A smooth particle mesh Ewald method

Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations

Plastic-degrading enzymes, particularly poly(ethylene terephthalate) (PET) hydrolases, have garnered significant attention in recent years as potential eco-friendly solutions for recycling plastic waste. However, understanding of their PET-degrading activity and influencing factors remains incomplete, impeding the development of uniform approaches for enhancing PET hydrolases for industrial applications. A key aspect of PET hydrolase engineering is optimizing the PET-hydrolysis reaction by lowering the associated free energy barrier. However, inconsistent findings have complicated these efforts. Therefore, our goal is to elucidate various aspects of enzymatic PET degradation by means of quantum mechanics/molecular mechanics (QM/MM) reaction simulations and analysis, focusing on the initial reaction step, acylation, in two thermophilic PET hydrolases, LCC and PES-H1, along with their highly active variants, LCCIG and PES-H1FY. Our findings highlight the impact of semiempirical QM methods on proton transfer energies, affecting the distinction between a two-step reaction involving a metastable tetrahedral intermediate and a one-step reaction. Moreover, we uncovered a concerted conformational change involving the orientation of the PET benzene ring, altering its interaction with the side-chain of the "wobbling" tryptophan from T-stacking to parallel π-π interactions, a phenomenon overlooked in prior research. Our study thus enhances the understanding of the acylation mechanism of PET hydrolases, in particular by characterizing it for the first time for the promising PES-H1FY using QM/MM simulations. It also provides insights into selecting a suitable QM method and a reaction coordinate, valuable for future studies on PET degradation processes.

Temperature behavior of the velocity autocorrelation function in large MD models of water

Velocity autocorrelation functions (VACFs) were calculated using the molecular dynamics method in the TIP4P/2005 and SPC/E water models of 157 464 molecules at temperatures ranging from 250 to 370 K. The large size of the models and the high accuracy of the calculations allow us to reliably compute the long-time tails of the VACFs, showing that they systematically change shape from hydrodynamic (argon-like) at high temperatures to that typical of supercooled liquids at low temperatures. These tails in the range of 2-10 ps can be well fitted by a combination of two power functions: At-3/2 - Bt-β (A, B > 0, β ≈ 2). It is found that the amplitude of the hydrodynamic asymptote, A, approaches zero as the temperature decreases, thereby rendering the negative power-law decay,-Bt-2, the dominant term within the specified time interval. The presence of a negative -Bt-2 decay in the time interval of 2-10 ps determines the specific shape of the VACF long-time tail of water, distinguishing it from ordinary simple liquids. The amplitude B, which is always non-zero, demonstrates a slight increase with rising temperature. At medium temperatures, weak but well-defined damped oscillations are observed on the VACF in the 0.5-2 ps interval.

Integrating protein interaction and pathway crosstalk network reveals a promising therapeutic approach for psoriasis through apoptosis induction

Psoriasis is a complex inflammatory skin disease manifested by altered proliferation and differentiation of keratinocytes with dysfunctional apoptosis. This study aimed to identify regulatory factors and comprehend the underlying mechanisms of inefficient apoptosis to open up promising therapeutic approaches. Incorporating human protein interactions, apoptosis proteins, and physical relationships of psoriasis-apoptosis proteins helped us to generate a psoriasis-apoptosis interaction (SAI) network. Subsequently, topological and functional analyses of the SAI network revealed effective proteins, functional modules, hub motifs, dysregulated pathways and transcriptional gene regulatory factors. Network pharmacology, molecular docking and molecular dynamics simulation methods identified the potential drug-target interactions. RELA, MAPK1, MAPK3, MMP9, IL1B, AKT1 and STAT1 were revealed as effective proteins. The MAPK1-MAPK3-RELA motif was identified as a hub regulator in the crosstalk between 41 pathways. Among all pathways, "lipid and atherosclerosis" was found to be the predominant pathway. Acetylcysteine, arsenic-trioxide, β-elemene, bortezomib and curcumin were identified as potential drugs to inhibit pathway crosstalk. Experimental verifications were performed using the literature search, GSE13355 and GSE14905 microarray datasets. Drug-protein-pathway interactions associated with apoptosis were deciphered. These findings highlight the role of hub motif-mediated pathway-pathway crosstalk associated with apoptosis in the complexity of psoriasis and suggest crosstalk inhibition as an effective therapeutic approach.

Dissociation of Nicotine from Acetylcholine-Binding Protein under Terahertz Waves Radiation

The binding of nicotine (NCT) to acetylcholine-binding protein (AChBP) plays an important role in synaptic transmission and neurotransmitter regulation. However, effectively regulating their binding or dissociation processes remains a challenging problem. In this study, we employed all-atom molecular dynamics (MD) simulations to systematically investigate the impact of external terahertz (THz) waves on the binding kinetics between AChBP and NCT. We first identified the key residues (i.e., W143) and the key interactions (i.e., hydrogen bonding and cation-π interaction) in AChBP-NCT binding without THz waves. We then investigated the binding and dissociation of charged NCT with AChBP at three different frequencies (i.e., 13.02, 21.44, 42.55 THz). Importantly, the predominant vibrational modes at 13.02 THz can drive the rotation of the pentagonal ring on NCT. This leads to the disruption of hydrogen bonds between NCT and W143 and a reduced likelihood of forming cation-π interactions, resulting in the dissociation of NCT from AChBP. Additionally, we further investigated the influence of electric field intensities on the dissociation kinetics and found that when the electric field intensity exceeds a critical value (∼0.60 V/nm), the probability of ligand dissociation gradually rises as the intensity increases. In general, this study contributes to a better understanding of the effects of THz waves on protein-ligand interactions, which might also shed some light on potential applications in nicotine addiction treatment and therapeutic strategies for neurodegenerative diseases.

14-3-3 phosphorylation inhibits 14-3-3θ's ability to regulate LRRK2 kinase activity and toxicity

LRRK2 mutations are among the most common genetic causes for Parkinson's disease (PD), and toxicity is associated with increased kinase activity. 14-3-3 proteins are key interactors that regulate LRRK2 kinase activity. Phosphorylation of the 14-3-3θ isoform at S232 is dramatically increased in human PD brains. Here we investigate the impact of 14-3-3θ phosphorylation on its ability to regulate LRRK2 kinase activity. Both wildtype and the non-phosphorylatable S232A 14-3-3θ mutant reduced the kinase activity of wildtype and G2019S LRRK2, whereas the phosphomimetic S232D 14-3-3θ mutant had minimal effects on LRRK2 kinase activity, as determined by measuring autophosphorylation at S1292 and T1503 and Rab10 phosphorylation. However, wildtype and both 14-3-3θ mutants similarly reduced the kinase activity of the R1441G LRRK2 mutant. 14-3-3θ phosphorylation did not promote global dissociation with LRRK2, as determined by co-immunoprecipitation and proximal ligation assays. 14-3-3s interact with LRRK2 at several phosphorylated serine/threonine sites, including T2524 in the C-terminal helix, which can fold back to regulate the kinase domain. Interaction between 14-3-3θ and phosphorylated T2524 LRRK2 was important for 14-3-3θ's ability to regulate kinase activity, as wildtype and S232A 14-3-3θ failed to reduce the kinase activity of G2019S/T2524A LRRK2. Finally, we found that the S232D mutation failed to protect against G2019S LRRK2-induced neurite shortening in primary cultures, while the S232A mutation was protective. We conclude that 14-3-3θ phosphorylation destabilizes the interaction of 14-3-3θ with LRRK2 at T2524, which consequently promotes LRRK2 kinase activity and toxicity.

