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Prates JLB, Lopes JR, Chin CM, Ferreira EI, Dos Santos JL, Scarim CB. Discovery of Novel Inhibitors of Cruzain Cysteine Protease of Trypanosoma cruzi. Curr Med Chem 2024; 31:2285-2308. [PMID: 37888814 DOI: 10.2174/0109298673254864230921090519] [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: 04/06/2023] [Revised: 07/11/2023] [Accepted: 08/15/2023] [Indexed: 10/28/2023]
Abstract
Chagas disease (CD) is a parasitic disease endemic in several developing countries. According to the World Health Organization, approximately 6-8 million people worldwide are inflicted by CD. The scarcity of new drugs, mainly for the chronic phase, is the main reason for treatment limitation in CD. Therefore, there is an urgent need to discover new targets for which new therapeutical agents could be developed. Cruzain cysteine protease (CCP) is a promising alternative because this enzyme exhibits pleiotropic effects by acting as a virulence factor, modulating host immune cells, and interacting with host cells. This systematic review was conducted to discover new compounds that act as cruzain inhibitors, and their effects in vitro were studied through enzymatic assays and molecular docking. Additionally, the advances and perspectives of these inhibitors are discussed. These findings are expected to contribute to medicinal chemistry in view of the design of new, safe, and efficacious inhibitors against Trypanosoma cruzi CCP detected in the last decade (2013-2022) to provide scaffolds for further optimization, aiming toward the discovery of new drugs.
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Affiliation(s)
- João Lucas Bruno Prates
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Chemistry Institute Araraquara, São Paulo State University (UNESP), SP, Brazil
| | - Juliana Romano Lopes
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Chung Man Chin
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Union of the Colleges of the Great Lakes (UNILAGO), School of Medicine, Advanced Research Center in Medicine, São José do Rio Preto, SP, Brazil
| | - Elizabeth Igne Ferreira
- LAPEN-Laboratory of Design and Synthesis of Chemotherapeutic Agents Potentially Active on Neglected Diseases, Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Jean Leandro Dos Santos
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Chemistry Institute Araraquara, São Paulo State University (UNESP), SP, Brazil
| | - Cauê Benito Scarim
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
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2
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Maltarollo VG, da Silva EB, Kronenberger T, Sena Andrade MM, de Lima Marques GV, Cândido Oliveira NJ, Santos LH, Oliveira Rezende Júnior CD, Cassiano Martinho AC, Skinner D, Fajtová P, M Fernandes TH, Silveira Dos Santos ED, Rodrigues Gazolla PA, Martins de Souza AP, da Silva ML, Dos Santos FS, Lavorato SN, Oliveira Bretas AC, Carvalho DT, Franco LL, Luedtke S, Giardini MA, Poso A, Dias LC, Podust LM, Alves RJ, McKerrow J, Andrade SF, Teixeira RR, Siqueira-Neto JL, O'Donoghue A, de Oliveira RB, Ferreira RS. Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors. Future Med Chem 2023; 15:959-985. [PMID: 37435731 DOI: 10.4155/fmc-2023-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
Aim: Discovery of novel SARS-CoV-2 main protease (Mpro) inhibitors using a structure-based drug discovery strategy. Materials & methods: Virtual screening employing covalent and noncovalent docking was performed to discover Mpro inhibitors, which were subsequently evaluated in biochemical and cellular assays. Results: 91 virtual hits were selected for biochemical assays, and four were confirmed as reversible inhibitors of SARS CoV-2 Mpro with IC50 values of 0.4-3 μM. They were also shown to inhibit SARS-CoV-1 Mpro and human cathepsin L. Molecular dynamics simulations indicated the stability of the Mpro inhibitor complexes and the interaction of ligands at the subsites. Conclusion: This approach led to the discovery of novel thiosemicarbazones as potent SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Thales Kronenberger
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Marina Mol Sena Andrade
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Gabriel V de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Nereu J Cândido Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucianna H Santos
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Celso de Oliveira Rezende Júnior
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Ana C Cassiano Martinho
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Institute of Organic Chemistry & Biochemistry, Academy of Sciences of the Czech Republic, Prague, 16610, Czech Republic
| | - Thaís H M Fernandes
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Eduardo da Silveira Dos Santos
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Poliana A Rodrigues Gazolla
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana P Martins de Souza
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Milene Lopes da Silva
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Fabíola S Dos Santos
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Stefânia N Lavorato
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, 47810-047, Brazil
| | - Ana C Oliveira Bretas
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Diogo Teixeira Carvalho
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucas Lopardi Franco
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Stephanie Luedtke
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Miriam A Giardini
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Antti Poso
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Larissa M Podust
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - James McKerrow
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Saulo F Andrade
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Róbson R Teixeira
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Anthony O'Donoghue
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Rafaela S Ferreira
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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3
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Santos VC, Leite PG, Santos LH, Pascutti PG, Kolb P, Machado FS, Ferreira RS. Structure-based discovery of novel cruzain inhibitors with distinct trypanocidal activity profiles. Eur J Med Chem 2023; 257:115498. [PMID: 37290182 DOI: 10.1016/j.ejmech.2023.115498] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Over 110 years after the first formal description of Chagas disease, the trypanocidal drugs thus far available have limited efficacy and several side effects. This encourages the search for novel treatments that inhibit T. cruzi targets. One of the most studied anti-T. cruzi targets is the cysteine protease cruzain; it is associated with metacyclogenesis, replication, and invasion of the host cells. We used computational techniques to identify novel molecular scaffolds that act as cruzain inhibitors. First, with a docking-based virtual screening, we identified compound 8, a competitive cruzain inhibitor with a Ki of 4.6 μM. Then, aided by molecular dynamics simulations, cheminformatics, and docking, we identified the analog compound 22 with a Ki of 27 μM. Surprisingly, despite sharing the same isoquinoline scaffold, compound 8 presented higher trypanocidal activity against the epimastigote forms, while compound 22, against the trypomastigotes and amastigotes. Taken together, compounds 8 and 22 represent a promising scaffold for further development of trypanocidal compounds as drug candidates for treating Chagas disease.
