine salt form of polyaniline

The development of antifouling membranes for water filtration applications is challenging. Conducting polymers can show enhanced antifouling characteristics by blending with various polymers, nanomaterials, and Ionic liquids (ILs). In this paper, we perform an all-atom molecular dynamics simulation on a conducting polymer polyaniline (PANI) immersed in IL-water mixtures. Two forms of PANI were considered, namely Emeraldine base (EB) and Emeraldine salt (ES) as well as two different water-mixed ILs are considered namely (a) 1-ethyl-3-methyl imidazolium [EMIM]+ hexafluorophosphate [PF6]- and (b) 1-ethyl-3-methyl imidazolium [EMIM]+ tetra-fluoroborate [BF4]-. We present various intra- and inter-molecular structural properties, solvation thermodynamics, and dynamic properties. We observe that with an increase in IL concentration, the radius of gyration (Rg) value shows a decrease for ES in pure state in both ILs; on the other hand, we see a minimal increase in the Rg values of EB in both ILs. The dihedral angle distribution analysis shows a combination of gauche and trans state for ES, whereas trans state is more pronounced for the case of EB in both water-IL mixtures. The radial distribution function (RDF) analysis between the ortho, meta carbons of the benzene rings, and the amine groups on ES with [BF4]- and [PF6]- show significant structural peaks. On the other hand, EB and ES show lower interaction with the water molecules. The number of hydrogen bonds (h-bonds) between polymer and water is higher for EB than ES in both IL-water mixtures. The hydrogen bond lifetime (τ) values show one-fold higher values for EB than ES. The self-diffusion coefficient (D) values of water show a decrease with an increase in IL concentration. The thermodynamic properties solvation enthalpy (ΔH) and excess molar volume (VmE) for both ES and EB show a more favorable solvation in [EMIM]+[BF4]- when compared to [EMIM]+[PF6]- with an increase in IL concentration. These observations are crucial for selecting ILs and designing sustainable polymers for antifouling membranes.

Biomimetic Vesicles with Designer Phospholipids Can Sense Environmental Redox Cues.

Cell-like materials that sense environmental cues can serve as next-generation biosensors and help advance the understanding of intercellular communication. Currently, bottom-up engineering of protocell models from molecular building blocks remains a grand challenge chemists face. Herein, we describe giant unilamellar vesicles (GUVs) with biomimetic lipid membranes capable of sensing environmental redox cues. The GUVs employ activity-based sensing through designer phospholipids that are fluorescently activated in response to specific reductive (hydrogen sulfide) or oxidative (hydrogen peroxide) conditions. These synthetic phospholipids are derived from 1,2-dipalmitoyl-rac-glycero-3-phosphocholine and they possess a headgroup with heterocyclic aromatic motifs. Despite their structural deviation from the phosphocholine headgroup, the designer phospholipids (0.5-1.0 mol %) mixed with natural lipids can vesiculate, and the resulting GUVs (7-20 μm in diameter) remain intact over the course of redox sensing. All-atom molecular dynamics simulations gave insight into how these lipids are positioned within the hydrophobic core of the membrane bilayer and at the membrane-water interface. This work provides a purely chemical method to investigate potential redox signaling and opens up new design opportunities for soft materials that mimic protocells.

Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds’ intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.

Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein

Cumulative global prevalence of the emergent monkeypox (MPX) infection in the non-endemic countries has been professed as a global public health predicament. Lack of effective MPX-specific treatments sets the baseline for designing the current study. This research work uncovers the effective use of known antiviral polyphenols against MPX viral infection, and recognises their mode of interaction with the target F13 protein, that plays crucial role in formation of enveloped virions. Herein, we have employed state-of-the-art machine learning based AlphaFold2 to predict the three-dimensional structure of F13 followed by molecular docking and all-atoms molecular dynamics (MD) simulations to investigate the differential mode of F13-polyphenol interactions. Our extensive computational approach identifies six potent polyphenols Rutin, Epicatechingallate, Catechingallate, Quercitrin, Isoquecitrin and Hyperoside exhibiting higher binding affinity towards F13, buried inside a positively charged binding groove. Intermolecular contact analysis of the docked and MD simulated complexes divulges three important residues Asp134, Ser137 and Ser321 that are observed to be involved in ligand binding through hydrogen bonds. Our findings suggest that ligand binding induces minor conformational changes in F13 to affect the conformation of the binding site. Concomitantly, essential dynamics of the six-MD simulated complexes reveals Catechin gallate, a known antiviral agent as a promising polyphenol targeting F13 protein, dominated with a dense network of hydrophobic contacts. However, assessment of biological activities of these polyphenols need to be confirmed through in vitro and in vivo assays, which may pave the way for development of new novel antiviral drugs.

