Free Energy Decomposition Research Articles

Structural and dynamic properties of the YTH domain in complex with N6‐methyladenosine RNA studied by accelerated molecular dynamics simulations

BackgroundN6‐methyl adenosine (m6A) modifications of mRNA and long non‐coding RNA (lncRNAs) are known to play a significant role in regulation of gene expression and organismal development. Besides writer and eraser proteins of this dynamic modification, the YT521‐B homology (YTH) domain can recognize the modification involved in numerous cellular processes. The function of proteins containing YTH domain and its binding mode with N6‐Methyladenosine RNA has attracted considerable attention. However, the structural and dynamic characteristics of the YTH domain in complex with m6A RNA is still unknown.MethodThis work presents results of accelerated molecular dynamics (aMD) simulations at the timescale of microseconds. Principal component analysis (PCA), molecular mechanics generalized Born surface area (MM/GBSA) calculations, contact analysis and contact‐based principal component analysis (conPCA) provide new insights into structure and dynamics of the YTH‐RNA complex.ResultsThe aMD simulations indicate that the recognition loop has a larger movement away from the binding pocket in the YTH‐A3 RNA than that in the YTH‐m6A3 RNA. In aMD trajectories of the apo YTH, there is a significant close‐open transition of the recognition loop, that is to say, the apo YTH can take both the closed and open structure. We have found that the YTH domain binds more favorably to the methylated RNA than the non‐methylated RNA. The per‐residue free energy decomposition and conPCA suggest that hydrophobic residues including W380, L383‐V385, W431‐P434, M437, and M441‐L442, may play important roles in favorable binding of the m6A RNA to the YTH domain, which is also supported by aMD simulations of a double mutated system (L383A/M437A).ConclusionThe results are in good agreement with higher structural stability of the YTH‐m6A RNA than that of the YTH‐A3 RNA. The addition of a methylation group on A3 can enhance its binding to the hydrophobic pocket in the YTH domain. Our simulations support a ‘conformational selection’ mechanism between the YTH‐RNA binding. This work may aid in our understanding of the structural and dynamic characteristics of the YTH protein in complex with the methylated RNA.

Initial decomposition mechanisms of 2,4,6-triamino-1,3,5-trinitrobenzene (TATB) and their kinetic isotope effect

2,4,6-triamino-1,3,5-trinitrobenzene (TATB) is an insensitive High Explosive (HE) that is widely studied to better understand the physical properties of safety and sensitivity of HE. A dominant initial decomposition mechanism of TATB is believed to be a dehydration reaction that forms mono- and di-furazans, although other mechanisms have been reported. In this work, seven initial decomposition mechanisms were modeled with ab initio simulations to calculate its free energy barriers, decomposition rates, and kinetic isotope effects. The energy barrier for mono-benzofurazan mechanisms was found to be high, >61 kcal/mol in the gas phase; however, the reaction energy can decrease significantly in a disordered condensed state. The predicted kinetic isotope effect ratio of the furazan mechanism was found to be kh/kd≈ 1.41 at 600 K, in agreement with the experiment. The NO2 scission mechanism was found to be an entropy-driven mechanism because the free energy barrier decreased significantly with temperature, making it the most energetically favorable mechanism at high temperatures in the gas phase. The results provide a better understanding of the atomistic decomposition mechanisms of TATB and may be useful for improving models of safety and sensitivity.

Molecular insights on PS-PLA1 lipase activity of human ABHD16B

The human alpha beta hydrolase domain (ABHD) proteins are ubiquitous and regulate the cellular lipids' anabolic and catabolic processes. The structural aspects for specific biochemical function of many ABHD proteins related to physiological disorders and its link to pathological conditions remain unknown. Here putative human ABHD16B protein was overexpressed in Saccharomyces cerevisiae for its biological activity. In-vitro enzymatic assay of the recombinant ABHD16B protein with fluorescently tagged glycerophospholipids revealed that the PLA1 activity is observed with phosphatidylserine (PS). In addition, it efficiently hydrolyzed monoacylglycerol over triacylglycerols. Further, molecular dynamic simulations and per residue binding free energy decomposition analysis revealed that the origin of PS-specific PLA1 activity of ABHD16B is due to the electrostatic interaction of the PS head group with K8, R319, and E178, which led to having the hydrogen bond interaction of sn-1 acyl chain ester to the catalytic site residues. Site-directed mutagenesis of the 245GXSXG249 motif of ABHD16B reduced the maximal lipase activity of PS and MAG. In summary, these results revealed that ABHD16B plays a vital role in PS selectivity that in turn, controls the specific subcellular pools of 2-LPS metabolism in the tissues at low pH.