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Affiliation(s)
- Viviane Corrêa Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Paulo Gaio Leite
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Lucianna Helene Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, CEP 21944-970, Brazil
| | - Peter Kolb
- Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Fabiana Simão Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafaela Salgado Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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4
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Martins LC, de Oliveira RB, Lameira J, Ferreira RS. Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism. J Chem Inf Model 2023; 63:1506-1520. [PMID: 36802548 DOI: 10.1021/acs.jcim.2c01566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Trypanosoma cruzi is a parasite that infects about 6-7 million people worldwide, mostly in Latin America, causing Chagas disease. Cruzain, the main cysteine protease of T. cruzi, is a validated target for developing drug candidates for Chagas disease. Thiosemicarbazones are one of the most relevant warheads used in covalent inhibitors targeting cruzain. Despite its relevance, the mechanism of inhibition of cruzain by thiosemicarbazones is unknown. Here, we combined experiments and simulations to unveil the covalent inhibition mechanism of cruzain by a thiosemicarbazone-based inhibitor (compound 1). Additionally, we studied a semicarbazone (compound 2), which is structurally similar to compound 1 but does not inhibit cruzain. Assays confirmed the reversibility of inhibition by compound 1 and suggested a two-step mechanism of inhibition. The Ki was estimated to be 36.3 μM and Ki* to be 11.5 μM, suggesting the pre-covalent complex to be relevant for inhibition. Molecular dynamics simulations of compounds 1 and 2 with cruzain were used to propose putative binding modes for the ligands. One-dimensional (1D) quantum mechanics/molecular mechanics (QM/MM) potential of mean force (PMF) and gas-phase energies showed that the attack of Cys25-S- on the C═S or C═O bond yields a more stable intermediate than the attack on the C═N bond of the thiosemicarbazone/semicarbazone. Two-dimensional (2D) QM/MM PMF revealed a putative reaction mechanism for compound 1, involving the proton transfer to the ligand, followed by the Cys25-S- attack at C═S. The ΔG and energy barrier were estimated to be -1.4 and 11.7 kcal/mol, respectively. Overall, our results shed light on the inhibition mechanism of cruzain by thiosemicarbazones.
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Affiliation(s)
- Luan Carvalho Martins
- Molecular Modeling and Drug Design Laboratory, Institute for Biological Sciences, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
| | - Renata Barbosa de Oliveira
- Pharmaceutical Products Department, Faculty of Pharmacy, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil
| | - Rafaela Salgado Ferreira
- Molecular Modeling and Drug Design Laboratory, Institute for Biological Sciences, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
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Caroli AP, Mansoldo FRP, Cardoso VS, Lage CLS, Carmo FL, Supuran CT, Beatriz Vermelho A. Are patents important indicators of innovation for Chagas disease treatment? Expert Opin Ther Pat 2023; 33:193-209. [PMID: 36786067 DOI: 10.1080/13543776.2023.2176219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
INTRODUCTION Chagas disease is a neglected, endemic disease in 21 countries, spreading to non-endemic countries too. Like other neglected diseases affecting primarily low- and middle-income countries, low investment and the absence of new chemical entities from the industry occurred. Increased knowledge about the parasite, drug targets, and vector control has been observed, but this was not translated into new drugs. The partnerships of pharmaceutical companies with academies and consolidated networks to increment the new drugs and treatment research in Chagas disease are shown. The current review analyzes in detail the patents dealing with compounds candidates for new drugs and treatment. The patent search was performed using Orbit Intelligence® software in the 2001-2021 period. AREAS COVERED The author focused specifically on patents for the treatment, the new candidates disclosed in the patents, and the barriers to innovation. EXPERT OPINION Patents in Chagas disease have been increasing in the last years, although they do not bring new compounds to an effective treatment.
