title: CD4-gp120 interaction interface - a gateway for HIV-1 infection in human: molecular network, modeling and docking studies.
abstract: The major causative agent for Acquired Immune Deficiency Syndrome (AIDS) is Human Immunodeficiency Virus-1 (HIV-1). HIV-1 is a predominant subtype of HIV which counts on human cellular mechanism virtually in every aspect of its life cycle. Binding of viral envelope glycoprotein-gp120 with human cell surface CD4 receptor triggers the early infection stage of HIV-1. This study focuses on the interaction interface between these two proteins that play a crucial role for viral infectivity. The CD4-gp120 interaction interface has been studied through a comprehensive protein-protein interaction network (PPIN) analysis and highlighted as a useful step towards identifying potential therapeutic drug targets against HIV-1 infection. We prioritized gp41, Nef and Tat proteins of HIV-1 as valuable drug targets at early stage of viral infection. Lack of crystal structure has made it difficult to understand the biological implication of these proteins during disease progression. Here, computational protein modeling techniques and molecular dynamics simulations were performed to generate three-dimensional models of these targets. Besides, molecular docking was initiated to determine the desirability of these target proteins for already available HIV-1 specific drugs which indicates the usefulness of these protein structures to identify an effective drug combination therapy against AIDS.
authors.affiliation: a Bioinformatics Infrastructure Facility , Sri Venkateswara College, University of Delhi , Benito Juarez Road, Dhaula Kuan, New Delhi 110021 , India.
authors.forename: Deeksha
authors.initials: D
authors.lastname: Pandey
authors.affiliation: a Bioinformatics Infrastructure Facility , Sri Venkateswara College, University of Delhi , Benito Juarez Road, Dhaula Kuan, New Delhi 110021 , India.
authors.forename: Avijit
authors.initials: A
authors.lastname: Podder
authors.affiliation: a Bioinformatics Infrastructure Facility , Sri Venkateswara College, University of Delhi , Benito Juarez Road, Dhaula Kuan, New Delhi 110021 , India.
authors.forename: Mansi
authors.initials: M
authors.lastname: Pandit
authors.affiliation: a Bioinformatics Infrastructure Facility , Sri Venkateswara College, University of Delhi , Benito Juarez Road, Dhaula Kuan, New Delhi 110021 , India.
authors.forename: Narayanan
authors.initials: N
authors.lastname: Latha
mesh_terms: D015704:CD4 Antigens / Q000737:chemistry / Q000378:metabolism*; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000378:metabolism*; D015700:HIV Envelope Protein gp41 / Q000737:chemistry / Q000378:metabolism; D015658:HIV Infections / Q000378:metabolism* / Q000821:virology; D015497:HIV-1 / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D062105:Molecular Docking Simulation / Q000379:methods*; D011487:Protein Conformation; D060066:Protein Interaction Maps; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000378:metabolism; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000378:metabolism
chemical_list: D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; C514787:gp41 protein, Human immunodeficiency virus 1; D054311:nef Gene Products, Human Immunodeficiency Virus; C514837:nef protein, Human immunodeficiency virus 1; D054322:tat Gene Products, Human Immunodeficiency Virus
keywords: CD4–gp120 interface; molecular dynamics simulations; protein–ligand docking; protein–protein interaction network; structure prediction