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Cuccioloni M, Bonfili L, Cecarini V, Cocchioni F, Petrelli D, Crotti E, Zanchi R, Eleuteri AM, Angeletti M. Structure/activity virtual screening and in vitro testing of small molecule inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase from gut methanogenic bacteria. Sci Rep 2020; 10:13150. [PMID: 32753591 PMCID: PMC7588429 DOI: 10.1038/s41598-020-70042-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Virtual screening techniques and in vitro binding/inhibitory assays were used to search within a set of more than 8,000 naturally occurring small ligands for candidate inhibitors of 8-hydroxy-5-deazaflavin:NADPH oxidoreductase (FNO) from Methanobrevibacter smithii, the enzyme that catalyses the bidirectional electron transfer between NADP+ and F420H2 during the intestinal production of CH4 from CO2. In silico screening using molecular docking classified the ligand-enzyme complexes in the range between - 4.9 and - 10.5 kcal/mol. Molecular flexibility, the number of H-bond acceptors and donors, the extent of hydrophobic interactions, and the exposure to the solvent were the major discriminants in determining the affinity of the ligands for FNO. In vitro studies on a group of these ligands selected from the most populated/representative clusters provided quantitative kinetic, equilibrium, and structural information on ligands' behaviour, in optimal agreement with the predictive computational results.
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Affiliation(s)
- Massimiliano Cuccioloni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
| | - Laura Bonfili
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Valentina Cecarini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Filippo Cocchioni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Dezemona Petrelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133, Milan, Italy
| | - Raffaella Zanchi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, 20133, Milan, Italy
| | - Anna Maria Eleuteri
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Mauro Angeletti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
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Drenth J, Trajkovic M, Fraaije MW. Chemoenzymatic Synthesis of an Unnatural Deazaflavin Cofactor That Can Fuel F420-Dependent Enzymes. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01506] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
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