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Affiliation(s)
- Andrea Pestana Caroli
- Federal University of Rio de Janeiro (UFRJ), Institute of Microbiology Paulo de Góes, BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Rio de Janeiro, Brazil
| | - Felipe R P Mansoldo
- Federal University of Rio de Janeiro (UFRJ), Institute of Microbiology Paulo de Góes, BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Rio de Janeiro, Brazil
| | - Veronica S Cardoso
- Federal University of Rio de Janeiro (UFRJ), Institute of Microbiology Paulo de Góes, BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Rio de Janeiro, Brazil
| | - Celso Luiz Salgueiro Lage
- National Institute of Intellectual Property (INPI), Graduate and Research Division, Rio de Janeiro-RJ, Brazil
| | - Flavia L Carmo
- Federal University of Rio de Janeiro (UFRJ), Institute of Microbiology Paulo de Góes, LEMM - Molecular Microbial Ecology Laboratory
| | - Claudiu T Supuran
- NEUROFARBA Department Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Alane Beatriz Vermelho
- Federal University of Rio de Janeiro (UFRJ), Institute of Microbiology Paulo de Góes, BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Rio de Janeiro, Brazil
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Screening the Pathogen Box to Discover and Characterize New Cruzain and TbrCatL Inhibitors. Pathogens 2023; 12:pathogens12020251. [PMID: 36839523 PMCID: PMC9967275 DOI: 10.3390/pathogens12020251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Chagas disease and Human African Trypanosomiasis, caused by Trypanosoma cruzi and T. brucei, respectively, pose relevant health challenges throughout the world, placing 65 to 70 million people at risk each. Given the limited efficacy and severe side effects associated with current chemotherapy, new drugs are urgently needed for both diseases. Here, we report the screening of the Pathogen Box collection against cruzain and TbrCatL, validated targets for Chagas disease and Human African Trypanosomiasis, respectively. Enzymatic assays were applied to screen 400 compounds, validate hits, determine IC50 values and, when possible, mechanisms of inhibition. In this case, 12 initial hits were obtained and ten were prioritized for follow-up. IC50 values were obtained for six of them (hit rate = 1.5%) and ranged from 0.46 ± 0.03 to 27 ± 3 µM. MMV687246 was found to be a mixed inhibitor of cruzain (Ki = 57 ± 6 µM) while MMV688179 was found to be a competitive inhibitor of cruzain with a nanomolar potency (Ki = 165 ± 63 nM). A putative binding mode for MMV688179 was obtained by docking. The six hits discovered against cruzain and TbrCatL are of great interest for further optimization by the medicinal chemistry community.
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From rational design to serendipity: Discovery of novel thiosemicarbazones as potent trypanocidal compounds. Eur J Med Chem 2022; 244:114876. [DOI: 10.1016/j.ejmech.2022.114876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/04/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022]
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8
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A decennary update on diverse heterocycles and their intermediates as privileged scaffolds for cathepsin B inhibition. Int J Biol Macromol 2022; 222:2270-2308. [DOI: 10.1016/j.ijbiomac.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/17/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
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9
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Abdelgawad MA, Bukhari SNA, Musa A, Elmowafy M, Elkomy MH, Nayl AA, El-Ghorab AH, Alsohaimi IH, Abdel-Bakky MS, Althobaiti IO, Altaleb HA, Omar HA, Abdelazeem AH, Zaki MA, Shaker ME, Elshemy HAH. New Sulfamethoxazole Derivatives as Selective Carbonic Anhydrase IX and XII Inhibitors: Design, Synthesis, Cytotoxic Activity and Molecular Modeling. Pharmaceuticals (Basel) 2022; 15:ph15091134. [PMID: 36145355 PMCID: PMC9501356 DOI: 10.3390/ph15091134] [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: 07/28/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
In this study new sulphamethoxazole derivatives (S1-S4, S6-S12, and S14-S22) were designed and synthesized and their structures were fully characterized and validated using NMR, mass, and IR spectroscopy, as well as elemental analyses. All new derivatives (S1-S22) were assayed against human carbonic anhydrase (hCAs IX and XII) for their inhibitory activities. hCAs IX and XII were chosen due to the fact that CAIX expression is recognized as a hypoxia marker with a poor prognosis in breast cancer. When compared to Dorzolamide HCl as a standard reference, derivatives S2, S3, S8, S9, and S15 had the most effective inhibition with low IC50 values. The active compounds were further evaluated against hCAs I and II inhibitory activity and compounds S8, S9 and S15 showed the least inhibitory effect compared to the reference standard, acetazolamide, indicating that their effect in normal cells is the lowest. Cell viability tests for the selected compounds were carried out on MCF7 (normoxia and hypoxia) and on the normal breast cell line (MCF10a) with Staurosporine as a standard. The results showed that compound S15 had a highly potent cytotoxic effect. Furthermore, cell cycle analysis results showed that compound S15 triggered cell cycle arrest and apoptosis in G1/S of MCF7 cancer cells. Finally, molecular docking was performed to point out the possible explanation for the vital structural features and key-interactions exerted by our ligands with hCAs IX and XII that might share additional designs and highlight possible leads for a hopeful anticancer agent. Consequently, sulphamethoxazole Derivative S15 could be the potential lead for emerging selective cytotoxic compounds directing h CAs IX and XII.