Effects of Normal and Lateral Electric Fields on Membrane Mechanical Properties

As a core component of biological and synthetic membranes, lipid bilayers are key to compartmentalizing chemical processes. Bilayer morphology and mechanical properties are heavily influenced by electric fields, such as those caused by biological ion concentration gradients. We present atomistic simulations exploring the effects of electric fields applied normally and laterally to lipid bilayers. We find that normal fields decrease membrane tension, while lateral fields increase it. Free energy perturbation calculations indicate the importance of dipole-dipole interactions to these tension changes, especially for lateral fields. We additionally show that membrane area compressibilities can be related to their cohesive energies, allowing us to estimate changes in membrane bending rigidity under applied fields. We find that normal and lateral fields decrease and increase bending rigidity, respectively. These results point to the use of directed electric fields to locally control membrane stiffness, thereby modulating associated cellular processes.

Trp-cage-1,1,1,3,3,3-Hexafluoro-2-propanol-Water Interactions in a Nanosphere at 298 K

MD simulations of the peptide Trp-cage dissolved in a solvent composed of 28% 1,1,1,3,3,3-hexafluoroisopropanol-water and contained within a nanosphere of 4.2 nm radius are described. To provide a thermal buffer, the nanosphere is submerged in a collection of liquid neopentane molecules, modeled as united atoms. It was found that the HFIP-water mixture demixes when confined under these conditions, with most of the fluoroalcohol becoming strongly associated with the walls of the nanosphere. The remaining HFIP interacts with the peptide and itself in the interior of the nanoshell. Diffusion of HFIP molecules near the surface of the nanoshell is limited, taking place over a small volume, while diffusion of the fluoroalcohol in the center of the nanoshell is more wide-ranging. By contrast, diffusion of the water in the solvent mixture appears to take place equivalently throughout the shell. The conformation of the peptide, distribution of solvent components around it, and the number and duration of the contacts with solvent molecules are calculated and contrasted to results previously reported for the bulk (non-nanocontained) system.

Development and assessment of novel pyrazole-thiadiazol hybrid derivatives as VEGFR-2 inhibitors: design, synthesis, anticancer activity evaluation, molecular docking, and molecular dynamics simulation

Cancer remains a significant health challenge globally, requiring the development of targeted chemotherapeutics capable of specifically inhibiting cancer cell growth. Angiogenesis is one of the key features of tumor growth and metastasis and is, therefore, an important target for the treatment of many tumors. The vascular endothelial growth factor (VEGF) signaling pathway has proven to be a promising lead in anticancer therapy due to the central role it plays in tumor angiogenesis. Vascular endothelial growth factor receptor-2 (VEGFR-2) is a key mediator in the signaling pathway regulating angiogenesis. Targeting VEGFR-2 may disrupt angiogenesis, leading to a reduction in tumor blood supply and tumor progression. The design, synthesis, and assessment of novel VEGFR-2 inhibitor derivatives are the focus of this study, with particular emphasis on incorporating the pyrazole-thiadiazol pharmacophore into the molecular structure. Taking advantage of the pharmacophoric properties of pyrazole and 1,3,4-thiadiazol, compounds with different substituents in the main structure were designed and synthesized. The compounds were also evaluated for antiproliferative activity against cancer cell lines. Compound 4e demonstrated the highest activity among all compounds, with an IC50 of 9.673 ± 0.399 μM against HT-29 cells and 23.081 ± 0.400 μM against NIH3T3 cells. To further support the inhibitory activity of compound 4e, an in silico study was performed. Compound 4e demonstrated strong binding to the active site of VEGFR-2 in molecular docking studies, forming hydrogen bonds with key amino acid residues. The stability of the compound in the enzyme's active site was demonstrated through molecular dynamics simulations.

Structural and mechanistic insights into a mesophilic prokaryotic Argonaute

Argonaute (Ago) proteins are programmable nucleases found in all domains of life, playing a crucial role in biological processes like DNA/RNA interference and gene regulation. Mesophilic prokaryotic Agos (pAgos) have gained increasing research interest due to their broad range of potential applications, yet their molecular mechanisms remain poorly understood. Here, we present seven cryo-electron microscopy structures of Kurthia massiliensis Ago (KmAgo) in various states. These structures encompass the steps of apo-form, guide binding, target recognition, cleavage, and release, revealing that KmAgo employs a unique DDD catalytic triad, instead of a DEDD tetrad, for DNA target cleavage under 5'P-DNA guide conditions. Notably, the last catalytic residue, D713, is positioned outside the catalytic pocket in the absence of guide. After guide binding, D713 enters the catalytic pocket. In contrast, the corresponding catalytic residue in other Agos has been consistently located in the catalytic pocket. Moreover, we identified several sites exhibiting enhanced catalytic activity through alanine mutagenesis. These sites have the potential to serve as engineering targets for augmenting the catalytic efficiency of KmAgo. This structural analysis of KmAgo advances the understanding of the diversity of molecular mechanisms by Agos, offering insights for developing and optimizing mesophilic pAgos-based programmable DNA and RNA manipulation tools.

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfation patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks to their unmatched microscopic resolution, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics force fields used in biosimulations to accurately capture sulfation-specific interactions is not well established, partly due to the intrinsic properties of GAGs that pose challenges for most experimental techniques. In this work, we evaluate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca2+ to sulfated moieties─N-methylsulfamate and methylsulfate─that resemble N- and O-sulfation found in GAGs, respectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06) and explicitly polarizable (Drude and AMOEBA) force fields, and derived new implicitly polarizable models through charge scaling (prosECCo75 and GLYCAM-ECC75) that are consistent with our developed "charge-scaling" framework. The calcium-sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations, which serve as a robust alternative to experiments. AIMD simulations indicate that the preferential Ca2+ binding mode to sulfated GAG groups is solvent-shared pairing. Only our scaled-charge models agree satisfactorily with the AIMD data, while all other force fields exhibit poorer agreement, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields display a notable disagreement with the AIMD data, likely attributed to difficulties in their optimization and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, which qualitatively disagrees with our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.

Identifying Potential Human Monoacylglycerol Lipase Inhibitors from the Phytoconstituents of Morinda Citrifolia L. Fruits by in silico Pharmacology and in vitro Study

Background

Human monoacylglycerol lipase (MGL) is accountable for the hydrolysis of 2-arachidonoylglycerol (2-AG), thus contributing pivotally to neuroprotection because 2-AG is the main source of arachidonic acid, the precursor of prostaglandins production. Inhibiting MGL reduces inflammatory damage in the ischemic brain and enhances cerebral blood flow. Plants have been reported for their neuroprotective effect, such as Morinda citrifolia on pentylenetetrazol (PTZ)-induced kindling seizures in mice, by reducing the seizures and restoring behavioral and biochemical changes, although the mechanism is not described.

Purpose

To evaluate the binding affinity and stability of phytoconstituents in M. citrifolia fruits toward human MGL (PDB ID 3PE6), compared to the known MGL inhibitors (JZL195 and ZYH). The in silico pharmacology study was validated by an in vitro study of the phytosterols and the ethanol extract of M. citrifolia fruits (EEMC) towards MGL.

Methods

Initially, nine phytoconstituents of M. citrifolia fruits were docked to the catalytic pocket of human MGL (PDB ID: 3PE6), and compounds with the best affinity were subjected to a molecular dynamic (MD) simulation. The in vitro study was performed using the MGL inhibitor screening assay kit.

