title: Structure, evolution and virtual screening of NDM-1 strain from Kolkata.
abstract: β-lactam antibiotics are utilised to treat bacterial infection. β-lactamase enzymes (EC 3.5.2.6) are produced by several bacteria and are responsible for their resistance to β-lactam antibiotics like penicillin, cephamycins and carbapenems. New Delhi Metallo-β-lactamase (NDM-1) is a gene that makes bacteria resistant to β-lactam antibiotics. Preparing a compound against NDM-1 will require additional investment and development by drug manufacturers as the current antibiotics will not treat patients with NDM-1 resistance. NDM-1 of Kolkata showed convergent-type evolution with other NDM-1 producing strains. The modelled structure exhibited α-β-α barrel-type domain along with Zn metallo-β-lactamase N-terminal domain. Compounds belonging to cephalosporins (relatively resistant to β-lactamase) and other antibiotics ceftaroline, ceftobiprole, piperacillin, penamecillin, azidocillin, cefonicid, tigecycline and colistin have exhibited better binding affinity with the modelled NDM-1.
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India.
authors.forename: Ganesh Chandra
authors.initials: GC
authors.lastname: Sahoo
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India.
authors.forename: Mukta
authors.initials: M
authors.lastname: Rani
authors.affiliation: Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research, Hajipur, India.
authors.forename: Yousuf
authors.initials: Y
authors.lastname: Ansari
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India.
authors.forename: Chanda
authors.initials: C
authors.lastname: Jha
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India.
authors.forename: Sindhuprava
authors.initials: S
authors.lastname: Rana
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India.
authors.forename: Manas Ranjan
authors.initials: MR
authors.lastname: Dikhit
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India.
authors.forename: Kanhu Charan
authors.initials: KC
authors.lastname: Moharana
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India.
authors.forename: Rakesh
authors.initials: R
authors.lastname: Kumar
authors.affiliation: BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna 800007, India; Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research, Hajipur, India.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Das
mesh_terms: D000900:Anti-Bacterial Agents / Q000138:chemical synthesis*; D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D004791:Enzyme Inhibitors / Q000138:chemical synthesis; D019143:Evolution, Molecular; D008956:Models, Chemical; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics* / Q000648:ultrastructure
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D001618:beta-Lactamases; C552864:beta-lactamase NDM-1
keywords: NDM–1 evolution; NDM–1 resistance; NDM–1 structure; alpha–beta–alpha barrel; antibiotics; azidocillin; beta–lactamase enzymes; carbapenems; cefonicid; ceftaroline; ceftobiprole; cephalosporins; cephamycins; colistin; modelling; penamecillin; penicillin; piperacillin; threading; tigecycline; virtual screening