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Affiliation(s)
- Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72431, Saudi Arabia
- Correspondence: ; Tel.: +96-65-9543-5214
| | - Syed N. A. Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72431, Saudi Arabia
| | - Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Mohammed Elmowafy
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Mohammed H. Elkomy
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - AbdElAziz. A. Nayl
- Department of Chemistry, College of Science, Jouf University, Sakaka 72341, Saudi Arabia
| | - Ahmed H. El-Ghorab
- Department of Chemistry, College of Science, Jouf University, Sakaka 72341, Saudi Arabia
| | | | - Mohamed Sadek Abdel-Bakky
- Department of Pharmacology and Toxicology, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ibrahim O. Althobaiti
- Department of Chemistry, College of Science and Arts, Jouf University, Sakaka 72341, Saudi Arabia
| | - Hamud A. Altaleb
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 41477, Saudi Arabia
| | - Hany A. Omar
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Ahmed H. Abdelazeem
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
- Pharmacy Department, College of Pharmacy, Riyadh Elm University, Riyadh 11681, Saudi Arabia
| | - Mohamed A. Zaki
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Mohamed E. Shaker
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Heba A. H. Elshemy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
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10
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Martinho ACC, Resende DDM, Landin ES, Dit Lapierre TJWJ, Bernardes TCD, Martins LC, Ferreira RS, Murta SMF, de Oliveira Rezende Júnior C. Synthesis, Design, and Structure-Activity Relationship of a Benzenesulfonylpiperazine Series Against Trypanosoma Cruzi. ChemMedChem 2022; 17:e202200211. [PMID: 35993440 DOI: 10.1002/cmdc.202200211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/19/2022] [Indexed: 11/09/2022]
Abstract
Chagas disease is a neglected tropical disease, endemic in Latin America and caused by the protozoan parasite Trypanosoma cruzi . Available treatments show low cure efficacy during the chronic phase of the disease and cause a series of side effects, reinforcing the need to develop new drugs against Chagas disease. In this work, we describe the optimization of a trypanocidal hit compound recently reported in phenotypic HTS studies against Trypanosoma cruzi . A hit-to-lead process was initiated and a structure-activity relationship against Trypanosoma cruzi was obtained after the synthesis and biological evaluation of 22 new benzenesulfonylpiperazine derivatives. From this SAR study, we identified three compounds with a promising predicted ADMET profile and potency comparable to the reference drug benznidazole, which are candidates for further development towards therapies for Chagas disease.
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Affiliation(s)
| | - Daniela de Melo Resende
- Fundação Oswaldo Cruz Instituto René Rachou: Fundacao Oswaldo Cruz Instituto Rene Rachou, René Rachou Institute, BRAZIL
| | - Emanuelly Silva Landin
- Federal University of Uberlandia: Universidade Federal de Uberlandia, Chemistry Institute, BRAZIL
| | | | | | - Luan Carvalho Martins
- Federal University of Minas Gerais: Universidade Federal de Minas Gerais, Biochemistry and immunology, BRAZIL
| | - Rafaela Salgado Ferreira
- Federal University of Minas Gerais: Universidade Federal de Minas Gerais, Biochemistry and immunology, BRAZIL
| | - Silvane Maria Fonseca Murta
- Oswaldo Cruz Foundation Rene Rachou Institute: Fundacao Oswaldo Cruz Instituto Rene Rachou, René Rachou Institute, BRAZIL
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11
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Espinosa-Bustos C, Ortiz Pérez M, Gonzalez-Gonzalez A, Zarate AM, Rivera G, Belmont-Díaz JA, Saavedra E, Cuellar MA, Vázquez K, Salas CO. New Amino Naphthoquinone Derivatives as Anti-Trypanosoma cruzi Agents Targeting Trypanothione Reductase. Pharmaceutics 2022; 14:pharmaceutics14061121. [PMID: 35745694 PMCID: PMC9228152 DOI: 10.3390/pharmaceutics14061121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 12/25/2022] Open
Abstract
To develop novel chemotherapeutic alternatives for the treatment of Chagas disease, in this study, a set of new amino naphthoquinone derivatives were synthesised and evaluated in vitro on the epimastigote and trypomastigote forms of Trypanosoma cruzi strains (NINOA and INC-5) and on J774 murine macrophages. The design of the new naphthoquinone derivatives considered the incorporation of nitrogenous fragments with different substitution patterns present in compounds with activity on T. cruzi, and, thus, 19 compounds were synthesised in a simple manner. Compounds 2e and 7j showed the lowest IC50 values (0.43 µM against both strains for 2e and 0.19 µM and 0.92 µM for 7j). Likewise, 7j was more potent than the reference drug, benznidazole, and was more selective on epimastigotes. To postulate a possible mechanism of action, molecular docking studies were performed on T. cruzi trypanothione reductase (TcTR), specifically at a site in the dimer interface, which is a binding site for this type of naphthoquinone. Interestingly, 7j was one of the compounds that showed the best interaction profile on the enzyme; therefore, 7j was evaluated on TR, which behaved as a non-competitive inhibitor. Finally, 7j was predicted to have a good pharmacokinetic profile for oral administration. Thus, the naphthoquinone nucleus should be considered in the search for new trypanocidal agents based on our hit 7j.