Structural Insights into the Interactions of Belumosudil with Rho-Associated Coiled-Coil Containing Protein Kinases 1 and 2 Based on Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculations

Rho-associated coiled-coil containing protein kinases (ROCKs) are members of the cyclic adenosine monophosphate-dependent protein kinase/protein kinase G/protein kinase C family that participates in a variety of important physiological functions, including smooth muscle contraction, cell proliferation, cell adhesion, migration, and inflammatory responses. In this study, we focused on ROCK1 and ROCK2, which are targets of the Food and Drug Administration-approved inhibitor 2-(3-(4-((1[Formula: see text]-Indazol-5-yl)amino)quinazolin-2-yl)phenoxy)-[Formula: see text]-isopropylacetamide (belumosudil). We constructed four representative belumosudil/ROCK complex structures by molecular docking. The interactions between belumosudil and ROCK were then investigated via molecular dynamics simulations and binding free energy calculations. It was found that belumosudil showed a stronger binding affinity toward ROCK2 than toward ROCK1. Binding free energy calculations and free energy decompositions suggested that the modification of various regions of the belumosudil structure may enhance its binding affinity with ROCK, in addition to improving the selectivity between ROCK1 and ROCK2. This work therefore provides useful information to aid future drug design.

Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study.

Phosphorylation, the most popular post-translational modification of tau protein, plays an important role in regulating tau physiological functions. However, aberrant phosphorylation attenuates the binding affinity of tau to a microtubule (MT), resulting in MT destabilization followed by accumulation of neurofibrillary tangles in the brain. There are in total 85 potential phosphorylation sites in a full-length tau protein, and about half of them are abnormal as they occur in tau of Alzheimer's disease (AD) brain only. In this work, we investigated the impact of abnormal Ser289, Ser293, and Ser289/Ser293 phosphorylation on tau R2-MT binding and the conformation of tau R2 using molecular dynamics simulation. We found that the phosphorylation significantly affected R2-MT interaction and reduced the binding affinity of tau R2 peptides to MTs. Free energy decomposition analysis suggested that the post-translational modified residues themselves made a significant contribution to destabilize tau repeat R2-MT binding. Therefore, the phosphorylation may attenuate the binding affinity of tau to MTs. Additionally, the phosphorylation also enhanced helix-coil transition of monomeric R2 peptides, which may result in the acceleration of tau aggregation. Since these phosphorylated sites have not been examined in previous experimental studies, our finding through all-atom molecular dynamics simulations and free energy analysis can inspire experimental scientists to investigate the impact of the phosphorylation on MT binding and aggregation of full-length tau and the pathological roles of the phosphorylation at those sites in AD development through in vitro/in vivo assays.

A structure-based virtual high-throughput screening, molecular docking, molecular dynamics and MM/PBSA study identified novel putative drug-like dual inhibitors of trypanosomal cruzain and rhodesain cysteine proteases.

Virtual screening a collection of ~ 25,000 ChemBridge molecule collection identified two nitrogenous heterocyclic molecules, 12 and 15, with potential dual inhibitory properties against trypanosomal cruzain and rhodesain cysteine proteases. Similarity search in DrugBank found the two virtual hits with novel chemical structures with unreported anti-trypanosomal activities. Investigations into the binding mechanism by molecular dynamics simulations for 100ns revealed the molecules were able to occupy the binding sites and stabilise the protease complexes. Binding affinities calculated using the MM/PBSA method for the last 20ns showed that the virtual hits have comparable binding affinities to other known inhibitors from literature suggesting both molecules as promising scaffolds with dual cruzain and rhodesain inhibition properties, i.e. 12 has predicted ΔGbind values of -38.1 and -38.2kcal/mol to cruzain and rhodesain, respectively, and 15 has predicted ΔGbind values of -34.4 and -25.8kcal/mol to rhodesain. Per residue binding free energy decomposition studies and visual inspection at 100ns snapshots revealed hydrogen bonding and non-polar attractions with important amino acid residues that contributed to the ΔGbind values. The interactions are similar to those previously reported in the literature. The overall ADMET predictions for the two molecules were favourable for drug development with acceptable pharmacokinetic profiles and adequate oral bioavailability.

