Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.

Discovery of Potential SARS-CoV-2M Protease Inhibitors by Virtual Screening,Molecular Dynamics,and Binding Free Energy Analyses

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)gained tremendous attention due to its high infectivity and pathogenicity.The 3-chymotrypsin-like hydrolase protease(Mpro)of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity.To better identify the drugs with potential in treating coronavirus disease 2019(COVID-19)caused by SARS-CoV-2 and according to the crystal structure of Mpro,we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials.As a result,9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2.Consequently,molecular dynamics(MD)simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro.The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes.Based on the binding free energy calculated by using MM/PBSA,Lopiravir,an inhibitor of human immunodeficiency virus(HIV)protease,is under investigation for the treatment of COVID-19 in combination with ritionavir,and it might inhibit Mpro effectively.Moreover,Ombitasvir,an inhibitor for non-structural protein 5 A of hepatitis C virus(HCV),has good inhibitory potency for Mpro.It is notable that the GS-6620 has a binding free energy,with respect to binding Mpro,comparable to that of ombitasvir.Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19,and that GS-6620 has good anti-SARS-CoV-2 activity.

Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments:The Influence of Force Field Polarisation and Capping

Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins.The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge)were investigated.Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding,peptide capping has the largest influence on the predicted free energy of binding.Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

Mechanism of inhibitor ADS-J1 and ADS-J2 binding to HIV-1 gp41

In order to analyze and explain the mechanism of the two small inhibitors （ADS-JI and ADS-J2） binding to HIV-1 gp41, a computational study is carried out to help identifying possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and characterize structures of binding complexes. The binding interactions of gp41-molecule and free energies of binding are obtained through molecular dynamics simulation and molecular mechanic/Poisson- Boitzmann surface area （ MM/PBSA ） calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point tbr further refinement of small molecular gp41 inhibitors.

Computational Analysis for Residue-Specific CDK2-Inhibitor Bindings

Cyclin-dependent kinase 2 (CDK2) is a key macromolecule in cell cycle regulation. In cancer cells, CDK2 is often overexpressed and its inhibition is an effective therapy of many cancers including breast carcinomas, leukemia, and lymphomas. Quantitative characterization of the interactions between CDK2 and its inhibitors at atomic level may provide a deep understanding of protein-inhibitor interactions and clues for more effective drug discovery. In this study, we have used the computational alanine scanning approach in combination with an efficient interaction entropy method to study the microscopic mechanism of binding between CDK2 and its 13 inhibitors. The total binding free energy from the method shows a correlation of 0.76?0.83 with the experimental values. The free energy component reveals two binding mode in the 13 complexes, namely van der Waals dominant, and electrostatic dominant. Decomposition of the total energy to per-residue contribution allows us to identify five hydrophobic residues as hot spots during the binding. Residues that are responsible for determining the strength of the binding were also analyzed.

Molecular Docking, 3D-QSAR and Molecular Dynamics Simulation Studies of Substituted Pyrimidines as Selective Covalent Janus Kinase 3 Inhibitors

Janus kinase 3（JAK3） is a member of Janus kinase（JAK） family, and it represents a promising target for the treatment of immune diseases and cancers. However, no highly selective inhibitors of JAK3 have been developed. For discovering the binding mechanism of JAK3 and these inhibitors, a molecular modeling study combining molecular docking, three-dimensional quantitative structure-activity relationships（3D-QSAR）, molecular dynamics and binding free energy calculations was performed on a series of pyrimidine-based compounds which could bind with the unique residue Cys909 of JAK3 kinase as the selective inhibitors of JAK3 in this work. The optimum Co MFA and Co MSIA models were generated based on the conformations obtained by molecular docking. The results showed that the models have satisfactory predicted capacity in both internal and external validation. Furthermore, a 50 ns molecular dynamics simulation was carried out to determine the detailed binding process of inhibitors with different activities. It was demonstrated that hydrogen bond interactions with Leu828, Glu903, Tyr904, Leu905 and Leu956 of JAK3 are significant for activity increase, and the Van der Waals interaction is mainly responsible for stable complex.

Inclusion Modes of Berberine with β-Cyclodextrin in Aqueous Solution

The possible inclusion modes of berberine（Berb） with β-cyclodextrin（BCD） in aqueous solution were predicted by molecular docking,molecular dynamics（MD） simulation and binding free energy calculations.Firstly,the molecular docking result reveals that the docking conformations of Berb appeared in two clusters ranked in two opposite orientations.Then,10 ns MD simulation was performed separately on the lowest energy conformation of each orientation（Mode I and Mode II） obtained by molecular docking.Moreover,based on the trajectories from MD simulation,the binding free energies of the two different modes were calculated by the Molecular Mechanics/Poisson Boltzmann surface area（MM/PBSA） method.Through analyzing the binding free energies of Berb with BCD,we found that Mode II was the preferential inclusion mode,which was in good agreement with the experimental result.In addition,the computed results show that the main impetus for the complex was the van der Waals interaction,but the solvation energy and the entropy change produced an adverse effect on the complex.