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Affiliation(s)
- Christian Espinosa-Bustos
- Departamento de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7820436, Chile;
| | - Mariana Ortiz Pérez
- Departamento de Parasitología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Nuevo León, Francisco Villa 20, General Escobedo 66054, Mexico;
| | - Alonzo Gonzalez-Gonzalez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro s/n, Reynosa 88710, Mexico; (A.G.-G.); (G.R.)
| | - Ana María Zarate
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile;
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro s/n, Reynosa 88710, Mexico; (A.G.-G.); (G.R.)
| | - Javier A. Belmont-Díaz
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, México City 14080, Mexico; (J.A.B.-D.); (E.S.)
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, México City 14080, Mexico; (J.A.B.-D.); (E.S.)
| | - Mauricio A. Cuellar
- Centro de Investigación Farmacopea Chilena, Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2340000, Chile;
| | - Karina Vázquez
- Departamento de Parasitología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Nuevo León, Francisco Villa 20, General Escobedo 66054, Mexico;
- Correspondence: (K.V.); (C.O.S.)
| | - Cristian O. Salas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago 7820436, Chile;
- Correspondence: (K.V.); (C.O.S.)
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12
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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13
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Santos VC, Campos ACB, Waldner BJ, Liedl KR, Ferreira RS. Impact of different protonation states on virtual screening performance against cruzain. Chem Biol Drug Des 2021; 99:703-716. [PMID: 34923756 DOI: 10.1111/cbdd.14008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/12/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022]
Abstract
The cysteine protease cruzain is a Chagas disease target, exploited in computational studies. However, there is no consensus on the protonation states of the active site residues Cys25, His162, and Glu208 at the enzyme's active pH range. We evaluated the impact of different protonation states of these residues on docking calculations. Through a retrospective study with cruzain inhibitors and decoys, we compared the performance of virtual screening using four grids, varying protonation states of Cys25, His162, and Glu208. Based on enrichment factors and ROC plots, docking with the four grids affected compound ranking and the overall charge of top-ranking compounds. Different grids can be complementary and synergistic, increasing the odds of finding different ligands with diverse chemical properties.
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Affiliation(s)
- Viviane Corrêa Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Augusto César Broilo Campos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, and Centre for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 82, Innsbruck, Tyrol, 6020, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Centre for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 82, Innsbruck, Tyrol, 6020, Austria
| | - Rafaela Salgado Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
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14
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Barbosa da Silva E, Rocha DA, Fortes IS, Yang W, Monti L, Siqueira-Neto JL, Caffrey CR, McKerrow J, Andrade SF, Ferreira RS. Structure-Based Optimization of Quinazolines as Cruzain and TbrCATL Inhibitors. J Med Chem 2021; 64:13054-13071. [PMID: 34461718 DOI: 10.1021/acs.jmedchem.1c01151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cysteine proteases, cruzain and TbrCATL (rhodesain), are therapeutic targets for Chagas disease and Human African Trypanosomiasis, respectively. Among the known inhibitors for these proteases, we have described N4-benzyl-N2-phenylquinazoline-2,4-diamine (compound 7 in the original publication, 1a in this study), as a competitive cruzain inhibitor (Ki = 1.4 μM). Here, we describe the synthesis and biological evaluation of 22 analogs of 1a, containing modifications in the quinazoline core, and in the substituents in positions 2 and 4 of this ring. The analogs demonstrate low micromolar inhibition of the target proteases and cidal activity against Trypanosoma cruzi with up to two log selectivity indices in counterscreens with myoblasts. Fourteen compounds were active against Trypanosoma brucei at low to mid micromolar concentrations. During the optimization of 1a, structure-based design and prediction of physicochemical properties were employed to maintain potency against the enzymes while removing colloidal aggregator characteristics observed for some molecules in this series.
