Molecular Simulation Study On The Binding Mechanism And Virtual Screening Of VGSC Inhibitors

At present,the problem of pain is widespread and challenging in the medical field,among which neuropathic pain,inflammatory pain and clinical operation pain are the most prominent problems.A large number of clinical experiments show that voltage gated sodium channels(VGSC)play an extremely important role in the production and development of pain,and have become a key target for current pain treatment.Inhibitors that produce analgesic effects based on interaction with VGSC can be divided into two types of selective inhibitors of VGSC and non-selective inhibitors of VGSC.Non-selective inhibitors of VGSC can bind with all subtypes of the VGSC.Among them,local anesthetics have the most prominent analgesic effect and show obvious advantages in pain treatment of clinical application.However,the local anesthetics in clinical use have obvious concentration dependence and side effects.In the study of VGSC selective inhibitors,Nav1.7 and Nav1.8 have become the hot targets for selective inhibitors of VGSC,because the excitatory development of neurons in abnormal neurons by them can lead to a variety of pain.Among them,the research on selective inhibitors of Nav1.7 is relatively mature,while there are few reports on selective inhibitors of Nav1.8,but a growing number of biological experiments show that Nav1.8 plays a key role in the occurrence of pain,which has attracted our attention.Nav1.7 is a target closely related to pain,and its crystal structure is currently resolved,which provides an important basis for studying the binding mechanism of local anesthetics to VGSC.In view of the limited reports of inhibitors of VGSC based on pain treatment for a long time,which could not meet the urgent needs of patients for pain treatment,and the specific mechanism of VGSC inhibitors is not clear,so further research of which is of great significance.In this paper,homologous modeling,molecular docking,virtual screening and molecular dynamics simulation were used to study the binding mechanism for local anesthetics of non-selective inhibitors of VGSC and the binding mechanism and virtual screening of selective inhibitors of Nav1.8.The main contents are as follows:(1)Molecular mechanisms studies for local anesthetic of non-selective inhibitor of VGSCLocal anesthetics play an indispensable role in the treatment of various acute and chronic pains.The new fluorine-substituted amide compounds combined by our research group showed good local anesthetic effects.In this experiment,representative active compounds with activity differences were selected for research.Given that the reported local anesthetics do not have selectivity for each subtype of the VGSC,and the the local anesthetic binding site of the subtypes of VGSC are the same and the residues of the binding site is quite similar.Therefore,this paper selected the newly reported human-derived crystal structure of Nav1.7 closely related to pain as the target protein,and used molecular docking,molecular dynamics simulations and free energy calculation methods to study the binding mechanism of local anesthetic inhibitors with Nav1.7,which provide an important theoretical basis for the design of new and efficient local anesthetic.It was found that Van der Waals and electrostatic interactions have important significance for the binding of inhibitors to Nav1.7,and residues Phe1748,Leu1449,Trp1332,Phe1452,and Ile1745 might be the key residues for local anesthetic to bind with Nav1.7.Besides,the structure of the compound in the protonated state is more stable in binding with Nav1.7,which might indicate that the protonated compound occupy a relatively dominant position when the compound plays a role.(2)Molecular mechanism and virtual screening of Nav1.8 selective inhibitorsStudies have reported that the Nav1.8 is an important target involved in neuropathic pain and inflammatory pain.Therefore,we selected a representative benzimidazole Nav1.8 selective inhibitor for a series of binding mechanisms and virtual screening studies.Since no Nav1.8 crystal structure has been reported,this work first used the homology modeling method to build the reliable structure of Nav1.8.Then,based on the Nav1.8 homology model,molecular docking,dynamic simulation,and calculation and decomposition of binding free energy were studied.It was found that hydrogen bonds and hydrophobic interactions play important roles in the binding of inhibitors to Nav1.8,and the residues Thr770,Ser1065,Phe1115,Trp697,Leu815,Phe818,and Phe771 migh be the key residues for ligand to bind with Nav1.8.In addition,to have hydrogen bond with Ser1065 could improve the biological activity of the compounds.Subsequently,based on the previous study results,we used a combined strategy of receptor-based and pharmacophore-based virtual screening to conduct a multi-conformation virtual screening study of Nav1.8 inhibitors in the internal entity library of the research group and 9 hits were selected.Finally,the molecular docking study was used to analyze the binding model of inhibitor to Nav1.8.It was found that these hits have novel skeleton,large optimization space,and are conducive to series of derivative synthesis of compounds using the splicing principle.Therefore,based on these structures of hits,optimization design and subsequent synthesis and activity evaluation work are carried out(in progress).