Dynamical characterization and multiple unbinding paths of two PreQ1 ligands in one pocket.

Riboswitches naturally regulate gene expression in bacteria by binding to specific small molecules. Class 1 preQ1 riboswitch aptamer is an important model not only for RNA folding but also as a target for designing small molecule antibiotics due to its well-known minimal aptamer domain. Here, we ran a total of 62.4 μs conventional and enhanced-sampling molecular dynamics (MD) simulations to characterize the determinants underlying the binding of the preQ1-II riboswitch aptamer to two preQ1 ligands in one binding pocket. Decomposition of binding free energy suggested that preQ1 ligands at α and β sites interact with four nucleotides (G5, C17, C18, and A30) and two nucleotides (A12 and C31), respectively. Mg2+ ions play a crucial role in both stabilizing the binding pocket and facilitating ligand binding. The flexible preQ1 ligand at the β site leads to the top of the binding pocket loosening and thus pre-organizes the riboswitch for ligand entry. Enhanced sampling simulations further revealed that the preQ1 ligand at the α site unbinds through two orthogonal pathways, which are dependent on whether or not a β site preQ1 ligand is present. One of the two preQ1 ligands has been identified in the binding pocket, which will aid to identify the second preQ1 Ligand. Our work provides new information for designing robust ligands.

Structural Dynamics of P‐Rex1 Complexed with Natural Leads Establishes the Protein as an Attractive Target for Therapeutics to Suppress Cancer Metastasis

Phosphatidylinositol 3,4,5‐trisphosphate‐ (PIP3‐) dependent Rac exchanger 1 (P‐Rex1) functions as Rho guanine nucleotide exchange factor and is activated by synergistic activity of Gβγ and PIP3 of the heterotrimeric G protein. P‐Rex1 activates Rac GTPases for regulating cell invasion and migration and promotes metastasis in several human cancers including breast, prostate, and skin cancer. The protein is a promising therapeutic target because of its multifunction roles in human cancers. Herein, the present study attempts to identify selective P‐Rex1 natural inhibitors by targeting PIP3‐binding pocket using large‐size multiple natural molecule libraries. Each library was filtered subsequently in FAF‐Drugs4 based on Lipinski’s rule of five (RO5), toxicity, and filter pan assay interference compounds (PAINS). The output hits were virtually screened at the PIP3‐binding pocket through PyRx AutoDock Vina and cross‐checked by GOLD. The best binders at the PIP3‐binding pocket were prioritized using a comparative analysis of the docking scores. Top‐ranked two compounds with high GOLD fitness score (>80) and lowest AutoDock binding energy (< ‐12.7 kcal/mol) were complexed and deciphered for molecular dynamics along with control‐P‐Rex1 complex to validate compound binding conformation and disclosed binding interaction pattern. Both the systems were seen in good equilibrium, and along the simulation time, the compounds are in strong contact with the P‐Rex1 PIP3‐binding site. Hydrogen bonding analysis towards simulation end identified the formation of 16 and 22 short‐ and long‐distance hydrogen bonds with different percent of occupancy to the PIP3 residues for compound I and compound 2, respectively. Radial distribution function (RDF) analysis of the key hydrogen bonds between the compound and the PIP3 residues demonstrated a strong affinity of the compounds to the mentioned PIP3 pocket. Additionally, MMGB/PBSA energies were performed that confirmed the dominance of Van der Waals energy in complex formation along with favorable contribution from hydrogen bonding. These findings were also cross‐validated by a more robust WaterSwap binding energy predictor, and the results are in good agreement with a strong binding affinity of the compounds for the protein. Lastly, the key contribution of residues in interaction with the compounds was understood by binding free energy decomposition and alanine scanning methods. In short, the results of this study suggest that P‐Rex1 is a good druggable target to suppress cancer metastasis; therefore, the screened druglike molecules of this study need in vitro and in vivo anti‐P‐Rex1 validation and may serve as potent leads to fight cancer.

In silico and invitro studies of potential inhibitors against Dengue viral protein NS5 Methyl Transferase from Ginseng and Notoginseng.