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Affiliation(s)
- Elany Barbosa da Silva
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil.,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Débora A Rocha
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Isadora S Fortes
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Wenqian Yang
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Ludovica Monti
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Jair L Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - James McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Saulo F Andrade
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Graduate Program in Agricultural and Environmental Microbiology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Rafaela S Ferreira
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
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15
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Arafet K, González FV, Moliner V. Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases. Chemistry 2021; 27:10142-10150. [PMID: 33852187 DOI: 10.1002/chem.202100892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/06/2023]
Abstract
A computational study of the two possible inhibition mechanisms of rhodesain cysteine protease by the dipeptidyl enoate Cbz-Phe-Leu-CH=CH-CO2 C2 H5 has been carried out by means of molecular dynamics simulations with hybrid QM/MM potentials. The low free energy barriers confirm that the Cys25 residue can attack both Cβ and C1 atoms of the inhibitor, confirming a dual mode of action in the inhibition of the rhodesain by enoates. According to the results, the inhibition process through the Cys25 attack on the Cβ atom of the inhibitor is an exergonic and irreversible process, while the inhibition process when Cys25 attacks on the C1 atom of the inhibitor is and exergonic but reversible process. The interactions between the inhibitor and rhodesain suggest that P2 is the most important fragment to consider in the design of new efficient inhibitors of rhodesain. These results may be useful for the design of new inhibitors of rhodesain and other related cysteine proteases based on dipeptidyl enoates scaffolds.
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Affiliation(s)
- Kemel Arafet
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
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16
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Anju A, Chaturvedi S, Chaudhary V, Pant P, Hussain F, Mishra AK. Virtual screening of quinoline derived library for SARS-COV-2 targeting viral entry and replication. J Biomol Struct Dyn 2021; 40:8464-8493. [PMID: 34032180 PMCID: PMC8171009 DOI: 10.1080/07391102.2021.1913228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic infection has claimed many lives and added to the social, economic, and psychological distress. The contagious disease has quickly spread to almost 218 countries and territories following the regional outbreak in China. As the number of infected populations increases exponentially, there is a pressing demand for anti-COVID drugs and vaccines. Virtual screening provides possible leads while extensively cutting down the time and resources required for ab-initio drug design. We report structure-based virtual screening of a hundred plus library of quinoline drugs with established antiviral, antimalarial, antibiotic or kinase inhibitor activity. In this study, targets having a role in viral entry, viral assembly, and viral replication have been selected. The targets include: 1) RBD of receptor-binding domain spike protein S 2) Mpro Chymotrypsin main protease 3) Ppro Papain protease 4) RNA binding domain of Nucleocapsid Protein, and 5) RNA Dependent RNA polymerase from SARS-COV-2. An in-depth analysis of the interactions and G-score compared to the controls like hydroxyquinoline and remdesivir has been presented. The salient results are (1) higher scoring of antivirals as potential drugs (2) potential of afatinib by scoring as better inhibitor, and (3) biological explanation of the potency of afatinib. Further MD simulations and MM-PBSA calculations showed that afatinib works best to interfere with the the activity of RNA dependent RNA polymerase of SARS-COV-2, thereby inhibiting replication process of single stranded RNA virus. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Anju Anju
- Department of Chemistry, University of Delhi, Delhi, India.,Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Shubhra Chaturvedi
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Vishakha Chaudhary
- Department of Chemistry, University of Delhi, Delhi, India.,Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
| | - Pradeep Pant
- Department of Chemistry, Indian Institute of Technology, New Delhi, India
| | | | - Anil Kumar Mishra
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization Brig, Delhi, India
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17
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Nunes PSG, da Silva G, Nascimento S, Mantoani SP, de Andrade P, Bernardes ES, Kawano DF, Leopoldino AM, Carvalho I. Synthesis, biological evaluation and molecular docking studies of novel 1,2,3-triazole-quinazolines as antiproliferative agents displaying ERK inhibitory activity. Bioorg Chem 2021; 113:104982. [PMID: 34020277 DOI: 10.1016/j.bioorg.2021.104982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022]
Abstract
ERK1/2 inhibitors have attracted special attention concerning the ability of circumventing cases of innate or log-term acquired resistance to RAF and MEK kinase inhibitors. Based on the 4-aminoquinazoline pharmacophore of kinases, herein we describe the synthesis of 4-aminoquinazoline derivatives bearing a 1,2,3-triazole stable core to bridge different aromatic and heterocyclic rings using copper-catalysed azide-alkyne cycloaddition reaction (CuAAC) as a Click Chemistry strategy. The initial screening of twelve derivatives in tumoral cells (CAL-27, HN13, HGC-27, and BT-20) revealed that the most active in BT-20 cells (25a, IC50 24.6 μM and a SI of 3.25) contains a more polar side chain (sulfone). Furthermore, compound 25a promoted a significant release of lactate dehydrogenase (LDH), suggesting the induction of cell death by necrosis. In addition, this compound induced G0/G1 stalling in BT-20 cells, which was accompanied by a decrease in the S phase. Western blot analysis of the levels of p-STAT3, p-ERK, PARP, p53 and cleaved caspase-3 revealed p-ERK1/2 and p-STA3 were drastically decreased in BT-20 cells under 25a incubation, suggesting the involvement of these two kinases in the mechanisms underlying 25a-induced cell cycle arrest, besides loss of proliferation and viability of the breast cancer cell. Molecular docking simulations using the ERK-ulixertinib crystallographic complex showed compound 25a could potentially compete with ATP for binding to ERK in a slightly higher affinity than the reference ERK1/2 inhibitor. Further in silico analyses showed comparable toxicity and pharmacokinetic profiles for compound 25a in relation to ulixertinib.
