title: An integrated in silico approach to design specific inhibitors targeting human poly(a)-specific ribonuclease.
abstract: Poly(A)-specific ribonuclease (PARN) is an exoribonuclease/deadenylase that degrades 3'-end poly(A) tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN's catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A) amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A) inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.
authors.affiliation: Bioinformatics and Medical Informatics Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Vlachakis
authors.forename: Athanasia
authors.initials: A
authors.lastname: Pavlopoulou
authors.forename: Georgia
authors.initials: G
authors.lastname: Tsiliki
authors.forename: Dimitri
authors.initials: D
authors.lastname: Komiotis
authors.forename: Constantinos
authors.initials: C
authors.lastname: Stathopoulos
authors.forename: Nikolaos A A
authors.initials: NA
authors.lastname: Balatsos
authors.forename: Sophia
authors.initials: S
authors.lastname: Kossida
mesh_terms: D020134:Catalytic Domain / Q000235:genetics; D003198:Computer Simulation; D015195:Drug Design; D005095:Exoribonucleases / Q000037:antagonists & inhibitors*; D011485:Protein Binding / Q000235:genetics; D013379:Substrate Specificity
chemical_list: D005095:Exoribonucleases