title: Delineating residues for haemolytic activities of snake venom cardiotoxin 1 from Naja naja as probed by molecular dynamics simulations and in vitro validations.
abstract: Cardiotoxins (CTXs) are single polypeptide chain consisting of 59-62 amino acids with four disulfide bridges and globular proteins of simple β-sheet folds. The CTXs are one of principal toxic components causing haemolysis and damaging various cells and belong to three-finger toxin (TFT) superfamily of snake venoms. However, there is no natural or synthetic small molecular inhibitor to the protein toxins to date. In the present study, modes of interaction of cardiotoxin 1 (CTX1) from Indian cobra (Naja naja) with heterogeneous erythrocyte membrane (EM) model system have been extensively examined by using all-atom molecular dynamics (MD) simulations in near physiological conditions and comprehensive analyses of the MD data revealed two distinct principal regions ('head groove' and 'loop groove') of the protein toxin for establishing structural interactions with the EM system. Moreover, combined analyses of data from high-throughput virtual screening of NCI small molecular database, in vitro haemolytic assays for top-hits of the chemical compounds against crude venom of Naja naja and as well CTXs purified from the venom and pharmacokinetic examinations on the chemical compounds retarding haemolytic activities of CTXs suggested that Etidronic acid and Zoledronic acid are promising prototypic chemical inhibitors to CTXs of snake venoms.
authors.affiliation: Structural Biology Lab, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Gorai
authors.affiliation: Structural Biology Lab, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India. Electronic address: sivaram@scbt.sastra.edu.
authors.forename: Thirunavukkarasu
authors.initials: T
authors.lastname: Sivaraman
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000931:Antidotes / Q000737:chemistry / Q000494:pharmacology*; D002784:Cholesterol / Q000737:chemistry; D004179:Cobra Cardiotoxin Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000302:isolation & purification / Q000633:toxicity; D004164:Diphosphonates / Q000737:chemistry / Q000494:pharmacology*; D004220:Disulfides / Q000737:chemistry; D004546:Elapid Venoms / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000302:isolation & purification / Q000633:toxicity; D017815:Elapidae / Q000378:metabolism; D004910:Erythrocyte Membrane / Q000737:chemistry / Q000187:drug effects; D012968:Etidronic Acid / Q000737:chemistry / Q000494:pharmacology*; D006461:Hemolysis / Q000187:drug effects; D057166:High-Throughput Screening Assays; D006801:Humans; D007093:Imidazoles / Q000737:chemistry / Q000494:pharmacology*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry; D010714:Phosphatidylethanolamines / Q000737:chemistry; D010718:Phosphatidylserines / Q000737:chemistry; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D054852:Small Molecule Libraries / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D014584:User-Computer Interface; D000077211:Zoledronic Acid
chemical_list: D000931:Antidotes; D004179:Cobra Cardiotoxin Proteins; D004164:Diphosphonates; D004220:Disulfides; D004546:Elapid Venoms; D007093:Imidazoles; D010713:Phosphatidylcholines; D010714:Phosphatidylethanolamines; D010718:Phosphatidylserines; D054852:Small Molecule Libraries; C057561:1-palmitoyl-2-oleoylphosphatidylethanolamine; D000077211:Zoledronic Acid; C042511:1,2-dioleoylphosphatidylserine; D002784:Cholesterol; D012968:Etidronic Acid; C028694:1-palmitoyl-2-oleoylphosphatidylcholine
keywords: Heterogeneous bilayer; Inhibitors; Molecular dynamics; RBC lysis; Snake venom