Dengue is a potentially deadly tropical infectious disease transmitted by mosquito vector Aedes aegypti with no antiviral drug available to date. Dengue NS5 protein is crucial for viral replication and is the most conserved among all four Dengue serotypes, making it an attractive drug target. Both Ginseng and Notoginseng extracts and isolates have been shown to be effective against various viral infections yet against Dengue Virus is understudied. We aim to identify potential inhibitors against Dengue NS5 Methyl transferase from small molecular compounds found in Ginseng and Notoginseng. A molecular docking model of Dengue NS5 Methyl transferase (MTase) domain was tested with decoys and then used to screen 91 small molecular compounds found in Ginseng and Notoginseng followed by Molecular dynamics simulations and the per-residue free energy decompositions based on molecular mechanics/Poisson-Boltzmann (generalised Born) surface area (MM/PB(GB)SA) calculations of the hit. ADME predictions and drug-likeness analyses were discussed to evaluate the viability of the hit as a drug candidate. To confirm our findings, invitro studies of antiviral activities against RNA and a E protein synthesis and cell toxicity were carried out. The virtual screening resulted in Isoquercitrin as a single hit. Further analyses of the Isoquercitrin-MTase complex show that Isoquercitrin can reside within both of the NS5 Methyl Transferase active sites; the AdoMet binding site and the RNA capping site. The Isoquercitrin is safe for consumption and accessible on multikilogram scale. Invitro studies showed that Isoquercitrin can inhibit Dengue virus by reducing viral RNA and viral protein synthesis with low toxicity to cells (CC50>20μM). Our work provides evidence that Isoquercitrin can serve as an inhibitor of Dengue NS5 protein at the Methyl Transferase domain, further supporting its role as an anti-DENV agent.

Inhibitory selectivity to the AKR1B10 and aldose reductase (AR): insight from molecular dynamics simulations and free energy calculations.

AKR1B10 is over-expressed in many cancer types and is related to chemotherapy resistance, which makes AKR1B10 a potential anti-cancer target. The high similarity of the protein structure between AKR1B10 and AR makes it difficult to develop highly selective inhibitors against AKR1B10. Understanding the interaction between AKR1B10 and inhibitors is very important for designing selective inhibitors of AKR1B10. In this study, Fidarestat, Zopolrestat, MK184 and MK204 bound to AKR1B10 and AR were used to investigate the selectivity mechanism. The results of MM/PBSA calculations show that van der Waals and electrostatic interaction provide the main contributions of the binding free energy. The hydrogen bonding between residues Y49 and H111 and inhibitors plays a pivotal role in contributing to the high inhibitory activity of AKR1B10 inhibitors. The π-π stacking interaction between residue W112 and inhibitor also plays a key role in the stability of inhibitors and AKR1B10, but W112 should keep its natural conformation to stabilize the inhibitor-AKR1B10 complex. Highly selective AKR1B10 inhibitors should have a bulky moiety like a phenyl group, which can change its binding with ABP in binding with AR and cannot change its binding with AKR1B10. The free energy decomposition shows that residues W21, V48, Y49, K78, W80, H111, R298 and V302 are beneficial to the stability of the inhibitor-AKR1B10. Our work will provide an important in silico basis for researchers to develop highly selective inhibitors of AKR1B10.

Theoretical Study on the Binding Properties of Inhibitors to Myeloid Cell Leukemia 1

Myeloid leukemia 1 (Mcl-1) is a key anti-apoptotic member of the Bcl-2 protein family, and its overexpression or upregulation has been found in numerous cancer cells, which not only leads to tumorigenesis mediated by apoptotic escape modality, but also causes resistance to multiple subsequent anti-cancer therapies. The development of small molecule inhibitors that specifically target Mcl-1 and restore the blocked apoptotic pathway in cancer cells has emerged as a realistic solution for oncology drug design. Therefore, an in-depth study of the mechanism of action of inhibitors with Mcl-1 is important for the design of efficient drugs targeting Mcl-1. In this study, using molecular dynamics (MD) simulations, correlation analysis and principal component analysis, we revealed that the binding of inhibitors significantly altered the kinetic behavior of Mcl-1 and led to a conformational rearrangement of Mcl-1. Subsequently, the molecular mechanics-generalized Born surface area (MM-GBSA) method was used to further explore the binding ability of different inhibitors to Mcl-1, and the results showed that the calculated binding free energies agreed well with the experimental values, and van der Waals interactions and electrostatic interactions provided the main favorable contribution in the binding of inhibitors to Mcl-1. Furthermore, the interaction analysis showed a large number of hydrophobic interactions and hydrogen bonding between the inhibitor and Mcl-1. Finally, the residues F228, M231, M250, V253, T266, L267 and F270 and R263 were identified by residue-based free energy decomposition calculations to provide important energetic contributions to the binding of the inhibitor to Mcl-1 and could be key targets for the design of Mcl-1 inhibitors.