Theoretical Investigating Mechanisms of Drug-Resistance Generated by Mutation-Induced Changes in Influenza Viruses

Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its highly conserved catalytic center structure,while resistance mutations have already generated.Here,a detailed investigation of the drug resistance mechanism caused by mutations was performed for subtype N9(A/H7N9).Molecular dynamics simulation and alanine-scanning-interaction-entropy method(ASIE)were used to explore the critical differences between N9 and Zanamivir(ZMR)before and after R294K mutation.The results showed that the mutation caused the hydrogen bond between Arg294 and ZMR to break,then the hydrogen bonding network was disrupted,leading to weakened binding ability and resistance.While in wild type(A/H7N9^(WT)),this hydrogen bond was initially stable.Meanwhile,N9 derived from A/H11N9 was obtained as an R292K mutation.Then the relative binding free energy of N9 with five inhibitors(SIA,DAN,ZMR,G28,and G39)was predicted,basically consistent with experimental values,indicating that the calculated results were reliable by ASIE.In addition,Arg292 and Tyr406 were hot spots in the A/H11N9^(WT)-drugs.However,Lys292 was not observed as a favorable contributing residue in A/H11N9^(R292K),which may promote resistance.In comparison,Tyr406 remained the hotspot feature when SIA,ZMR,and G28 binding to A/H11N9^(R292K).Combining the two groups,we speculate that the resistance was mainly caused by the disruption of the hydrogen bonding network and the transformation of hotspots.This study could guide novel drug delivery of drug-resistant mutations in the treatment of A/H_(x)N9.

Effect of Residue Mutation on the Electrostatic Potential in EcClC

The effect of mutation of strongly conserved porelining residues in the chloride channel EcClC on the electrostatic potential and binding free energy of the chloride ion was studied using explicit protein-membrane structures. Electrostatic potential distribution and binding free energy of the chloride ion at different binding sites in the wild-type and mutated EcClC were calculated with APBS. The potential data reveal that the electrostatic potential around the selectivity filter, especially around the site Sext and Scen becomes more negative as the residue R147 was mutated to C147. The electrostatic binding free energy shows that the binding free energy of the chloride ion at all binding sites becomes more positive as R147 was mutated. It follows that mutation of R147 decreases ion stabilization at binding sites and affects channel＇s gating.

Computational Investigation on the Ethylene-induced Esterase from Citrus Sinensis

In order to understand the interaction between ethylene-induced esterase（EIE, EC 3.1.1.） from Citrus sinensis and α-naphthyl acetate, a3D model of EIE was generated based on the crystal structure of the tobacco salicylic acid binding protein 2（SABP2）. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model was obtained and its reliability was further assessed. In this study, the docking results show that the main-chain amide of residue His85 and residue Vall8 can form hydrogen bonds to the carbonyl oxygen group of α-naphthyl acetate. MM-PBSA method was applied to calculating the binding free energy between EIE mutants and α-naphthyl acetate. Our calculated binding free energy of each of the two mutant complexes is increased compared with that of the one of the wild type, which is unfavorable to the reaction. It is well consistent with the experimental data. The above results clearly indicate that His85 and Vail8 in EIE function as the oxyanion role and take part in the catalytic reaction. The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of EIE and other members of the plant α/β hydrolases.

Inhibiting the oligomerization of mycobacterial DNA-directed RNA polymerase(RNAP)using natural compound via in-silico techniques

Mycobacterium tuberculosis(Mtb)is responsible for the spread of tuberculosis(TB).The current study employed virtual screening of 2569 natural compounds against the DNA-directed RNA polymerase(RNAP)of Mtb to identify the possible binders that can inhibit its function.The in-silico methodology included molecular docking to the compounds,further,the stability and flexibility of the best complexes were studied using molecular dynamics simulation,the MM/GBSA binding free energy technique with energy decomposition,PCA,FEL,steered MD simulation,and umbrella sampling.Individual virtual screenings were conducted for the five RNAP subunits(chains A,B,C,D,and E)to identify a compound capable of inhibiting RNAP oligomerization.A promising compound,isoestradiol 3-benzoate,exhibited a low binding score(−7.28kcal/mol to−8.21kcal/mol)and showed binding ability with all subunits of the protein.Thus,the five complexes with isoestradiol 3-benzoate were selected for molecular dynamics simulation analysis.Furthermore,RMSD showed that isoestradiol 3-benzoate bound with chain E showed the lowest RMSD of 0.49nm,while with chains A and B it had the most stable and consistent conformations with RMSD of 1.75nm and 1.2nm,respectively.The H-bond between isoestradiol 3-benzoate and chains C and E showed the highest occupancy(58.27%,45.33%,and 50.80%,42.25%,11.75%).Moreover,the MMPBSA technique showed that isoestradiol 3-benzoate had a strong association with chains B and C(ΔGbind=−126.25±2.03 and−129.27±2.25).Additionally,free energy decomposition,PCA,FEL-steered MD simulation,and umbrella sampling were also performed to validate the association of the ligand with the protein.Isoestradiol 3-benzoate binds strongly to chains B and E;therefore,it should be considered as viable candidate for inhibiting the formation of RNAP protein complex,concluded in this study.

