Molecular Dynamics Simulations Study Of The Binding And Recognition Mechanism Of Transcription Factor TvMyb And Anaplastic Lymphoma Kinase With Ligands

With the development of the times,mankind has overcome many diseases through modern medicine,but contemporary human health still faces many major disease threats,such as infectious diseases,cancer,etc.Infectious diseases are diseases that can be transmitted from person to person or from human to animal by pathogens and are widely prevalent.One of the most widespread non-viral sexually transmitted infections worldwide is Trichomonas vaginalis,which according to the World Health Organization infects approximately 170 million people each year.Cancer is a major threat to contemporary human health,and according to the World Health Organization,it will kill approximately 10 million people worldwide in 2020.Cancer research has always been one of the major concerns of researchers worldwide,but with increasing life expectancy and changing lifestyles,the annual incidence of cancer continues to increase worldwide.1.Molecular dynamics simulation study of the binding and recognition mechanism of transcription factor tvMyb2 to MRE-2f gene fragment in ap65-1 geneTrichomonas vaginalis,an anaerobic protozoan parasite with flagella,is the causative agent of vaginal trichomoniasis.Trichomonas vaginalis is usually found in the vagina of women,and infection is usually associated with significant symptoms and an increased risk of adverse pregnancy outcomes and cervical cancer.Trichomonas vaginalis completes its parasitism by secreting a series of adhesion proteins that attach to the epithelial cells of the vagina.The adhesion protein AP65-1,which is important for its parasitic process,is transcribed from the ap65-1 gene.The transcription factor tvMyb2 regulates the transcriptional process by binding to two different Myb recognition elements（MRE）,MRE-2f and MRE-1,of the ap65-1 gene.This chapter focuses on the binding process of the transcription factor tvMyb2 to the MRE-2f gene fragment.To clarify the binding and recognition mechanism between tvMyb2 and MRE-2f gene fragments at the atomic level,the details of the interaction between tvMyb2 and its mutants K51A,R84A and R87A,respectively,with MRE-2f gene fragments are investigated in this chapter using molecular dynamics simulations combined with MM-GBSA binding free energy calculations.We found that the introduction of DNA causes a decrease in the relative motion of the R2 and R3structural domains of tvMyb2 and a decrease in conformational flexibility.Combined with the results of free energy calculations,it was shown that van der Waals interactions are the main driving force of the binding process of tvMyb2 to the MRE-2f gene fragment.The polar amino acid residues（K49,K51,R84,K138 and N139）can form specific hydrogen bonds with the MRE-2f gene fragment and make an important contribution to the recognition process;the polar amino acid residues（K48,K49,K72,R87,Q85,R89,K91 and R120）can form non-specific hydrogen bonds with MRE-2f and the resulting hydrogen bond network The hydrogen bonding network constituted by MRE-2f contributes positively to the stable binding of the two.The difference in the binding ability of transcription factor tvMyb2 and its mutants to the MRE-2f gene fragment is mainly due to polar interactions and is mainly manifested by the local disruption of the hydrogen bonding network in the mutant.This work obtained microscopic information on the binding of tvMyb2 and MRE-2f gene fragments at the atomic level,which provides reliable theoretical support for understanding the binding and recognition mechanism.2.Molecular dynamics simulation study of the binding and recognition mechanism of transcription factor tvMyb2 to MRE-1 gene fragment in ap65-1 geneThe ap65-1 gene of Trichomonas vaginalis contains two discrete Myb recognition elements（MREs）,MRE-2f and MRE-1.MRE-2f and MRE-1 are interspersed among several closely adjacent DNA elements in the ap65-1 promoter region and together regulate the transcriptional process of the ap65-1 gene.In this chapter,we focus on the binding process between tvMyb2 and the MRE-1 gene fragment,another Myb recognition element in the ap65-1 gene.In the work of this chapter,we used molecular dynamics simulations combined with MM-GBSA binding free energy calculations to study the details of the interaction between tvMyb2 and the MRE-1gene fragment.We found that electrostatic interactions are the main driving force of the binding process of tvMyb2 to the MRE-1 gene fragment.The polar amino acid residues（K49,R84,K138 and N139）can form specific hydrogen bonds with the MRE-2f gene fragment and make an important contribution to the recognition process of the two;the polar amino acid residues（K51,Q85,R87,R89,Y93 and R140）can form non-specific hydrogen bonds with MRE-1 and the resulting hydrogen bond network makes a positive contribution to the stable binding of the two The hydrogen bonding network formed by The difference in the