Molecular dynamics study on the behavior and binding mechanism of target protein Transgelin-2 with its agonist TSG12 for anti-asthma drug discovery

Transgelin-2 (TG2) is a novel promising therapeutic target for the treatment of asthma as it plays an important role in relaxing airway smooth muscles and reducing pulmonary resistance in asthma. The compound TSG12 is the only reported TG2 agonist with in vivo anti-asthma activity. However, the dynamic behavior and ligand binding sites of TG2 and its binding mechanism with TSG12 remain unclear. In this study, we performed 12.6 μs molecular dynamics (MD) simulations for apo-TG2 and TG2-TSG12 complex, respectively. The results suggested that the apo-TG2 has 4 most populated conformations, and that its binding of the agonist could expand the conformation distribution space of the protein. The simulations revealed 3 potential binding sites in 3 most populated conformations, one of which is induced by the agonist binding. Free energy decomposition uncovered 8 important residues with contributions stronger than −1 kcal/mol. Computational alanine scanning for the important residues by 100 ns conventional MD simulation for each mutated TG2-TSG12 complexes demonstrated that E27, R49 and F52 are essential residues for the agonist binding. These results should be helpful to understand the dynamic behavior of TG2 and its binding mechanism with the agonist TSG12, which could provide some structural insights into the novel mechanism for anti-asthma drug development.

Identification of potential inhibitors of omicron variant of SARS-Cov-2 RBD based virtual screening, MD simulation, and DFT.

Emergence of the SARS-CoV-2 Omicron variant of concern (VOC; B.1.1.529) resulted in a new peak of the COVID-19 pandemic, which called for development of effective therapeutics against the Omicron VOC. The receptor binding domain (RBD) of the spike protein, which is responsible for recognition and binding of the human ACE2 receptor protein, is a potential drug target. Mutations in receptor binding domain of the S-protein have been postulated to enhance the binding strength of the Omicron VOC to host proteins. In this study, bioinformatic analyses were performed to screen for potential therapeutic compounds targeting the omicron VOC. A total of 92,699 compounds were screened from different libraries based on receptor binding domain of the S-protein via docking and binding free energy analysis, yielding the top 5 best hits. Dynamic simulation trajectory analysis and binding free energy decomposition were used to determine the inhibitory mechanism of candidate molecules by focusing on their interactions with recognized residues on receptor binding domain. The ADMET prediction and DFT calculations were conducted to determine the pharmacokinetic parameters and precise chemical properties of the identified molecules. The molecular properties of the identified molecules and their ability to interfere with recognition of the human ACE2 receptors by receptor binding domain suggest that they are potential therapeutic agents for SARS-CoV-2 Omicron VOC.

Aggregation propensities of proteins with varying degrees of disorder.

The hydration thermodynamics of a globular protein (AcP), three intrinsically disordered protein regions (1CD3, 1MVF, 1F0R) and a fully disordered protein (α-synuclein) is studied by an approach that combines an all-atom explicit water molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. The variation in hydration free energy with percentage disorder of the selected proteins is investigated through its nonelectrostatic and electrostatic components. A decrease in hydration free energy is observed with an increase in percentage disorder, indicating favorable interactions of the disordered proteins with the solvent. This confirms the role of percentage disorder in determining the aggregation propensity of proteins which is measured in terms of the hydration free energy in addition to their respective mean net charge and mean hydrophobicity. The hydration free energy is decoupled into energetic and entropic terms. A residue-wise decomposition analysis of the hydration free energy for the selected proteins is evaluated. The decomposition shows that the disordered regions contribute more than the ordered ones for the intrinsically disordered protein regions. The dominant role of electrostatic interactions is confirmed from the residue-wise decomposition of the hydration free energy. The results depict that the negatively charged residues contribute more to the total hydration free energy for the proteins with negative mean net charge, while the positively charged residues contribute more for proteins with positive mean net charge.

Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations.