Thermodynamic consequences of stapling side-chains on a peptide ligand using a lactam-bridge: A theoretical study on anti-angiogenic peptides targeting VEGF.

Peptides are promising therapeutic agents for various biological targets due to their high efficacy and low toxicity, and the design of peptide ligands with high binding affinity to the target of interest is of utmost importance in peptide-based drug design. Introducing a conformational constraint to a flexible peptide ligand using a side-chain lactam-bridge is a convenient and efficient method to improve its binding affinity to the target. However, in general, such a small structural modification to a flexible ligand made with the intent of lowering the configurational entropic penalty for binding may have unintended consequences in different components of the binding enthalpy and entropy, including the configurational entropy component, which are still not clearly understood. Toward probing this, we examine different components of the binding enthalpy and entropy as well as the underlying structure and dynamics, for a side-chain lactam-bridged peptide inhibitor and its flexible analog forming complexes with vascular endothelial growth factor (VEGF), using all-atom molecular dynamics simulations. It is found that introducing a side-chain lactam-bridge constraint into the flexible peptide analog led to a gain in configurational entropy change but losses in solvation entropy, solute internal energy, and solvation energy changes upon binding, pinpointing the opportunities and challenges in drug design. The present study features an interplay between configurational and solvation entropy changes, as well as the one between binding enthalpy and entropy, in ligand-target binding upon imposing a conformational constraint into a flexible ligand.

Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling.

HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56-77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.

Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations

The SNAP receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin mediate neurotransmitter release by forming tight SNARE complexes that fuse synaptic vesicles with the plasma membranes in microseconds. Membrane fusion is generally explained by the action of proteins on macroscopic membrane properties such as curvature, elastic modulus, and tension, and a widespread model envisions that the SNARE motifs, juxtamembrane linkers, and C-terminal transmembrane regions of synaptobrevin and syntaxin-1 form continuous helices that act mechanically as semirigid rods, squeezing the membranes together as they assemble ("zipper") from the N to the C termini. However, the mechanism underlying fast SNARE-induced membrane fusion remains unknown. We have used all-atom molecular dynamics simulations to investigate this mechanism. Our results need to be interpreted with caution because of the limited number and length of the simulations, but they suggest a model of membrane fusion that has a natural physicochemical basis, emphasizes local molecular events over general membrane properties, and explains extensive experimental data. In this model, the central event that initiates fast (microsecond scale) membrane fusion occurs when the SNARE helices zipper into the juxtamembrane linkers which, together with the adjacent transmembrane regions, promote encounters of acyl chains from both bilayers at the polar interface. The resulting hydrophobic nucleus rapidly expands into stalk-like structures that gradually progress to form a fusion pore, aided by the SNARE transmembrane regions and without clearly discernible intermediates. The propensity of polyunsaturated lipids to participate in encounters that initiate fusion suggests that these lipids may be important for the high speed of neurotransmitter release.

Repurposing Drugs to Modulate Sortilin: Structure-Guided Strategies Against Atherogenesis, Coronary Artery Disease, and Neurological Disorders.

Sortilin (SORT1) is a multifunctional protein intricately involved in atherogenesis, coronary artery disease (CAD), and various neurological disorders. It has materialized as a potential pharmacological target for therapeutic development due to its diverse biological roles in pathological processes. Despite its central role under these conditions, effective therapeutic strategies targeting SORT1 remain challenging. In this study, we introduce a drug repurposing strategy guided by structural insights to identify potent SORT1 inhibitors with broad therapeutic potential. Our approach combines molecular docking, virtual screening, and molecular dynamics (MD) simulations, enabling the systematic evaluation of 3648 FDA-approved drugs for their potential to modulate SORT1. The investigation reveals a subset of repurposed drugs exhibiting highly favorable binding profiles and stable interactions within the binding site of SORT1. Notably, two hits, ergotamine and digitoxin, were carefully chosen based on their drug profiles and subjected to analyze their interactions with SORT1 and stability assessment via all-atom MD simulations spanning 300 ns (ns). The structural analyses uncover the complex binding interactions between these identified compounds and SORT1, offering essential mechanistic insights. Additionally, we explore the clinical implications of repurposing these compounds as potential therapeutic agents, emphasizing their significance in addressing atherogenesis, CAD, and neurological disorders. Overall, this study highlights the efficacy of structure-guided drug repurposing and provides a solid foundation for future research endeavors aimed at the development of effective therapies targeting SORT1 under diverse pathological conditions.