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Affiliation(s)
| | - Gabriel da Silva
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sofia Nascimento
- Radiopharmacy Center, Nuclear and Energy Research Institute (IPEN/CNEN-SP), São Paulo, São Paulo, Brazil
| | | | - Peterson de Andrade
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson Soares Bernardes
- Radiopharmacy Center, Nuclear and Energy Research Institute (IPEN/CNEN-SP), São Paulo, São Paulo, Brazil
| | - Daniel Fábio Kawano
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Andreia Machado Leopoldino
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ivone Carvalho
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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18
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Silva LR, Guimarães AS, do Nascimento J, do Santos Nascimento IJ, da Silva EB, McKerrow JH, Cardoso SH, da Silva-Júnior EF. Computer-aided design of 1,4-naphthoquinone-based inhibitors targeting cruzain and rhodesain cysteine proteases. Bioorg Med Chem 2021; 41:116213. [PMID: 33992862 DOI: 10.1016/j.bmc.2021.116213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 12/26/2022]
Abstract
Chagas disease and Human African Trypanosomiasis (HAT) are caused by Trypanosoma cruzi and T. brucei parasites, respectively. Cruzain (CRZ) and Rhodesain (RhD) are cysteine proteases that share 70% of identity and play vital functions in these parasites. These macromolecules represent promising targets for designing new inhibitors. In this context, 26 CRZ and 5 RhD 3D-structures were evaluated by molecular redocking to identify the most accurate one to be utilized as a target. Posteriorly, a virtual screening of a library containing 120 small natural and nature-based compounds was performed on both of them. In total, 14 naphthoquinone-based analogs were identified, synthesized, and biologically evaluated. In total, five compounds were active against RhD, being three of them also active on CRZ. A derivative of 1,4-naphthoquinonepyridin-2-ylsulfonamide was found to be the most active molecule, exhibiting IC50 values of 6.3 and 1.8 µM for CRZ and RhD, respectively. Dynamic simulations at 100 ns demonstrated good stability and do not alter the targets' structures. MM-PBSA calculations revealed that it presents a higher affinity for RhD (-25.3 Kcal mol-1) than CRZ, in which van der Waals interactions were more relevant. A mechanistic hypothesis (via C3-Michael-addition reaction) involving a covalent mode of inhibition for this compound towards RhD was investigated by covalent molecular docking and DFT B3LYP/6-31 + G* calculations, exhibiting a low activation energy (ΔG‡) and providing a stable product (ΔG), with values of 7.78 and - 39.72 Kcal mol-1, respectively; similar to data found in the literature. Nevertheless, a reversibility assay by dilution revealed that JN-11 is a time-dependent and reversible inhibitor. Finally, this study applies modern computer-aided techniques to identify promising inhibitors from a well-known chemical class of natural products. Then, this work could inspire other future studies in the field, being useful for designing potent naphthoquinones as RhD inhibitors.
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Affiliation(s)
- Leandro Rocha Silva
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Ari Souza Guimarães
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Jadiely do Nascimento
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Igor José do Santos Nascimento
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil
| | - Elany Barbosa da Silva
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - James H McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sílvia Helena Cardoso
- Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil.
