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Ruatta SM, Prada Gori DN, Fló Díaz M, Lorenzelli F, Perelmuter K, Alberca LN, Bellera CL, Medeiros A, López GV, Ingold M, Porcal W, Dibello E, Ihnatenko I, Kunick C, Incerti M, Luzardo M, Colobbio M, Ramos JC, Manta E, Minini L, Lavaggi ML, Hernández P, Šarlauskas J, Huerta García CS, Castillo R, Hernández-Campos A, Ribaudo G, Zagotto G, Carlucci R, Medrán NS, Labadie GR, Martinez-Amezaga M, Delpiccolo CML, Mata EG, Scarone L, Posada L, Serra G, Calogeropoulou T, Prousis K, Detsi A, Cabrera M, Alvarez G, Aicardo A, Araújo V, Chavarría C, Mašič LP, Gantner ME, Llanos MA, Rodríguez S, Gavernet L, Park S, Heo J, Lee H, Paul Park KH, Bollati-Fogolín M, Pritsch O, Shum D, Talevi A, Comini MA. Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro. Front Pharmacol 2023; 14:1193282. [PMID: 37426813 PMCID: PMC10323144 DOI: 10.3389/fphar.2023.1193282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence. Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy -performed in a large and diverse chemolibrary- complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening. Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12-20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7-45 μM). Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known "garbage in, garbage out" machine learning principle.
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Affiliation(s)
- Santiago M. Ruatta
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Denis N. Prada Gori
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Martín Fló Díaz
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Franca Lorenzelli
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Karen Perelmuter
- Cell Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucas N. Alberca
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carolina L. Bellera
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrea Medeiros
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gloria V. López
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Ingold
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Williams Porcal
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Vascular Biology and Drug Discovery Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Estefanía Dibello
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Irina Ihnatenko
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Conrad Kunick
- PVZ—Center of Pharmaceutical Engineering, Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marcelo Incerti
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Martín Luzardo
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Maximiliano Colobbio
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Juan Carlos Ramos
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Manta
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Química Fina, Facultad de Química, Instituto Polo Tecnológico de Pando, Universidad de la República, Montevideo, Uruguay
| | - Lucía Minini
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Laura Lavaggi
- Laboratorio de Química Biológica Ambiental, Sede Rivera, Centro Universitario Regional Noreste, Universidad de la República, Montevideo, Uruguay
| | - Paola Hernández
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jonas Šarlauskas
- Life Sciences Centre, Department of Xenobiotic Biochemistry, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | | | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Renzo Carlucci
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Noelia S. Medrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo R. Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maitena Martinez-Amezaga
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carina M. L. Delpiccolo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Ernesto G. Mata
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química Rosario (IQUIR) UNR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Laura Scarone
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Posada
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Gloria Serra
- Departamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | | | - Kyriakos Prousis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia Detsi
- Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Mauricio Cabrera
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Guzmán Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| | - Adrián Aicardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Nutrición Clínica, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Verena Araújo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
- Departamento de Alimentos, Escuela de Nutrición, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, Uruguay
| | | | - Melisa E. Gantner
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel A. Llanos
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Santiago Rodríguez
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
| | - Luciana Gavernet
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Soonju Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Jinyeong Heo
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Honggun Lee
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Kyu-Ho Paul Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | | | - Otto Pritsch
- Laboratory of Immunovirology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo A. Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
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Irabuena C, Scarone L, de Souza GE, Aguiar ACC, Mendes GR, Guido RVC, Serra G. Synthesis and antiplasmodial assessment of nitazoxanide and analogs as new antimalarial candidates. Med Chem Res 2022; 31:426-435. [PMID: 35106047 PMCID: PMC8794615 DOI: 10.1007/s00044-021-02843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 10/26/2022]
Abstract
During the last years, the progression to control malaria disease seems to be slowed and WHO (World Health Organization) reported a modeling analysis with the prediction of the increase in malaria morbidity and mortality in sub-Saharan Africa during the COVID-19 pandemic. A rapid way to the discovery of new drugs could be carried out by performing investigations to identify drugs based on repurposing of "old" drugs. The 5-nitrothiazole drug, Nitazoxanide was shown to be active against intestinal protozoa, human helminths, anaerobic bacteria, viruses, etc. In this work, Nitazoxanide and analogs were prepared using two methodologies and evaluated against P. falciparum 3D7. A bithiazole analog, showed attractive inhibitory activity with an EC50 value of 5.9 μM, low propensity to show toxic effect against HepG2 cells at 25 μM, and no cross-resistance with standard antimalarials.
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Affiliation(s)
- Camila Irabuena
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, General Flores 2124, CC1157 Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Laura Scarone
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, General Flores 2124, CC1157 Montevideo, Uruguay
| | - Guilherme Eduardo de Souza
- São Carlos Institute of Physics, University of Sao Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo 13563-120 Brazil
| | - Anna Caroline Campos Aguiar
- São Carlos Institute of Physics, University of Sao Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo 13563-120 Brazil
| | - Giovana Rossi Mendes
- São Carlos Institute of Physics, University of Sao Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo 13563-120 Brazil
| | - Rafael Victorio Carvalho Guido
- São Carlos Institute of Physics, University of Sao Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo 13563-120 Brazil
| | - Gloria Serra
- Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República, General Flores 2124, CC1157 Montevideo, Uruguay
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