Results

The best binding affinity and stability toward human MGL were shown by stigmasterol and beta-sitosterol, and the MM-PBSA total binding energy of stigmasterol and beta-sitosterol to MGL is stronger than that of JZL195 and ZYH. Moreover, beta-sitosterol and EEMC inhibit MGL with an IC50 value of, respectively, 8.10 μg/mL and 196.20 μg/mL, while JZL195 shows an IC50 of 0.028 μg/mL.

Conclusion

Beta-sitosterol of Morinda citrifolia fruits may have the potential to protect human neurons by occupying the catalytic site of human MGL, thus competitively inhibiting the substrate of the enzyme. However, the inhibitory activity towards human MGL is lower than JZL195.

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern

One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into β-sheets, and F2 peptides partially fold into an α-helical structure. The β-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although β-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of β-sheets spanning both leaflets of the bilayer.

Computational investigation of the effects of polymer grafting on the effective interaction between silica nanoparticles in water

Understanding and control of the effective interaction between nanoscale building blocks (colloids or nanoparticles) dispersed in a solvent is an important prerequisite for the development of bottom-up design strategies for soft functional materials. Here, we have employed all-atom molecular dynamics simulations to investigate the impact of polymer grafting on the solvent-mediated effective interaction between the silica nanoparticles (Si-NPs) in water, and in turn, on its bulk structural and thermodynamic properties. We found that the nature of the short grafting polymers [characterized by their interaction with water (hydrophobicity or hydrophilicity) and molecular weight] has a profound effect on the range and strength of the effective interaction between the Si-NPs. The hydrophobic polymer [such as polyethylene (PE)]-grafting of Si-NP gives rise to a more attractive interaction between the Si-NPs compared to the hydrophilic polymer [such as polyethylene glycol (PEG)] and non-grafted cases. This study further provides fundamental insights into the molecular origin of the observed behavior of the effective pair interactions between the grafted Si-NPs. For PE-grafted Si-NPs, the confined water (water inside the cavity formed by a pair of Si-NPs) undergoes a partial dewetting transition on approaching below a critical inter-particle separation leading to a stronger attractive interaction. Furthermore, we report that the effective attraction between the PE-grafted Si-NPs can be reliably controlled by changing the grafting PE density. We have also investigated the bulk structural and thermodynamic behavior of the coarse-grained Si-NP system where the particles interact via effective interaction in the absence of water. We believe that the insights gained from this work are important prerequisites for formulating rational bottom-up design strategies for functional materials where nano- (or, colloidal) particles are the building blocks.

The retinal chromophore environment in an inward light-driven proton pump studied by solid-state NMR and hydrogen-bond network analysis

Inward proton pumping is a relatively new function for microbial rhodopsins, retinal-binding light-driven membrane proteins. So far, it has been demonstrated for two unrelated subgroups of microbial rhodopsins, xenorhodopsins and schizorhodopsins. A number of recent studies suggest unique retinal-protein interactions as being responsible for the reversed direction of proton transport in the latter group. Here, we use solid-state NMR to analyze the retinal chromophore environment and configuration in an inward proton-pumping Antarctic schizorhodopsin. Using fully 13C-labeled retinal, we have assigned chemical shifts for every carbon atom and, assisted by structure modelling and molecular dynamics simulations, made a comparison with well-studied outward proton pumps, identifying locations of the unique protein-chromophore interactions for this functional subclass of microbial rhodopsins. Both the NMR results and molecular dynamics simulations point to the distinctive polar environment in the proximal part of the retinal, which may result in a hydration pattern dramatically different from that of the outward proton pumps, causing the reversed proton transport.

High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method

Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes. Molecular dynamics (MD) simulation is a useful complement as it provides the spatial detail that native MS cannot offer. However, MD simulations performed in the gas phase have suffered from rapidly increasing computational costs with the system size. The primary bottleneck is the calculation of electrostatic forces, which are effective over long distances and must be explicitly computed for each atom pair, precluding efficient use of methods traditionally used to accelerate condensed-phase simulations. As a result, MD simulations have been unable to match the capacity of MS in probing large multimeric protein complexes. Here, we apply the fast multipole method (FMM) for computing the electrostatic forces, recently implemented by Kohnke et al. (J. Chem. Theory Comput., 2020, 16, 6938-6949), showing that it significantly enhances the performance of gas-phase simulations of large proteins. We assess how to achieve adequate accuracy and optimal performance with FMM, finding that it expands the accessible size range and time scales dramatically. Additionally, we simulate a 460 kDa ferritin complex over microsecond time scales, alongside complementary ion mobility (IM)-MS experiments, uncovering conformational changes that are not apparent from the IM-MS data alone.

Structural insights into the allosteric effects of the antiepileptic drug topiramate on the CaV2.3 channel

The R-type voltage-gated calcium channel CaV2.3 is predominantly located in the presynapse and is implicated in distinct types of epileptic seizures. It has consequently emerged as a molecular target in seizure treatment. Here, we determined the cryo-EM structure of the CaV2.3-α2δ1-β1 complex in the topiramate-bound state at a 3.0 Å resolution. We provide a snapshot of the binding site of topiramate, a widely prescribed antiepileptic drug, on a voltage-gated ion channel. The binding site is located at an intracellular juxtamembrane hydrophilic cavity. Further structural analysis revealed that topiramate may allosterically facilitate channel inactivation. These findings provide fundamental insights into the mechanism underlying the inhibitory effect of topiramate on CaV and NaV channels, elucidating a previously unseen modulator binding site and thus pointing toward a route for the development of new drugs.

A Patent-Pending Ointment Containing Extracts of Five Different Plants Showed Antinociceptive and Anti-Inflammatory Mechanisms in Preclinical Studies

Background/Objectives: The antinociceptive and anti-inflammatory effects of a patent-pending ointment containing plant extracts from Eucalyptus globulus, Curcuma longa, Hamamelis virginiana, Echinacea purpurea, and Zingiber officinale were evaluated. Methods: Plant extracts were chemically characterized by gas chromatography-mass spectroscopy. The antinociceptive activity of the ointment was assessed using the hot plate, tail flick, and formalin tests, whereas the anti-inflammatory activity was measured using the acute and chronic TPA-induced ear edema tests. Mechanisms of action were evaluated using inhibitors from signaling pathways related to pain response and by using histological analysis and assessing the expression and activity of pro-inflammatory mediators. Results: The ointment showed antinociceptive and anti-inflammatory effects like those observed with diclofenac gel (1.16% v/v) and ketoprofen gel (2.5% v/v). The antinociceptive actions of the ointment are mediated by the possible participation of the opiodergic system and the nitric oxide pathway. The anti-inflammatory response was characterized by a decrease in myeloperoxidase (MPO) activity and by a reduction in ear swelling and monocyte infiltration in the acute inflammation model. In the chronic model, the mechanism of action relied on a decrease in pro-inflammatory mediators such as COX-2, IL-1β, TNF-α, and MPO. An in-silico study with myristic acid, one of the compounds identified in the ointment's plant mixture, corroborated the in vivo results. Conclusions: The ointment showed antinociceptive activities mediated by the decrease in COX-2 and NO levels, and anti-inflammatory activity due to the reduction in IL-1β and TNFα levels, a reduction in MPO activity, and a decrease in NF-κB and COX-2 expression.