binding ability of transcription factor tvMyb2 and its mutants with MRE-1 is mainly due to polar interactions and is mainly manifested by the local disruption of the hydrogen bonding network in the mutants.tvMyb2 and the two Myb binding elements differ in their binding modes mainly due to the different hydrogen bonding networks.The K51 residue plays an important role in the difference between the two hydrogen bonding networks:during the binding of tvMyb2 to MRE-2f,the K51 residue forms a specific hydrogen bond K51-T（1’）,which plays a recognition role;during the binding of tvMyb2 to MRE-1the specific hydrogen bond disappears and the K51 residue forms a non-specific hydrogen bond K51-T（8）,which helps to stabilize the complex conformation.This work obtained microscopic information on the binding of tvMyb2 and MRE-1 gene fragments at the atomic level,which provides reliable theoretical support for understanding the binding and recognition mechanism of both.3.Molecular dynamics simulation study of the binding and recognition mechanism of transcription factor tvMyb3 to MRE-1 gene fragment in ap65-1 geneThe transcription factor tvMyb3 is a Myb protein that regulates the transcription of the adhesion protein 65-1 in Trichomonas vaginalis together with the transcription factor tvMyb2.tvMyb3 protein has a unique C-terminal structure that contains aβ-hairpin structure and a DNA signaling region.In this chapter,we focus on the binding process between tvMyb3 and the MRE-1 gene fragment of ap65-1 gene.In the work of this chapter,we used molecular dynamics simulations combined with MM-GBSA binding free energy calculations to investigate in depth the details of the interaction between tvMyb2 and the MRE-1 gene fragment.We found that the tvMyb3 protein recognizes and binds to the MRE-1 gene fragment through a series of hydrogen bonding and hydrophobic interactions,and that the Myb structural domain,which is similar to that of the tvMyb protein in the same family,plays a relatively similar role in recognizing and binding to the MRE-1 gene fragment.The uniqueβ-hairpin structure of the transcription factor tvMyb3 plays an important role in binding and recognizing the MRE-1 gene fragment.Subsequently,we reconstructed the C-terminal DNA signaling region of tvMyb3 and found that this DNA-binding signaling region forms a more stableα-helix structure,which plays an important role in the binding process of tvMyb3 to the MRE-1 gene fragment.This work has obtained microscopic information on the binding of tvMyb3 and MRE-1 gene fragments at the atomic level,which provides reliable theoretical support for understanding the binding and recognition mechanism of both.4.Molecular dynamics of the Anaplastic lymphoma kinase and its mutations with its three important drugsAnaplastic lymphoma kinase（ALK）is a receptor tyrosine kinase that has been used as a therapeutic target for a variety of cancers,including non-small cell lung cancer,neuroblastoma,and breast cancer,and several inhibitors targeting the ALK protein are now licensed for marketing by FDA.Despite the multitude of available inhibitors,the therapeutic efficacy of various inhibitors has been significantly reduced by the accumulation of acquired drug-resistant mutations.Although a large amount of experimental data related to drug resistance mutations have been reported,the structural determinants of the mechanisms of drug resistance mutations remain poorly defined.Here,we applied molecular dynamics simulations and NEB simulations to investigate the interactions between wild-type ALK protein and three important drug resistance mutants（L1198F,G1123S and G1202R）and three important marketed inhibitors（Ceritinib,Alectinib and Lorlatinib）in order to compare the mechanisms of resistance caused by the three resistance mutations and to provide a molecular-level explanation of the principle of inhibitors overcome specific resistance mutations.The results show that the G1123S mutant alters the binding pocket in different ways to make Ceritinib lost its stability and that both Alectinib and Lorlatinib can overcome the G1123S mutant by avoiding conformational changes in the binding pocket.The L1198F mutant is resistant to all three inhibitors,mainly because the altered side chain of the L1198F mutation occupies what would otherwise be an important drug recognition pocket E₀.The G1202R mutant establishes a series of polar interactions and closes the entrance to a portion of the binding pocket of ALK through the polar interaction network.Lorlatinib can induce changes in the polar interaction network of the G1202R mutant to break through the blockage of the G1202R mutant and enter the binding pocket without obstacle.This study elucidates the molecular mechanisms of three drug-resistance mutants,and on this basis,we propose the molecular-level mechanisms of three different inhibitors overcome these drug-resistant mutations.This study can also provide an important theoretical basis for a new strategy of structure based ALK drug design.