Inhibition of CK2 Activity by TCDD via Binding to ATP-competitive Binding Site of Catalytic Subunit： Insight from Computational Studies

Alternative mechanisms of toxic effects induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin（TCDD）, instead of the binding to aryl hydrocarbon receptor（AhR）, have been taken into consideration. It has been recently shown that TCDD reduces rapidly the activity of CK2（casein kinase II） both in vivo and in vitro. It is found that TCDD has high molecular similarities to the known inhibitors of CK2 catalytic subunit（CK2a）. This suggests that TCDD could also be an ATP-competitive inhibitor of CK2a. In this work, docking TCDD to CK2 was carried out based on the two structures of CK2a from maize and human, respectively. The binding free energies of the predicted CK2a-TCDD complexes estimated by the molecular mechanics/Poisson-Boltzmann surface area（MM/PBSA） method are from -85.1 kJ/mol to -114.3 kJ/mol for maize and are from -96.1 kJ/mol to -118.2 kJ/mol for human, which are comparable to those estimated for the known inhibitor and also ATP with CK2a. The energetic analysis also reveals that the van der Waals interaction is the dominant contribution to the binding free energy. These results are also useful for designing new drugs for a target of overexpressing CK2 in cancers.

Computational Characterization of Binding of Small Molecule Inhibitors to HIV-1 gp41

Developing orally available small molecule inhibitors of HIV-1 fusion has attracted significant interest over many years. Frey had recently reported several synthetic compounds which are experimentally shown to inhibit cell-cell fusion in the low micromolar range. We carried out computational study to help identify possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and to characterize structures of binding complexes. The detailed gp41-molecule binding interactions and free energies of binding are obtained through mo- lecular dynamics simulation and MM-PBSA calculation. Specific molecular interactions in the gp41-inhibitor com- plexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of small molecular gp41 inhibitors.

Identifying potential compounds from Bacopa monnieri(brahmi)against coxsackievirus A16 RdRp targeting HFM disease(tomato flu)

Hand,foot,and mouth disease(HFMD),primarily instigated by Coxsackievirus A16(CVA16),poses a serious health concern,necessitating effective therapeutic interventions.The RNA-dependent RNA polymerase(RdRp)of CVA16 emerges as a promising drug target for HFMD treatment.This study presents an in-silico pipeline for the identification of potential RdRp inhibitors against CVA16.A library of 91 natural compounds derived from Bacopa monnieri(brahmi)was virtually screened against the CVA16 RdRp.Here,Bacobitacin D emerged as a promising hit molecule,forming 8 hydrogen bonds including key catalytic site residues(Asp^(238)and Asp^(329))within the RdRp active site.Further,molecular dynamics(MD)simulations and MM/GBSA binding free energy calculations was applied on the top three hits that were selected based on exhaustive docking scores(≤-9.55 kcal/mol).Bacobitacin D exhibited sustainable stability,as evidenced by minimal deviation(RMSD=0.75±0.02 nm)during a 100 ns MD simulation.Importantly,Bacopaside IV exhibited the lowestΔGTOTAL binding free energy(-23.70 kcal/mol),while Bacobitacin D displayed a comparableΔGTOTAL of19.14 kcal/mol.Structural interpretation of the most populated cluster derived from MD simulations showed direct interactions of Bacobitacin D with pivotal catalytic residues,including Asp^(238)and Ser^(289).This comprehensive study confirmed Bacobitacin D as a potent inhibitor of CVA16 RdRp,offering a potential avenue for therapeutic intervention against HFMD.Experimental validation is required to confirm the inhibitory action of Bacobitacin D against HFMD.

Structural and dynamic properties of the YTH domain in complex with N^(6)-methyladenosine RNA studied by accelerated molecular dynamics simulations

Background:N^(6)-methyladenosine(m^(6)A)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 N^(6)-methyladenosine RNA has attracted considerable attention.However,the structural and dynamic characteristics of the YTH domain in complex with m^(6)A RNA is still unknown.Method:This 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.Results:The 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-m^(6)A3 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 nonmethylated 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 m^(6)A RNA to the YTH domain,which is also supported by aMD simulations of a double mutated system(L383A/M437A).Conclusion:The results are in good agreement with higher structural stability of the YTH-m^(6)A 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.