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Fernandes PO, Dias ALT, Dos Santos Júnior VS, Sá Magalhães Serafim M, Sousa YV, Monteiro GC, Coutinho ID, Valli M, Verzola MMSA, Ottoni FM, Pádua RMD, Oda FB, Dos Santos AG, Andricopulo AD, da Silva Bolzani V, Mota BEF, Alves RJ, de Oliveira RB, Kronenberger T, Maltarollo VG. Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. J Chem Inf Model 2024; 64:1932-1944. [PMID: 38437501 DOI: 10.1021/acs.jcim.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The application of computer-aided drug discovery (CADD) approaches has enabled the discovery of new antimicrobial therapeutic agents in the past. The high prevalence of methicillin-resistantStaphylococcus aureus(MRSA) strains promoted this pathogen to a high-priority pathogen for drug development. In this sense, modern CADD techniques can be valuable tools for the search for new antimicrobial agents. We employed a combination of a series of machine learning (ML) techniques to select and evaluate potential compounds with antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA strains. In the present study, we describe the antibacterial activity of six compounds against MSSA and MRSA reference (American Type Culture Collection (ATCC)) strains as well as two clinical strains of MRSA. These compounds showed minimal inhibitory concentrations (MIC) in the range from 12.5 to 200 μM against the different bacterial strains evaluated. Our results constitute relevant proven ML-workflow models to distinctively screen for novel MRSA antibiotics.
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Affiliation(s)
- Philipe Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Anna Letícia Teotonio Dias
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Valtair Severino Dos Santos Júnior
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Yamara Viana Sousa
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Gustavo Claro Monteiro
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Isabel Duarte Coutinho
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Marilia Valli
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Marina Mol Sena Andrade Verzola
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Flaviano Melo Ottoni
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Rodrigo Maia de Pádua
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Fernando Bombarda Oda
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - André Gonzaga Dos Santos
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - Adriano Defini Andricopulo
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Vanderlan da Silva Bolzani
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Ricardo José Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
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Qin B, Chen Y, Yang K, Wang R, Yu L, Wang N, Liu S. An Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS) Method for Qualifying DAPB in Rat Plasma and Application to Pharmacokinetic Studies. Molecules 2024; 29:541. [PMID: 38276619 PMCID: PMC10818329 DOI: 10.3390/molecules29020541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
DAPB, a new molecule including danshensu, borneol, and a mother nucleus of ACEI (Angiotensin-converting enzyme inhibitors), is being developed as an antihypertensive candidate compound. A rapid, accurate, and sensitive ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was established and validated for the determination of DAPB in rat plasma. Chromatographic separation was performed on an Agilent SB-C18 column after protein precipitation by acetonitrile with a mobile phase consisting of acetonitrile and deionized water with 0.02% formic acid and 5 mM NH4F (v/v) at a flow rate of 0.2 mL/min. Quantification was performed using electrospray positive ionization mass spectrometry in the multiple reaction monitoring (MRM) mode. The method was linear over the range of 2-1000 ng/mL. The intra- and inter-day precision was within 12%, with accuracies less than 7%. Stability was within the acceptable limits under various storage and processing conditions. No apparent matrix effect was detected. The validated method was applied to the pre-clinical pharmacokinetic study of DAPB after oral administration of 30 mg/kg and intravenous administration of 6 mg/kg in rats.
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Affiliation(s)
- Bei Qin
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Yunmei Chen
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Kuan Yang
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Rong Wang
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Lili Yu
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Nana Wang
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Shaojing Liu
- Xi’an Key Laboratory for Research and Development of Innovative Multi-Target Antihypertensive Drugs, Xi’an Innovative Antihypertensive Drugs International Science and Technology Cooperation Base, Xi’an Medical University, Xi’an 710021, China; (Y.C.); (K.Y.); (R.W.); (L.Y.); (N.W.); (S.L.)
- Institute of Drug Research, Xi’an Medical University, Xi’an 710021, China
- College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
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