Exploring the influence of pore shape on conductance and permeation

There are increasing numbers of ion channel structures featuring heteromeric subunit assembly, exemplified by synaptic α1βB glycine and α4β2 nicotinic receptors. These structures exhibit inherent pore asymmetry, but the relevance of this to function is unknown. Furthermore, molecular dynamics simulations performed on symmetrical homomeric channels often lead to thermal distortion whereby conformations of the resulting ensemble are also asymmetrical. When functionally annotating ion channels, researchers often rely on minimal constrictions determined via radius-profile calculations performed with computer programs, such as HOLE or CHAP, coupled with an assessment of pore hydrophobicity. However, such tools typically employ spherical probe particles, limiting their ability to accurately capture pore asymmetry. Here, we introduce an algorithm that employs ellipsoidal probe particles, enabling a more comprehensive representation of the pore geometry. Our analysis reveals that the use of nonspherical ellipsoids for pore characterization provides a more accurate and easily interpretable depiction of conductance. To quantify the implications of pore asymmetry on conductance, we systematically investigated carbon nanotubes with varying degrees of pore asymmetry as model systems. The conductance through these channels shows surprising effects that would otherwise not be predicted with spherical probes. The results have broad implications not only for the functional annotation of biological ion channels but also for the design of synthetic channel systems for use in areas such as water filtration. Furthermore, we make use of the more accurate characterization of channel pores to refine a physical conductance model to obtain a heuristic estimate for single-channel conductance. The code is freely available, obtainable as pip-installable python package and provided as a web service.

Flavonoid-Quinoxaline Hybrid Compounds as Cathepsin Inhibitors Against Fascioliasis

Fasciola hepatica is a parasitic trematode that infects livestock animals and humans, causing significant health and economic burdens worldwide. The extensive use of anthelmintic drugs has led to the emergence of resistant parasite strains, posing a threat to treatment success. The complex life cycle of the liver fluke, coupled with limited funding and research interest, have hindered progress in drug discovery. Our group has been working in drug development against this parasite using cathepsin proteases as molecular targets, finding promising compound candidates with in vitro and in vivo efficacy. Here, we evaluated hybrid molecules that combine two chemotypes, chalcones and quinoxaline 1,4-di- N-oxides, previously found to inhibit F. hepatica cathepsin Ls and tested their in vitro activity with the isolated targets and the parasites in culture. These molecules proved to be good cathepsin inhibitors and to kill the juvenile parasites at micromolar concentrations. Also, we performed molecular docking studies to analyze the compounds-cathepsins interface, finding that the best inhibitors interact at the active site cleft and contact the catalytic dyad and residues belonging to the substrate binding pockets. We conclude that the hybrid compounds constitute promising scaffolds for the further development of new fasciolicidal compounds.

Computational investigation of novel synthetic analogs of C-1'β substituted remdesivir against RNA-dependent RNA-polymerase of SARS-CoV-2

Remdesivir, a C-nucleotide prodrug binds to the viral RNA-dependent-RNA polymerase (RdRp) and inhibits the viral replication by terminating RNA transcription prematurely. It is reported in literature that interaction between the C-1'β-CN moiety of Remdesivir (RDV) and the Ser861 residue in RdRp enzyme, causes a delayed chain termination during the RNA replication process and is one of the important aspect of its mechanism of action. In the pursuance of increasing the biological activity of RDV and enhancing the SAR studies, against RNA viruses, we have designed its fourteen C1'β substituted analogs, 10 -23 bearing 4/5-membered heterocyclic rings. The docking and 100 ns molecular dynamics (MD) simulations of 10-23 to the RdRp protein (PDB ID: 7L1F) revealed important interactions between 2',3'-diol, oxo group of phosphoramidate, nitrogen residues of heterocyclic rings of synthetic molecules with Arg555, Arg553, Ser759, Cys622, Asn691, Asp623 amino acid residues of protein. The docking score of 2-ethylbutyl ((S)-(((2R,3S,4R,5R)-5-(4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl)-3,4-dihydroxy-5-(1H-1,2,3-triazol-4-yl)tetrahydrofuran-2-yl)methoxy)(phenoxy)phosphoryl)-L-alaninate, 11 was found to be the higher than RDV among 14 new compounds i.e. -5.20 kcal/mol. Out of 3 compounds, 10, 12 and 13 submitted for MD simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis, trifluoro-oxadiazole derivative, 13 showed higher binding energy as compared to Remdesivir. The predicted ADMET properties of 14 compounds showed their potential for being drug candidates. The present study suggests that substitution at the C1'β position by 4/5-membered rings plays an important role in the interactions between nucleoside/tide and target protein.

Integrative determination of the atomic structure of mutant huntingtin exon 1 fibrils implicated in Huntington's disease

Neurodegeneration in Huntington's disease (HD) is accompanied by the aggregation of fragments of the mutant huntingtin protein, a biomarker of disease progression. A particular pathogenic role has been attributed to the aggregation-prone huntingtin exon 1 (HTTex1), generated by aberrant splicing or proteolysis, and containing the expanded polyglutamine (polyQ) segment. Unlike amyloid fibrils from Parkinson's and Alzheimer's diseases, the atomic-level structure of HTTex1 fibrils has remained unknown, limiting diagnostic and treatment efforts. We present and analyze the structure of fibrils formed by polyQ peptides and polyQ-expanded HTTex1 in vitro. Atomic-resolution perspectives are enabled by an integrative analysis and unrestrained all-atom molecular dynamics (MD) simulations incorporating experimental data from electron microscopy (EM), solid-state NMR, and other techniques. Alongside the use of prior data, we report new magic angle spinning NMR studies of glutamine residues of the polyQ fibril core and surface, distinguished via hydrogen-deuterium exchange (HDX). Our study provides a new understanding of the structure of the core as well as surface of aggregated HTTex1, including the fuzzy coat and polyQ-water interface. The obtained data are discussed in context of their implications for understanding the detection of such aggregates (diagnostics) as well as known biological properties of the fibrils.

Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy

Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion.

Activation of automethylated PRC2 by dimerization on chromatin

Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 is associated with transcriptionally repressed chromatin and is established when PRC2 is allosterically activated upon methyl-lysine binding by the regulatory subunit EED. Automethylation of the catalytic subunit enhancer of zeste homolog 2 (EZH2) stimulates its activity by an unknown mechanism. Here, we show that human PRC2 forms a dimer on chromatin in which an inactive, automethylated PRC2 protomer is the allosteric activator of a second PRC2 that is poised to methylate H3 of a substrate nucleosome. Functional assays support our model of allosteric trans-autoactivation via EED, suggesting a previously unknown mechanism mediating context-dependent activation of PRC2. Our work showcases the molecular mechanism of auto-modification-coupled dimerization in the regulation of chromatin-modifying complexes.

Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion

Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.

Molecular basis of the urate transporter URAT1 inhibition by gout drugs

Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood1. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population2-4. The human urate transporter 1 (URAT1) is responsible for the reabsorption of ~90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout5. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown5. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the novel compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.

Sickle Cell Hemoglobin "Drugged" with Cyclic Peptides Is Aggregation Incompetent

Sickle cell disease (SCD) is a monogenic blood disorder associated with a mutation in the hemoglobin subunit β gene encoding for the β-globin of normal adult hemoglobin (HbA). This mutation transcribes into a Glu-β6 → Val-β6 substitution in the β-globins, inducing the polymerization of this hemoglobin form (HbS) when in the T-state. Despite advances in stem cell and gene therapy, and the recent approval of a new antisickling drug, therapeutic limitations persist. Herein, we demonstrate through molecular dynamics and umbrella sampling, that (unrestrained) blockage of the hydrophobic pocket involved in the lateral contact of the HbS fibers by 5-mer cyclic peptides, recently proposed as SCD aggregation inhibitors (Neto, V.; J. Med. Chem. 2023, 66, 16062-16074), is enough to turn the dimerization of HbS thermodynamically unfavorable. Among these potential drugs, some exhibit an estimated pocket abandonment probability of around 15-20% within the simulations' time frame, and an impressive specificity toward the mutated Val-β6. Additionally, we show that the dimerization can be thermodynamically unfavored by blocking a nearby region while the pocket remains vacant. These results are compared with curcumin, an antisickling molecule and a pan-assay interference compound, with a good binding affinity for different proteins and protein domains. Our results confirm the potential of some of these cyclic peptides as antisickling drug candidates to reduce the concentration of aggregation-competent HbS.

