95508 20210902121733.0 doi 10.1371/journal.pcbi.1007898 sideral 119580 ART-2020-119580 eng Lans, Isaías In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target 2020 Access copy available to the general public Unrestricted New treatments for diseases caused by antimicrobial-resistant microorganisms can be developed by identifying unexplored therapeutic targets and by designing efficient drug screening protocols. In this study, we have screened a library of compounds to find ligands for the flavin-adenine dinucleotide synthase (FADS) -a potential target for drug design against tuberculosis and pneumonia- by implementing a new and efficient virtual screening protocol. The protocol has been developed for the in silico search of ligands of unexplored therapeutic targets, for which limited information about ligands or ligand-receptor structures is available. It implements an integrative funnel-like strategy with filtering layers that increase in computational accuracy. The protocol starts with a pharmacophore-based virtual screening strategy that uses ligand-free receptor conformations from molecular dynamics (MD) simulations. Then, it performs a molecular docking stage using several docking programs and an exponential consensus ranking strategy. The last filter, samples the conformations of compounds bound to the target using MD simulations. The MD conformations are scored using several traditional scoring functions in combination with a newly-proposed score that takes into account the fluctuations of the molecule with a Morse-based potential. The protocol was optimized and validated using a compound library with known ligands of the Corynebacterium ammoniagenes FADS. Then, it was used to find new FADS ligands from a compound library of 14, 000 molecules. A small set of 17 in silico filtered molecules were tested experimentally. We identified five inhibitors of the activity of the flavin adenylyl transferase module of the FADS, and some of them were able to inhibit growth of three bacterial species: C. ammoniagenes, Mycobacterium tuberculosis, and Streptococcus pneumoniae, where the last two are human pathogens. Overall, the results show that the integrative VS protocol is a cost-effective solution for the discovery of ligands of unexplored therapeutic targets. info:eu-repo/semantics/openAccess by http://creativecommons.org/licenses/by/3.0/es/ 4.475 2020 MATHEMATICAL & COMPUTATIONAL BIOLOGY 8 / 58 = 0.138 2020 Q1 T1 BIOCHEMICAL RESEARCH METHODS 16 / 77 = 0.208 2020 Q1 T1 2.628 2020 Cellular and Molecular Neuroscience 2020 Q1 Computational Theory and Mathematics 2020 Q1 Ecology 2020 Q1 Molecular Biology 2020 Q1 Genetics 2020 Q1 Modeling and Simulation 2020 Q1 Ecology, Evolution, Behavior and Systematics 2020 Q1 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Anoz-Carbonell, Ernesto Universidad de Zaragoza (orcid)0000-0002-6649-9153 Palacio-Rodríguez, Karen Aínsa, José Antonio Universidad de Zaragoza (orcid)0000-0003-2076-844X Medina, Milagros Universidad de Zaragoza (orcid)0000-0001-8743-0182 Cossio, Pilar 1011 630 Universidad de Zaragoza Dpto. Microb.Ped.Radio.Sal.Pú. Área Microbiología 1002 060 Universidad de Zaragoza Dpto. Bioq.Biolog.Mol. Celular Área Bioquímica y Biolog.Mole. 16, 8 (2020), e1007898 1-24 PLoS Comput. Biol. PLoS computational biology 1553-734X 2111964 http://zaguan.unizar.es/record/95508/files/texto_completo.pdf Versión publicada 515746 http://zaguan.unizar.es/record/95508/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:95508 articulos driver 2021-09-02-09:37:01 ARTICLE