title: A combined in silico/in vitro approach unveils common molecular requirements for efficient BVDV RdRp binding of linear aromatic N-polycyclic systems.
abstract: In this work, we present and discuss a comprehensive set of both newly and previously synthesized compounds belonging to 5 distinct molecular classes of linear aromatic N-polycyclic systems that efficiently inhibits bovine viral diarrhea virus (BVDV) infection. A coupled in silico/in vitro investigation was employed to formulate a molecular rationale explaining the notable affinity of all molecules to BVDV RNA dependent RNA polymerase (RdRp) NS5B. We initially developed a three-dimensional common-feature pharmacophore model according to which two hydrogen bond acceptors and one hydrophobic aromatic feature are shared by all molecular series in binding the viral polymerase. The pharmacophoric information was used to retrieve a putative binding site on the surface of the BVDV RdRp and to guide compound docking within the protein binding site. The affinity of all compounds towards the enzyme was scored via molecular dynamics-based simulations, showing high correlation with in vitro EC50 data. The determination of the interaction spectra of the protein residues involved in inhibitor binding highlighted amino acids R295 and Y674 as the two fundamental H-bond donors, while two hydrophobic cavities HC1 (residues A221, I261, I287, and Y289) and HC2 (residues V216, Y303, V306, K307, P408, and A412) fulfill the third pharmacophoric requirement. Three RdRp (K263, R295 and Y674) residues critical for drug binding were selected and mutagenized, both in silico and in vitro, into alanine, and the affinity of a set of selected compounds towards the mutant RdRp isoforms was determined accordingly. The agreement between predicted and experimental data confirmed the proposed common molecular rationale shared by molecules characterized by different chemical scaffolds in binding to the BVDV RdRp, ultimately yielding compound 6b (EC50 = 0.3 μM; IC50 = 0.48 μM) as a new, potent inhibitor of this Pestivirus.
authors.affiliation: Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Muroni 23A, 07100 Sassari, SS, Italy. Electronic address: acarta@uniss.it.
authors.forename: A
authors.initials: A
authors.lastname: Carta
authors.affiliation: Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Muroni 23A, 07100 Sassari, SS, Italy.
authors.forename: I
authors.initials: I
authors.lastname: Briguglio
authors.affiliation: Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Muroni 23A, 07100 Sassari, SS, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Piras
authors.affiliation: Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Muroni 23A, 07100 Sassari, SS, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Corona
authors.affiliation: Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, via Muroni 23A, 07100 Sassari, SS, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Ibba
authors.affiliation: Molecular Simulations Engineering (MOSE) Laboratory, DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Piazzale Europa 1, 32127 Trieste, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Laurini
authors.affiliation: Molecular Simulations Engineering (MOSE) Laboratory, DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Piazzale Europa 1, 32127 Trieste, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Fermeglia
authors.affiliation: Molecular Simulations Engineering (MOSE) Laboratory, DEA, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy; National Interuniversity Consortium for Material Science and Technology (INSTM), Research Unit MOSE-DEA, University of Trieste, Piazzale Europa 1, 32127 Trieste, Italy. Electronic address: sabrina.pricl@di3.units.it.
authors.forename: S
authors.initials: S
authors.lastname: Pricl
authors.affiliation: Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P.le Aldo Moro, 5, 00185 Roma, Italy.
authors.forename: N
authors.initials: N
authors.lastname: Desideri
authors.affiliation: Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P.le Aldo Moro, 5, 00185 Roma, Italy.
authors.forename: E M
authors.initials: EM
authors.lastname: Atzori
authors.affiliation: Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
authors.forename: P
authors.initials: P
authors.lastname: La Colla
authors.affiliation: Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Collu
authors.affiliation: Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
authors.forename: I
authors.initials: I
authors.lastname: Delogu
authors.affiliation: Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Loddo
mesh_terms: D000818:Animals; D000998:Antiviral Agents / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites / Q000235:genetics; D001912:Bovine Virus Diarrhea-Mucosal Disease / Q000188:drug therapy / Q000517:prevention & control; D002417:Cattle; D001908:Diarrhea Viruses, Bovine Viral / Q000187:drug effects* / Q000201:enzymology; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism* / Q000494:pharmacology; D012324:RNA-Dependent RNA Polymerase / Q000187:drug effects / Q000378:metabolism*
chemical_list: D000998:Antiviral Agents; D011084:Polycyclic Aromatic Hydrocarbons; D012324:RNA-Dependent RNA Polymerase
keywords: Aromatic N-polycyclic systems; Bovine viral diarrhea virus (BVDV); Imidazo[4,5-g]quinoline; Pyrido[2,3-g]quinoxaline; RNA-dependent RNA polymerase (RdRp) inhibitors