Cholesterol inhibits oxygen permeation through biological membranes: mechanism against double-bond peroxidation

The presence of oxygen molecules (O2) in biological membranes promotes lipid peroxidation of phospholipids with unsaturated acyl chains. On the other hand, cholesterol is considered to be an antioxidant molecule as it has a significant barrier effect on the permeation of O2 across membranes. However, a comprehensive explanation of how cholesterol affects the distribution and diffusion of O2 within lipid bilayers is yet to be established. In this study, we investigated the interaction of oxygen molecules with polyunsaturated lipid bilayers using molecular dynamics (MD) simulations. The degree of lipid unsaturation and the concentration of cholesterol were varied to study the permeation of O2. The free energy profile of O2 diffusing from the water phase to the lipid bilayer was calculated using biased umbrella MD simulations. The results show that O2 passively translocates into the membrane without changing the physical properties of the bilayer. Interestingly, in the unsaturated lipid bilayers the presence of cholesterol led to a significantly decreased permeation of O2 and an increase in the lipid chain order. Our results indicate that the hydroxyl groups of cholesterol strongly interact with the O2 molecules effectively inhibiting interactions between the oxygens and the double bonds in unsaturated lipid tails. In addition, a linear relationship between permeation and the ratio of membrane thickness and area per lipid was found. These insights can help our understanding of how the degree of unsaturation in a lipid tail and cholesterol affect lipid peroxidation at the molecular level.

Dynamic allostery drives autocrine and paracrine TGF-β signaling

TGF-β, essential for development and immunity, is expressed as a latent complex (L-TGF-β) non-covalently associated with its prodomain and presented on immune cell surfaces by covalent association with GARP. Binding to integrin αvβ8 activates L-TGF-β1/GARP. The dogma is that mature TGF-β must physically dissociate from L-TGF-β1 for signaling to occur. Our previous studies discovered that αvβ8-mediated TGF-β autocrine signaling can occur without TGF-β1 release from its latent form. Here, we show that mice engineered to express TGF-β1 that cannot release from L-TGF-β1 survive without early lethal tissue inflammation, unlike those with TGF-β1 deficiency. Combining cryogenic electron microscopy with cell-based assays, we reveal a dynamic allosteric mechanism of autocrine TGF-β1 signaling without release where αvβ8 binding redistributes the intrinsic flexibility of L-TGF-β1 to expose TGF-β1 to its receptors. Dynamic allostery explains the TGF-β3 latency/activation mechanism and why TGF-β3 functions distinctly from TGF-β1, suggesting that it broadly applies to other flexible cell surface receptor/ligand systems.

Examining Hemin and its Derivatives: Induction of Heme-Oxygenase-1 Activity and Oxidative Stress in Breast Cancer Cells through Collaborative Experimental Analysis and Molecular Dynamics Simulations

Hemin triggers intracellular reactive oxygen species (ROS) accumulation and enhances heme oxygenase-1 (HOX-1) activity, indicating its potential as an anticancer agent, though precise control of its intracellular levels is crucial. The study explores the impact of hemin and its derivatives, hemin-tyrosine, and hemin-styrene (H-Styr) conjugates on migration, HOX-1 expression, specific apoptosis markers, mitochondrial functions, and ROS generation in breast cancer cells. Molecular docking and dynamics simulations were used to understand the interactions among HOX-1, heme, and the compounds. Hemin outperforms its derivatives in inducing HOX-1 expression, exhibiting pro-oxidative effects and reducing cell migration. Molecular simulations show that heme binds favorably to HOX-1, followed by the other compounds, primarily through van der Waals and electrostatic forces. However, only van der Waals forces determine the H-Styr complexation. These interactions, influenced by metalloporphyrin characteristics, provide insights into HOX-1 regulation and ROS generation, potentially guiding the development of breast cancer therapies targeting oxidative stress.

Substrate interactions guide cyclase engineering and lasso peptide diversification

Lasso peptides are a diverse class of naturally occurring, highly stable molecules kinetically trapped in a distinctive [1]rotaxane conformation. How the ATP-dependent lasso cyclase constrains a relatively unstructured substrate peptide into a low entropy product has remained a mystery owing to poor enzyme stability and activity in vitro. In this study, we combined substrate tolerance data with structural predictions, bioinformatic analysis, molecular dynamics simulations and mutational scanning to construct a model for the three-dimensional orientation of the substrate peptide in the lasso cyclase active site. Predicted peptide cyclase molecular contacts were validated by rationally engineering multiple, phylogenetically diverse lasso cyclases to accept substrates rejected by the wild-type enzymes. Finally, we demonstrate the utility of lasso cyclase engineering by robustly producing previously inaccessible variants that tightly bind to integrin αvβ8, which is a primary activator of transforming growth factor β and, thus, an important anti-cancer target.

On the composition and isomerism effect in the thermal and structural properties of choline chloride/hydroxyphenol deep eutectic solvents

We have carried out a comparative study on three sets of eutectic mixtures based on choline chloride (ChCl) and hydroxyphenol isomers having two hydroxyl groups in the ortho-, meta-, and para-positions of the aromatic ring, namely catechol (Cate), resorcinol (Reso), and hydroquinone (Hydro), respectively. Differential scanning calorimetry highlighted a different thermal behavior of the mixtures depending on the composition and precursor isomerism. These systems behave as deep eutectic solvents (DESs) with the exception of the ChCl/Cate mixture at a 1 : 0.75 molar ratio, the ChCl/Reso mixtures at 1 : 2 and 1 : 3 molar ratios, and the ChCl/Hydro mixture at a 1 : 3 molar ratio. Infrared spectroscopy measurements and molecular dynamics simulations show that the stronger hydrogen-bonding (H-bonding) in the mixed states compared to the pure precursors is key for the formation of a DES. This interaction is mostly reliant on interconnected chloride anion coordination shells thanks to the two hydroxyl groups of the hydroxyphenol molecules, which can bridge between different anions to form an extended H-bond network. This structural arrangement maximizes the interactions and is enhanced by the 1 : 0.75 and 1 : 1 molar ratios, while increasing the hydroxyphenol concentration translates into a lowering of the total number of H-bonds formed in the mixture. This is the basis for the different thermal behavior and points to nearly equimolar compositions between the components, as ideally suited to achieve a DES from these precursors. The obtained insights are able to explain the structure-property relationships for the studied systems and are deemed useful for more conscious development of these inherently tuneable solvents.

