Molecular Dynamics Simulations Study On The Interaction Mechanism Of HIF-2 And Matriptase With Its Inhibitors

Protein is the most important part of the life.The recognition process between protein receptor and ligand plays an important role in physiological function.Therefore,in order to understand the regulation of the life,it is vital to explore the interaction and recognition mechanism between protein receptor and ligand,which could provide theoretical support for new drug development as well.At present,it is challenging to study protein complex structure-fuction relationship by experimental methods.With the fast development on computational and theoretical simulation methods,such as molecular dynamics and molecular docking,have become essential means to explore the mechanism between protein and ligand during dynamic process.In this manuscript,molecular dynamics simulations are utilized to carry out systematic and detailed theoretical research on hypoxia-inducible factor(HIF-2)and the interaction mechanism of Matriptase with inhibitor,respectively.The main content is as follows 1.Theoretical study on the interaction mechanism of chiral inhibitor with HIF-2 heterodimerCellular response to oxygen availability plays a vital role in mammalian survival,physiological homeostasis and disease progression.In human cells,the hypoxia-inducible factors HIF-2? is one of major mediators for pathological hypoxia response.Misregulation of this system is often correlated with increased levels of HIF-2?,which can form the heterodimerization with aryl hydrocarbon receptor nuclear translocator(ARNT)has been linked to promote the expression of protumorigenic pathways.It can be an opportunity that the inhibition of HIF-2 heterodimerization can effectively control the development of tumor.Studies demonstrated a class of tetrazole containing chiral inhibitors could stereoselectively disrupt the HIF-2 dimerization and reduce the target gene expression.In this work,molecular dynamics(MD)simulations combined with adaptive steered molecular dynamics(ASMD)simulations were used to investigate stereoselective interrupting mechanism of HIF-2.Our results decipher that the binding of(S,R)-24 begets the significant conformation changes of ?-sheets on HIF-2? and interrupts the HIF-2?/ARNT heterodimerization,which may be attributed to the disruption of the hydrogen bond and salt bridge interactions formed by the four foremost residues(Asp240,Arg247,Glu362,and Arg366)and the destruction of hydrophobic interactions on the binding interface.In contrast,the binding of(R,S)-24 does not disrupt protein dimerization and causes the motion of F? helix in HIF-2? PAS-B domain to further change the major tunnel for ligand ingress and engress.The present work clarifies the effect of different stereostructure of inhibitors on HIF-2 heterodimerization,which may conduce to develop highly potent antagonists for intervening the HIF-2-driven tumors.2.Theoretical study on the interaction mechanism of inhibitors PT2399 and 0X3 with HIF-2 heterodimerRecently,targeting hypoxia-inducible factors HIF-2 is currently considered to be the most direct way for the therapy of clear cell renal cell carcinoma(ccRCC).In the above studies,we found that HIF-2 has certain structural selectivity to inhibitors,so what are the effects of functional groups on HIF-2 heterodimer.To this end,Conventional molecular dynamics(MD)simulations and molecular docking were performed to investigate the effects of preclinical inhibitor PT2399 and artificial inhibitor 0X3 on three HIF-2 heterodimer models.Our repeated simulation results reveal that the preclinical inhibitor PT2399 has strong ability to disrupt the heterodimerization of three HIF-2 models.The potential inhibiton mechanism may be that the binding of inhibitors in HIF-2? causes the the local conformational changes of binding interface,it will further disrupts the crucial hydrogen bond and hydrophobic interactions of interdomain of HIF-2 heterodimer.While the ability of 0X3 to destroy the dimerization of the three models is weaker than that of PT2399.It can be found that PT2399 with dominant substituents(cyano,fluorine,sulfuryl and hydroxyl)is more preferred than 0X3 as HIF-2 inhibitor,these substituents play a crucial role in involving more hydrogen bond interactions with residues of interface(His248,His293,Tyr278,Tyr281)and then cause the larger structural change of protein.This study may provide a deeper atomic-level insight into the effect of on-target inhibitors on HIF-2 heterodimer,which is expected to contribute to further rational design of effective ccRCC drugs.3.Theoretical study on the interaction mechanism of matriptase with two classes of inhibitorsMatriptase,as a Type II transmembrane serine protease,is overexpressed in many human cancers and proved to contribute to the tumor development.Up to now,many promising anti-cancer drugs have been developed.However,the detailed structure-function relationship between inhibitors and matriptase remains elusive.In this work,molecular dynamics simulation and binding free energy calculations were performed to investigate the biochemistry behaviors of two class inhibitors binding to matriptase.The results indicate that the van der Waals interaction is the major driving force for ligand binding.The results clearly identify the two class inhibitors exist different binding modes:the Pyridyl Bis(oxy)dibenzimidamide inhibitors(CJ-672 and CJ-730)bind into the S1 pocket and the anion cavity,and is mainly stabilized by hydrogen bonding;and the amidinophenylalanine inhibitors(N4A and F4D)bind into the S1 pocket,S2,S1' cavity,they are mainly stabilized by hydrophobic interaction.Moreover,the key residues responsible for achieving strong binding have been identified,including Asp189,Phe99,Gly216,Gly219 and Trp215.we have mastered some important and favorable interaction patterns between matriptase and inhibitors.Our findings would be helpful for understanding the interaction mechanism between the inhibitor and matriptase and afford important guidance for the rational design of potent matriptase inhibitors.