Molecular Dynamics Study On The Interaction Mechanism Of Small Molecule Inhibitors To BRD4 And SARS-CoV-2 Main Protease

Proteins are indispensable components of living organisms and play a critical role in their life processes.Abnormal expression of proteins leads to the emergence of many malignant diseases,such as cervical cancer,esophageal cancer and leukemia.Small molecule inhibitors targeting proteins can specifically block the signaling pathways necessary for tumor growth,thus providing a practical solution for the treatment of related diseases.In addition,small molecule inhibitors have good drug-forming and pharmacokinetic properties,showing great advantages in the process of drug development,and have become a popular research topic in the life sciences.Therefore,it is significant to the study of the interaction mechanism between small molecule inhibitors and target proteins for drug development and design.In this paper,the binding mechanism of two target proteins(bromodomain-containing protein 4 and SARS-CoV-2 main protease)to small molecule inhibitors was investigated,which is expected to provide useful theoretical information for the development of efficient inhibitors.Bromodomain-containing protein 4(BRD4)has an important role in cell proliferation and cell cycle progression,and its dysfunction is associated with tumor development,which has become a potential target for cancer treatment.BRD4 contains two tandem bromodomains(BD1and BD2),and selective inhibition of BD1 or BD2 can provide more effective regimen for the treatment of some diseases.The molecular mechanism of selective binding of inhibitors SG3-179,GSK778 and GSK620 to BD1 and BD2 was investigated using multiple replica molecular dynamics(MRMD)simulations and binding free energy calculations.The results show that inhibitor binding has different effects on the internal dynamics behavior of BD1 and BD2,and that BD1 exhibits stronger structural flexibility than BD2.In addition,binding free energy calculations indicated that entropic contributions,electrostatic interactions and van der Waals interactions are key factors in the selective binding of BD1 and BD2 by SG3-179,GSK778 and GSK620.The free energy decomposition method was used to calculate the energy contribution of i between individual residues and the inhibitor.It was found that the energy differences between inhibitor and residues(W81,W374),(P82,P375),(Q85,K378),(V87,V380),(L92,L385),(N93,G386),(L94,L387),(C136,C429),(N140,N433),(K141,P434),(D144,H437)and(I146,V439)in(BD1,BD2)drive the selective binding of the inhibitor to BD1 and BD2,and they can serve as effective targets for the development of high selective inhibitors against BD1 or BD2.The relevant information can provide some theoretical guidance to improve the selectivity of inhibitors for BD1 and BD2.The pneumonia outbreak caused by the SARS-CoV-2 virus poses a serious threat to human health and the world economy.Development of safe and highly effective antiviral drugs is of great significance for treatment of COVID-19.The main protease(Mpro)of SARS-CoV-2 is a key enzyme for viral replication and transcription,and has become an ideal target for the development of antiviral drugs.In this study,we analyzed the internal dynamics and conformational changes of the Mpro induced by the binding of three inhibitors YTV,YSP and YU4,using multiple replicaaccelerated molecular dynamics(MR-aMD)simulations,dynamic cross-correlation matrix(DCCM)calculations and principal component(PC)analysis.The results of DCCM calculations and PC analysis indicated that inhibitor binding significantly affects dynamic behavior of Mpro and resulted in conformational rearrangement of the Mpro.The molecular mechanics-Poisson Boltzmann surface area(MM-PBSA)method was used to calculate the binding ability of YTV,YSP,and YU4 to the Mpro.The results showed that the substitution of the tert-butanol group by methylbenzene and trifluoromethyl groups enhances the binding ability of YSP and YU4 to the Mpro compared to YTV.Furthermore,the energy contribution of individual residues and interaction network analysis revealed that residues T25,L27,H41,M49,N142,G143,C145,M165,E166 and Q189 formed massive hydrophobic interactions and hydrogen bonding interactions with the inhibitor,which provided important energy contributions to the binding of the inhibitor to the Mpro.The present work is expected to provide a theoretical reference for the development of efficient inhibitors targeting the Mpro.By now,molecular dynamics simulations,principal component analysis and free energy of binding calculations have become powerful tools for investigating the mechanism of inhibitortarget protein binding,exploring the conformational changes of proteins and identifying the key sites of inhibitor binding.We expect that the work in this paper will help to further explore the mechanism of inhibitor-target protein interaction and understand the protein conformational changes induced by inhibitor binding,and also provide a theoretical basis for the development of efficient inhibitors.