The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present an investigation of HCV NS3/4A inhibitors based on a sulfonamidobenzamide scaffold. Inhibitor interactions with HCV NS3/4A were explored by molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. All of the inhibitors adopt similar molecular docking poses in the catalytic site of the protease that are stabilized by hydrogen bond interactions with G137 and the catalytic S139, which are known to be important for potency and binding stability. The quantitative assessments of binding free energies from MM/PBSA correlate well with the experimental results, with a high coefficient of determination, R2 of 0.92. Binding free energy decomposition analyses elucidate the different contributions of Q41, F43, H57, R109, K136, G137, S138, S139, A156, M485, and Q526 in binding different inhibitors. The importance of these sidechain contributions was further confirmed by computational alanine scanning mutagenesis. In addition, the sidechains of K136 and S139 show crucial but distinct contributions to inhibitor binding with HCV NS3/4A. The structural basis of the potency has been elucidated, demonstrating the importance of the R155 sidechain conformation. This extensive exploration of binding energies and interactions between these compounds and HCV NS3/4A at the atomic level should benefit future antiviral drug design.

Design of transition metal carbonitrides (MCNs) as promising anchoring and high catalytic performance materials for lithium-sulfur batteries

The challenges faced by the application of lithium-sulfur (Li-S) batteries with high specific capacity and high energy density include the shuttle effect, which reduces the rate of sulfur reduction reaction (SRR), the difficulty of decomposition of insoluble Li2S during charging, and poor conductivity during charging and discharging. Herein, the adsorption, catalytic and electrical properties of a new class of two-dimensional transition metal carbonitrides (MCNs) have been systematically investigated as candidate cathodes for Li-S batteries. Density functional theory (DFT) calculations combined with van der Waals (vdW) interaction analysis show that TiCN and VCN can effectively suppress the shuttle effect with different solvents. The analysis of the Gibbs free energy and Li2S decomposition energy barrier of the lithiation process show that TiCN and VCN can significantly accelerate the decomposition of Li2S and sulfur reduction reaction, and improves the battery cycle performance. Moreover, the quantum conductivity (G) and density of state (DOS) of the VCN cathode during the whole charge-discharge process indicate that the electrode always has good conductivity. Based on these advantages, VCN is considered as a potential high-performance cathode material for Li-S batteries. This research has a certain guiding effect on the application of two-dimensional (2D) carbon and nitrogen materials in Li-S batteries.

Discovery of novel inhibitors targeting nematode chitinase CeCht1: Virtual screening, biological evaluation, and molecular dynamics simulation.

Plant-parasitic nematodes are a main limiting factor for worldwide agriculture. To reduce the global burden of nematode infections, chemical nematicides are still the most effective methods to manage nematodes. With the increasing resistance of nematodes, the development of new anti-nematicides drug is urgent. Nematode chitinases are found to play important roles in various physiological functions, such as larva moulting, hatching from eggshell, and host infection. Inhibition of nematode chitinase is considered a promising strategy for the development of eco-friendly nematicides. In this study, to develop novel nematode chitinase CeCht1 inhibitors, virtual screening of the ZINC database was performed using the pesticide-likeness rules, pharmacophore-based and docking-based approach in turn. Compounds HAU-4 and HAU-7 were identified as potent CeCht1 inhibitors with the IC50 values of 4.2μM and 10.0μM, respectively. Moreover, molecular dynamics simulations combined with binding free energy and free energy decomposition calculations were conducted to investigate the basis for the potency of the two inhibitors toward CeCht1. This work gives an insight into the future rational development of novel and potent nematode chitinase inhibitors.

The effect of genotype variation and M423 resistance mutations to the binding of phosphonomidate-based inhibitor IDX17119 with the thumb-II domain of Hepatitis C virus RdRp: an integrated molecular dynamics and binding free energy study

ABSTRACT The IDX17119 is a phosphonomidate-based pan-genotypic non-nucleoside inhibitor of Hepatitis C Virus (HCV) NS5B RdRp thumb-II domain. IDX17119 exhibits significant antiviral activity against HCV genotype (GT) 1a, 2a, 3a and 4a. The molecular docking analysis was performed to understand the binding and intermolecular interactions of the IDX17119 molecule at the thumb-II domain of 1a, 2a, 3a and 4a GT NS5B RdRps. The molecular dynamics simulation has been performed to determine the stability of the ligand–protein complexes. We found GT 1a complex is relatively stable compared with other drug-receptor complexes. The binding free energy calculations and free energy decomposition analysis were carried out for all the complexes, the result revealed that the increase in the unfavourable polar contribution affects the binding of IDX17119 with GT 2a NS5B RdRp compared with all other complexes. In addition to this, the effect of mutation at M423 site (M423T/V) alters the conformation and activity of the IDX17119 molecule.