Size-dependent acidity of aqueous nano-aerosols

Understanding the accurate acidity of nano-aerosols is important for the research on atmospheric chemistry. Herein, we propose the contributions from both the aerosol size and multiphase buffer effect to the steady-state acidity of nano-aerosols at a constant aerosol water content (AWC) through molecular simulations. As increasing of the aerosol size, the solvation free energy (SFE, ΔGs) became more negative (decreasing by 3-130 kcal mol-1 for different types of species) and Henry's law constant (H) apparently increased (from e6 to e16 mol m-3 Pa-1) in the nano-aerosols compared to that in bulk solutions. The lower SFE led to lower solute pKa and pKb values; thus, the acidity of HSO4- and HNO3 and the alkalinity of NH3 showed positive relations with the aerosol size. The lower H also increased the pKa of gaseous solutes, leading to a decrease in the acidity of HNO3 and a shift from alkaline to acidic for the NH4+/NH3 buffer pair in the nano-aerosols. The present study revealed the relationship between aerosol acidity and solvent size from a microscopic perspective. Specifically, the acidity of aerosols containing HSO4-/SO42- and HNO3/NO3- decreased with an increase in their radii, whereas aerosols containing NH4+/NH3 exhibited an opposite trend. This phenomenon can be attributed to the disappearance of the interfacial effect with an increase in the size of the aerosols. The above conclusions are of great significance for studying the pH-dependent multi-phase chemical processes in aerosols.

CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation

Lipid nanobubbles with different gas cores may integrate the biocompatibility of lipids, powerful physicochemical properties of nanobubbles, and therapeutic effects of gas molecules, which thus promote enormous biomedical applications such as ultrasound molecular imaging, gene/drug delivery, and gas therapy. In order for further more precise applications, the exact molecular mechanisms for the interactions between lipid nanobubbles and biological systems should be studied. Molecular dynamics (MD) simulation provides a powerful computational tool for this purpose. However, previous state-of-the-art MD simulations of free gas nanobubble/lipid nanobubble employed the vacuum as their gas cores, which is not suitable for studying the interactions between functional lipid nanobubbles and biological systems and revealing the biological roles of gas molecules. Hence, in this work, we developed and optimized the CHARMM36 all-atom gas parameters for six gases including N2, O2, H2, CO, CO2, and SO2, which accurately reproduced the gas density at different pressures as well as the spontaneous formation of gas nanobubbles. Subsequent applications of these gas parameters for lipid nanobubble simulations also reproduced the self-assembly process of the lipid nanobubble. We further developed a Python script to generate all-atom lipid nanobubble simulation systems, which was proven to be efficient for all-atom MD simulations of lipid nanobubbles and to be able to capture the exact dynamics of gas molecules at the gas-lipid and lipid-water interfaces of the lipid nanobubble. In summary, the all-atom gas models proposed in this work are suitable for simulating free gas nanobubbles and lipid nanobubbles, which are supposed to overcome the shortcomings of previous state-of-the-art MD simulations with the vacuum replacing the gas core and play key roles in revealing the molecular-level interactions between lipid nanobubbles and biological systems.

Engineering an Ancestral Glycosyltransferase for Biosynthesis of 2-Phenylethyl-β-d-Glucopyranoside and Salidroside

Phenylethanoid glycosides (PhGs) are naturally occurring glycosides derived from plants with various biological activities. Glycosyltransferases catalyze the production of PhGs from phenylethanols via a transglycosylation reaction. The low activity and stability of glycosyltransferase limit its industrial application. An ancestral glycosyltransferase, UGTAn85, with heat resistance, alkali resistance, and high stability was resurrected using ancestral sequence reconstruction technology. This enzyme can efficiently convert phenylethanols to PhGs. The optimal reaction temperature and pH for UGTAn85 were found to be 70 °C and pH 10.0, respectively. This study employed a combination of structure-guided rational design and co-evolution analysis to enhance its catalytic activity. Potential mutation sites were identified through computer-aided design, including homology modeling, molecular docking, Rosetta dock design, molecular dynamics simulation, and co-evolution analysis. By targeted mutagenesis, the UGTAn85 mutant Q23E/N65D exhibited a 2.2-fold increase in enzyme activity (11.85 U/mg) and elevated affinity (Km = 0.11 mM) for 2-phenylethanol compared to UGTAn85. Following a fed-batch reaction, 36.16 g/L 2-phenylethyl-β-d-glucopyranoside and 51.49 g/L salidroside could be produced within 24 h, respectively. The findings in this study provide a new perspective on enhancing the stability and activity of glycosyltransferases, as well as a potential biocatalyst for the industrial production of PhGs.

Molecular interactions of photosystem I and ZIF-8 in bio-nanohybrid materials

Bio-nanohybrid devices featuring natural photocatalysts bound to a nanostructure hold great promise in the search for sustainable energy conversion. One of the major challenges of integrating biological systems is protecting them against harsh environmental conditions while retaining, or ideally enhancing their photophysical properties. In this mainly computational work we investigate an assembly of cyanobacterial photosystem I (PS I) embedded in a metal-organic framework (MOF), namely the zeolitic imidazolate framework ZIF-8. This complex has been reported experimentally [Bennett et al., Nanoscale Adv., 2019, 1, 94] but so far the molecular interactions between PS I and the MOF remained elusive. We show via absorption spectroscopy that PS I remains intact throughout the encapsulation-release cycle. Molecular dynamics (MD) simulations further confirm that the encapsulation has no noticeable structural impact on the photosystem. However, the MOF building blocks frequently coordinate to the Mg2+ ions of chlorophylls in the periphery of the antenna complex. High-level quantum mechanical calculations reveal charge-transfer interactions, which affect the excitonic network and thereby may reversibly change the fluorescence properties of PS I. Nevertheless, our results highlight the stability of PS I in the MOF, as the reaction center remains unimpeded by the heterogeneous environment, paving the way for applications in the foreseeable future.

Understanding the stability and dynamics of influenza a H5N1 polymerase PB2 CAP-Binding domain in complex with natural compounds for antiviral drug discovery

Influenza A virus, particularly the H5N1 strain, poses a significant threat to public health due to its ability to cause severe respiratory illness and its high mortality rate. Traditional antiviral drugs targeting influenza A virus have faced challenges such as drug resistance and limited efficacy. Therefore, new antiviral compounds are needed to be discovered and developed. This study concentrated on examining the stability and behavior of the H5N1 polymerase PB2 CAP-binding domain when interacting with natural compounds, aiming to identify potential candidates for antiviral drug discovery. Through the virtual screening process, four lead compounds, ZINC000096095464, ZINC000044404209, ZINC000001562130, and ZINC000059779788, were selected, and these compounds showed binding energies -9.6, -9.4, -9.3, and -9.2 kcal/mol, respectively. When complexed with PB2, the ligand showed acceptable binding stability due to significant bond formation. However, during the 200ns MD simulation analysis, three (ZINC000096095464, ZINC000044404209, and ZINC000059779788) showed significant stability, which was proven by the trajectory analysis. The Rg-RMSD-based FEL plot showed significant structural stability due to stable conformers. The free-binding energy calculation also validates the stability of these complexes. This study offers valuable insights into the stability and dynamics of the H5N1 polymerase PB2 CAP-binding domain in complexes with natural compounds. These findings highlight the potential of these natural compounds as antiviral agents against the H5N1 influenza virus. Furthermore, this research contributes to the broader field of influenza virus treatment by demonstrating the effectiveness of computational methods in predicting and evaluating the stability and dynamics of potential drug candidates.

Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces

Performing reliable computer simulations of elementary processes occurring at metal-water interfaces is pivotal for novel catalyst design in sustainable energy applications. Computational catalyst design hinges on the ability to reliably and efficiently compute the potential energy surface (PES) of the system. Due to the large system sizes needed for studying processes at liquid water-metal interfaces, these systems can currently not be described using density functional theory (DFT). In this work, we used a hybrid quantum mechanical, molecular mechanical, and machine learning potential for studying the adsorption behavior of phenol, atomic hydrogen, 2-butanol, and 2-butanone on the (0001) facet of Ru under reducing conditions when Ru is not oxidized. Specifically, we describe the adsorbate and the surrounding metal atoms at the DFT level of theory. Here, we also considered the electrostatic field effect of the water molecules on adsorbate-metal interactions. Next, for the water-water and water-adsorbate interactions, we used established classical force fields. Finally, for the water-Ru surface interaction, for which no reliable force fields have been published, we used Behler-Parrinello high-dimensional neural network potentials (HDNNPs). Employing this setup, we used our explicit solvation for metal surface (eSMS) approach to compute the aqueous-phase effect on the low-coverage adsorption of selected molecules and atoms on the (0001) facet of Ru. In agreement with previous experimental and computational studies of oxygenated molecules over transition metal facets, we found that liquid water destabilizes the tested adsorbates on Ru(0001). Interestingly, our findings indicate that adsorbates on Ru are less affected by the presence of an aqueous phase than on other transition metals (e.g., Pt), highlighting the necessity of experimental investigations of Ru-based catalytic systems in liquid water.

Comprehensive Computational Investigation of the Porphyrin-Based COF as a Nanocarrier for Delivering Anti-Cancer Drugs: A Combined MD Simulation and DFT Calculation

As nanomaterials have gained prominence in drug delivery technology, exploring their feasibility through computational methods is beneficial before practical tests. In this study, we aim to evaluate the capability of the porphyrin-based covalent organic framework COF-366 as a nanocarrier for two anticancer drugs, irinotecan (IRI) and doxorubicin (DOX). The optimal binding conformation of the drug molecules on the COF surface was predicted by using molecular docking. Subsequently, molecular dynamic simulation (MD) was performed to assess the adsorption mechanism of drug molecules on the COF in the aqueous environment. The free energy of adsorption for DOX and IRI was estimated to be -20.07 and -23.89 kcal/mol, respectively. The adsorption of both drugs on the COF surface is mainly influenced by the π-π interaction. Furthermore, density functional theory (DFT) calculation, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM) analyses were employed to investigate the structural stability of Drug@COF complexes and gain a detailed understanding of the interaction between them at the molecular level. Based on DFT results, it was found that in addition to π-π interaction, the bis-piperidine-phenylene interaction affects the adsorption of IRI on the COF surface. Moreover, the diffusion behavior of the drug molecule inside the COF pore was simulated using a ten-layer COF. Based on the mean square displacement analysis, the diffusion coefficients of DOX and IRI within the COF pore were calculated to be 108 and 97 um2/s, respectively. This computational study sheds light on how different types of interactions between the drug molecule and COF affect the adsorption and diffusion process. Our findings validated that the porphyrin-based COF-366 can serve as a nanobased platform for delivering DOX and IRI.

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.

High-Speed Atomic Force Microscopy Reveals Fluctuations and Dimer Splitting of the N-Terminal Domain of GluA2 Ionotropic Glutamate Receptor-Auxiliary Subunit Complex

α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid glutamate receptors (AMPARs) enable rapid excitatory synaptic transmission by localizing to the postsynaptic density of glutamatergic spines. AMPARs possess large extracellular N-terminal domains (NTDs), which are crucial for AMPAR clustering at synaptic sites. However, the dynamics of NTDs and the molecular mechanism governing their synaptic clustering remain elusive. Here, we employed high-speed atomic force microscopy (HS-AFM) to directly visualize the conformational dynamics of NTDs in the GluA2 subunit complexed with TARP γ2 in lipid environments. HS-AFM videos of GluA2-γ2 in the resting and activated/open states revealed fluctuations in NTD dimers. Conversely, in the desensitized/closed state, the two NTD dimers adopted a separated conformation with less fluctuation. Notably, we observed individual NTD dimers transitioning into monomers, with extended monomeric states in the activated/open state. Molecular dynamics simulations provided further support, confirming the energetic stability of the monomeric NTD states within lipids. This NTD-dimer splitting resulted in subunit exchange between the receptors and increased the number of interaction sites with synaptic protein neuronal pentraxin 1 (NP1). Moreover, our HS-AFM studies revealed that NP1 forms a ring-shaped octamer through N-terminal disulfide bonds and binds to the tip of the NTD. These findings suggest a molecular mechanism in which NP1, upon forming an octamer, is secreted into the synaptic region and binds to the tip of the GluA2 NTD, thereby bridging and clustering multiple AMPARs. Thus, our findings illuminate the critical role of NTD dynamics in the synaptic clustering of AMPARs and contribute valuable insights into the fundamental processes of synaptic transmission.

All-Atom Membrane Builder via Multiscale Simulation

I present an automated and flexible tool designed for constructing bilayer membranes at all-atom (AA) resolution. The builder initiates the construction and equilibration of bilayer membranes at Martini coarse-grained (CG) resolution, followed by resolution enhancement to the atomic level using the accompanying backmapping tool. Notably, this tool enables users to create bilayer membranes with user-defined lipid compositions and protein structures, while also offering the flexibility to accommodate new lipid types. To assess the simplicity and robustness of the tool, I demonstrate the construction of several membranes incorporating protein structures. The tool is freely available at github.com/ksy141/mstool.

Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning

Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and principal component analysis (PCA) were carried out to probe the effect of G12C and binding of three partners NF1, RAF1, and SOS1 on the conformation alterations of KRAS4B. DL reveals that G12C and binding of partners result in alterations in the contacts of key structure domains, such as the switch domains SW1 and SW2 together with the loops L4, L5, and P-loop. Binding of NF1, RAF1, and SOS1 constrains the structural fluctuation of SW1, SW2, L4, and L5; on the contrary, G12C leads to the instability of these four structure domains. The analyses of free energy landscapes (FELs) and PCA also show that binding of partners maintains the stability of the conformational states of KRAS4B while G12C induces greater mobility of the switch domains SW1 and SW2, which produces significant impacts on the interactions of GTP with SW1, L4, and L5. Our findings suggest that partner binding and G12C play important roles in the activity and allosteric regulation of KRAS4B, which may theoretically aid in further understanding the function of KRAS4B.

Polymyxin B1 in the E. coli inner membrane: a complex story of protein and lipopolysaccharide mediated insertion

The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for 'last-resort' antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD) including long-timescale coarse-grained (CG) and all-atom (AA) simulations to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.

High terephthalic acid purity: Effective polyethylene terephthalate degradation process based on pH regulation with dual-function hydrolase

Eco-friendly enzymatic-recycling has been widely utilized in tackling plastic pollution. However, the limited activity on the polyethylene terephthalate (PET) degradation product mono-hydroxyethyl terephthalate (MHET) leads to the formation of heterogeneous hydrolysis products, resulting in PET downcycling. Herein, by applying a dual-function PET hydrolase IsPETasePA with balanced PET and MHET degradation efficiency, an effective PET hydrolysis process was developed to enhance the terephthalic acid (TPA) product purity. Firstly, the impact of pH on the catalytic activity of IsPETasePA revealed that the pH reduction caused by TPA generation hindered the complete conversion of MHET to TPA. Further investigation of the catalytic mechanism showed that the pH-induced protonation of His208 in the catalytic triad destabilized the interaction between IsPETasePA and MHET. Thus, by introducing pH regulation strategy on the bifunctional IsPETasePA, the single-enzyme process could achieve high-purity TPA recovery (>99 %). Overall, this work ensured the high-quality PET enzymatic-recycling for effectively addressing plastic pollution.

