title: Computational Analysis of the Domain Architecture and Substrate-Gating Mechanism of Prolyl Oligopeptidases from Shewanella woodyi and Identification of Probable Lead Molecules.
abstract: Prolyl oligopeptidases (POPs) are serine proteases found in prokaryotes and eukaryotes which hydrolyze the peptide bond containing proline. The current study focuses on the analysis of POP sequences, their distribution and domain architecture in Shewanella woodyi, a Gram-negative, luminous bacterium which causes celiac sprue and similar infections in marine organisms. The POP undergoes huge interdomain movement, which allows possible route for the entry of any substrate. Hence, it offers an opportunity to understand the mechanism of substrate gating by studying the domain architecture and possibility to identify a probable drug target. In the present study, the POP sequence was retrieved from GenBank database and the best homologous templates were identified by PSI-BLAST search. The three-dimensional structures of the closed and open forms of POP from S. woodyi, which are not available in native form, were generated by homology modeling. The ideal lead molecules were screened by computer-aided virtual screening, and the binding potential of the best leads toward the target was studied by molecular docking. The domain architecture of the POP revealed that it has a propeller domain consists of [Formula: see text]-sheets, surrounded by [Formula: see text]-helices and [Formula: see text] hydrolase domain with catalytic triad containing Ser-564, Asp-646 and His-681. The hypothetical models of open and closed POP showed backbone RMSD value of 0.56 and 0.65 Å, respectively. Ramachandran plot of the open and closed POP conformations accounts for 99.4 and 98.7 % residues in the favoured region, respectively. Our study revealed that propeller domain comes as an insert between N-terminal and C-terminal [Formula: see text] hydrolase domain. Molecular docking, drug likeness properties and ADME prediction suggested that KUC-103481N and Pramiracetum can be used as probable lead molecules toward the POP from S. woodyi.
authors: R&D Centre, Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, 560 078, India.
authors: Priya
authors: P
authors: Patil
authors: R&D Centre, Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, 560 078, India. sinoshskariya@gmail.com.|Visvesvaraya Technological University, Belgaum, Karnataka, India. sinoshskariya@gmail.com.
authors: Sinosh
authors: S
authors: Skariyachan
authors: National Centre for Biological Sciences, GKVK campus, Bangalore, Karnataka, 560065, India.
authors: Eshita
authors: E
authors: Mutt
authors: Department of Bioengineering and Therapeutic Sciences, Helen Diller Family Comprehensive Cancer, University of California, San Francisco, 1450 3rd St., San Francisco, CA, 94158, USA.
authors: Swati
authors: S
authors: Kaushik
mesh_terms: D019295:Computational Biology / Q000379:methods*; D062105:Molecular Docking Simulation; D000085822:Prolyl Oligopeptidases; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism*; D057057:Serine Proteases / Q000737:chemistry / Q000378:metabolism; D020592:Shewanella / Q000201:enzymology*
chemical_list: D057057:Serine Proteases; D012697:Serine Endopeptidases; D000085822:Prolyl Oligopeptidases
keywords: -propeller; Domain architecture; Probable drug target; Probable lead molecules; Prolyl oligopeptidases; Serine proteases; Shewanella woodyi; hydrolase