Heterologous expression of family GH11 Aspergillus niger xylanase B (AnXylB11) in Pichia pastoris and competitive inhibition by riceXIP: An experimental and simulation study

The family GH11 Aspergillus niger JL15 xylanase B (AnXylB11) was heterologously expressed in Pichia pastoris X33. The recombinant AnXylB11 (reAnXylB11) was secreted into the culture medium with a molecular weight of approximately 33.0 kDa. The optimal temperature and pH of reAnXylB11 were 40 ℃ and 5.0, respectively. reAnXylB11 released xylobiose (X2)-xylohexaose (X6) from beechwood xylan, with xylotriose (X3) as the primary product. The hydrolysates showed significant antioxidant activity. reAnXylB11 was also competitively inhibited by recombinant rice xylanase inhibitory protein (rePriceXIP), with an inhibition constant (Ki) of 106.9 nM. Molecular dynamics (MD) simulations, non-covalent interactions (NCI), and binding free energy calculation and decomposition were conducted to decipher the interactional features between riceXIP and AnXyB11. Representative conformation of riceXIP-AnXylB11 complex showed that a U-shaped long loop between α4 and β5 (K143-L152) of riceXIP was protruded into the catalytic groove and formed tight interaction with many key residues of AnXylB11. The binding free energy of riceXIP-AnXylB11 was calculated to be − 46.1 ± 10.5 kcal/mol, with Coulomb and van der Waals forces contributing the most. NCI analysis showed that the hydrogen bonding networks such as R148riceXIP-E98AnXyl11B, K143riceXIP-D138AnXyl11B and R148riceXIP-E189AnXyl11B provided terrific contributions to the interface interaction. The Laplacian of electron density values of atom pairs R148riceXIP@ 2HH1-E89AnXylB11@OE2 and N142riceXIP@ 1HD2-D138AnXylB11@OD1 were 0.12190 and 0.16009 a.u., respectively. Exploring the interactional features between xylanase and inhibitor protein may aid in constructing mutant xylanase that is insensitive to xylanase inhibitory proteins (XIs).

A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

The pandemic of COVID-19 severe acute respiratory syndrome, which was fatal for millions of people worldwide, triggered the race to understand in detail the molecular mechanisms of this disease. In this work, the differences of interactions between the SARS-CoV/SARS-CoV-2 Receptor binding domain (RBD) and the human Angiotensin Converting Enzyme 2 (ACE2) receptor were studied using in silico tools. Our results show that SARS-CoV-2 RBD is more stable and forms more interactions with ACE2 than SARS-CoV. At its interface, three stable binding patterns are observed and named red-K31, green-K353 and blue-M82 according to the central ACE2 binding residue. In SARS-CoV instead, only the first two binding patches are persistently formed during the MD simulation. Our MM/GBSA calculations indicate the binding free energy difference of about 2.5 kcal/mol between SARS-CoV-2 and SARS-CoV which is compatible with the experiments. The binding free energy decomposition points out that SARS-CoV-2 RBD–ACE2 interactions of the red-K31 (-23.5~pm ~0.2~kcal/mol) and blue-M82 (-9.1~pm ~0.1~kcal/mol) patterns contribute more to the binding affinity than in SARS-CoV (-1.8~pm ~0.02~kcal/mol for red-K31), while the contribution of the green-K353 pattern is very similar in the two strains (-17.8~pm ~0.2~kcal/mol and -22.7~pm ~0.1~kcal/mol for SARS-CoV-2 and SARS-CoV, respectively). Five groups of mutations draw our attention at the RBD–ACE2 binding interface, among them, the mutation –PPA469-471/GVEG482-485 has the most important and favorable impact on SARS-CoV-2 binding to the ACE2 receptor. These results, highlighting the molecular differences in the binding between the two viruses, contribute to the common knowledge about the new corona virus and to the development of appropriate antiviral treatments, addressing the necessity of ongoing pandemics.