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis

Anti-COVID19 drugs, such as nirmatrelvir, have been developed targeting the SARS-CoV-2 main protease, Mpro, based on the critical requirement of its proteolytic processing of the viral polyproteins into functional proteins essential for viral replication. However, the emergence of SARS-CoV-2 variants with Mpro mutations has raised the possibility of developing resistance against these drugs, likely due to therapeutic targeting of the Mpro catalytic site. An alternative to these drugs is the development of drugs that target an allosteric site distant from the catalytic site in the protein that may reduce the chance of the emergence of resistant mutants. Here, we combine computational analysis with in vitro assay and report the discovery of a potential allosteric site and an allosteric inhibitor of SARS-CoV-2 Mpro. Specifically, we identified an Mpro metastable state with a deformed catalytic site harboring potential allosteric sites, raising the possibility that stabilization of this metastable state through ligand binding can lead to the inhibition of Mpro activity. We then performed a computational screening of a library (∼4.2 million) of drug-like compounds from the ZINC database and identified several candidate molecules with high predicted binding affinity. MD simulations showed stable binding of the three top-ranking compounds to the putative allosteric sites in the protein. Finally, we tested the three compounds in vitro using a BRET-based Mpro biosensor and found that one of the compounds (ZINC4497834) inhibited the Mpro activity. We envisage that the identification of a potential allosteric inhibitor of Mpro will aid in developing improved anti-COVID-19 therapy.

Divergent mechanisms of steroid inhibition in the human ρ1 GABAA receptor

ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive disorders. Endogenous neuroactive steroids including β-estradiol and pregnenolone sulfate negatively modulate the function of ρ1 GABAA receptors, but their inhibitory mechanisms are not clear. By combining five cryo-EM structures with electrophysiology and molecular dynamics simulations, we characterize binding sites and negative modulation mechanisms of β-estradiol and pregnenolone sulfate at the human ρ1 GABAA receptor. β-estradiol binds in a pocket at the interface between extracellular and transmembrane domains, apparently specific to the ρ subfamily, and disturbs allosteric conformational transitions linking GABA binding to pore opening. In contrast, pregnenolone sulfate binds inside the pore to block ion permeation, with a preference for activated structures. These results illuminate contrasting mechanisms of ρ1 inhibition by two different neuroactive steroids, with potential implications for subtype-specific gating and pharmacological design.

Exploring the molecular mechanism of ginseng against anthracycline-induced cardiotoxicity based on network pharmacology, molecular docking and molecular dynamics simulation

BACKGROUND

Previous clinical and basic studies have revealed that ginseng might have cardioprotective properties against anthracycline-induced cardiotoxicity (AIC). However, the underlying mechanism of ginseng action against AIC remains insufficiently understood. The aim of this study was to explore the related targets and pathways of ginseng against AIC using network pharmacology, molecular docking, cellular thermal shift assay (CETSA) and molecular dynamics (MD) simulations.

RESULTS

Fourteen drug-disease common targets were identified. Enrichment analysis showed that the AGE-RAGE in diabetic complications, fluid shear stress and atherosclerosis, and TNF signaling pathway were potentially involved in the action of ginseng against AIC. Molecular docking demonstrated that the core components including Kaempferol, beta-Sitosterol, and Fumarine had notable binding activity with the three core targets CCNA2, STAT1, and ICAM1. Furthermore, the stable complex of STAT1 and Kaempferol with favorable affinity was further confirmed by CETSA and MD simulation.

CONCLUSIONS

This study suggested that ginseng might exert their protective effects against AIC through the derived effector compounds beta-Sitosterol, Kaempferol and Fumarine by targeting CCNA2, STAT1, and ICAM1, and modulating AGE-RAGE in diabetic complications, fluid shear stress and atherosclerosis, and TNF signaling pathways.

Phosphorylation of cytosolic hPGK1 affects protein stability and ligand binding: implications for its subcellular targeting in cancer

Human phosphoglycerate kinase 1(hPGK1) is a key glycolytic enzyme that regulates the balance between ADP and ATP concentrations inside the cell. Phosphorylation of hPGK1 at S203 and S256 has been associated with enzyme import from the cytosol to the mitochondria and the nucleus respectively. These changes in subcellular locations drive tumorigenesis and are likely associated with site-specific changes in protein stability. In this work, we investigate the effects of site-specific phosphorylation on thermal and kinetic stability and protein structural dynamics by hydrogen-deuterium exchange (HDX) and molecular dynamics (MD) simulations. We also investigate the binding of 3-phosphoglycerate and Mg-ADP using these approaches. We show that the phosphomimetic mutation S256D reduces hPGK1 kinetic stability by 50-fold, with no effect of the mutation S203D. Calorimetric studies of ligand binding show a large decrease in affinity for Mg-ADP in the S256D variant, whereas Mg-ADP binding to the WT and S203D can be accurately investigated using protein kinetic stability and binding thermodynamic models. HDX and MD simulations confirmed the destabilization caused by the mutation S256D (with some long-range effects on stability) and its reduced affinity for Mg-ADP due to the strong destabilization of its binding site (particularly in the apo-state). Our research provides evidence suggesting that modifications in protein stability could potentially enhance the translocation of hPGK1 to the nucleus in cancer. While the structural and energetic basis of its mitochondrial import remain unknown.

A cardioviral 2C-ATP complex structure reveals the essential role of a conserved arginine in regulation of cardioviral 2C activity

2C is a highly conserved picornaviral non-structural protein with ATPase activity and plays a multifunctional role in the viral life cycle as a promising target for anti-picornavirus drug development. While the structure-function of enteroviral 2Cs have been well studied, cardioviral 2Cs remain largely uncharacterized. Here, an endogenous ATP molecule was identified in the crystal structure of 2C from encephalomyocarditis virus (EMCV, Cardiovirus A). The ATP is bound into the ATPase active site with a unique compact conformation. Notably, the γ-phosphate of ATP directly interacts with Arg311 (conserved in cardioviral 2Cs), and its mutation significantly inhibits the ATPase activity. Unexpectedly, this mutation remarkably promotes 2C self-oligomerization and viral replication efficiency. Molecular dynamic simulations showed that the Arg311 side chain is highly dynamic, indicating it may function as a switch between the activation state and the inhibition state of ATPase activity. A hexameric ring model of EMCV 2C full length indicated that the C-terminal helix may get close to the N-terminal amphipathic helices to form a continuous positive region for RNA binding. The RNA-binding studies of EMCV 2C revealed that the RNA length is closely associated with the RNA-binding affinities and indicated that the substrate may wrap around the outer surface of the hexamer. Our studies provide a biochemical framework to guide the characterization of EMCV 2C and the essential role of arginine in cardioviral 2C functions.

IMPORTANCE

Encephalomyocarditis virus (Cardiovirus A) is the causative agent of the homonymous disease, which may induce myocarditis, encephalitis, and reproductive disorders in various mammals. 2C protein is functionally indispensable and a promising target for drug development involving broad-spectrum picornaviral inhibitors. Here, an endogenous ATP molecule with a unique conformation was discovered by a combination of protein crystallography and high-performance liquid chromatography in the encephalomyocarditis virus (EMCV) 2C structure. Biochemical and structural characterization analysis of EMCV 2C revealed the critical role of conserved Arg311 in ATPase activity and self-oligomerization of EMCV 2C. The viral replication kinetics and infectivity study suggested that the residue negatively regulated the infectivity titer and virus encapsulation efficiency of EMCV and is, therefore, crucial for 2C protein to promote viral replication. Our systemic structure-function analysis provides unique insights into the function and regulation mechanism of cardioviral 2C protein.