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19
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Yepes AF, Quintero‐Saumeth J, Cardona‐Galeano W. Biologically Active Quinoline‐Hydrazone Conjugates as Potential
Trypanosoma cruzi
DHFR‐TS Inhibitors: Docking, Molecular Dynamics, MM/PBSA and Drug‐Likeness Studies. ChemistrySelect 2021. [DOI: 10.1002/slct.202100238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrés F. Yepes
- Chemistry of Colombian Plants, Institute of Chemistry, Faculty of Exact and Natural Sciences University of Antioquia-UdeA, Calle 70 No. 52-21, A.A 1226 Medellín Colombia
| | - Jorge Quintero‐Saumeth
- University of Pamplona Faculty of Basic Sciences, Pamplona, Colombia, Km 1 Vía Bucaramanga Ciudad Universitaria Pamplona Colombia
| | - Wilson Cardona‐Galeano
- Chemistry of Colombian Plants, Institute of Chemistry, Faculty of Exact and Natural Sciences University of Antioquia-UdeA, Calle 70 No. 52-21, A.A 1226 Medellín Colombia
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20
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Rosas-Jimenez JG, Garcia-Revilla MA, Madariaga-Mazon A, Martinez-Mayorga K. Predictive Global Models of Cruzain Inhibitors with Large Chemical Coverage. ACS OMEGA 2021; 6:6722-6735. [PMID: 33748586 PMCID: PMC7970485 DOI: 10.1021/acsomega.0c05645] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Chagas disease affects 8-11 million people worldwide, most of them living in Latin America. Moreover, migratory phenomena have spread the infection beyond endemic areas. Efforts for the development of new pharmacological therapies are paramount as the pharmacological profile of the two marketed drugs currently available, nifurtimox and benznidazole, needs to be improved. Cruzain, a parasitic cysteine protease, is one of the most attractive biological targets due to its roles in parasite survival and immune evasion. In this work, we compiled and curated a database of diverse cruzain inhibitors previously reported in the literature. From this data set, quantitative structure-activity relationship (QSAR) models for the prediction of their pIC50 values were generated using k-nearest neighbors and random forest algorithms. Local and global models were calculated and compared. The statistical parameters for internal and external validation indicate a significant predictability, with q loo 2 values around 0.66 and 0.61 and external R 2 coefficients of 0.725 and 0.766. The applicability domain is quantitatively defined, according to QSAR good practices, using the leverage and similarity methods. The models described in this work are readily available in a Python script for the discovery of novel cruzain inhibitors.
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Affiliation(s)
- Jose Guadalupe Rosas-Jimenez
- Division
de Ciencias Naturales y Exactas, Universidad
de Guanajuato, Guanajuato 36050, Mexico
- Instituto
de Quimica, Universidad Nacional Autonoma
de Mexico, Mexico
City 04510, Mexico
| | - Marco A. Garcia-Revilla
- Division
de Ciencias Naturales y Exactas, Universidad
de Guanajuato, Guanajuato 36050, Mexico
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21
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Zuma AA, de Souza W. Chagas Disease Chemotherapy: What Do We Know So Far? Curr Pharm Des 2021; 27:3963-3995. [PMID: 33593251 DOI: 10.2174/1381612827666210216152654] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/13/2021] [Indexed: 11/22/2022]
Abstract
Chagas disease is a Neglected Tropical Disease (NTD), and although endemic in Latin America, affects around 6-7 million people infected worldwide. The treatment of Chagas disease is based on benznidazole and nifurtimox, which are the only available drugs. However, they are not effective during the chronic phase and cause several side effects. Furthermore, BZ promotes cure in 80% of the patients in the acute phase, but the cure rate drops to 20% in adults in the chronic phase of the disease. In this review, we present several studies published in the last six years, which describes the antiparasitic potential of distinct drugs, from the synthesis of new compounds aiming to target the parasite, as well as the repositioning and the combination of drugs. We highlight several compounds for having shown results that are equivalent or superior to BZ, which means that they should be further studied, either in vitro or in vivo. Furthermore, we stand out the differences in the effects of BZ on the same strain of T. cruzi, which might be related to methodological differences such as parasite and cell ratios, host cell type and the time of adding the drug. In addition, we discuss the wide variety of strains and also the cell types used as a host cell, which makes it difficult to compare the trypanocidal effect of the compounds.
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Affiliation(s)
- Aline Araujo Zuma
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho, 373, Centro de Ciências da Saúde, Cidade Universitária, Ilha do Fundão, 21491-590, Rio de Janeiro, RJ. Brazil
| | - Wanderley de Souza
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro. Av. Carlos Chagas Filho, 373, Centro de Ciências da Saúde, Cidade Universitária, Ilha do Fundão, 21491-590, Rio de Janeiro, RJ. Brazil
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22
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Albino SL, da Silva JM, de C Nobre MS, de M E Silva YMS, Santos MB, de Araújo RSA, do C A de Lima M, Schmitt M, de Moura RO. Bioprospecting of Nitrogenous Heterocyclic Scaffolds with Potential Action for Neglected Parasitosis: A Review. Curr Pharm Des 2020; 26:4112-4150. [PMID: 32611290 DOI: 10.2174/1381612826666200701160904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/24/2020] [Indexed: 11/22/2022]
Abstract
Neglected parasitic diseases are a group of infections currently considered as a worldwide concern. This fact can be attributed to the migration of these diseases to developed and developing countries, associated with therapeutic insufficiency resulted from the low investment in the research and development of new drugs. In order to overcome this situation, bioprospecting supports medicinal chemistry in the identification of new scaffolds with therapeutically appropriate physicochemical and pharmacokinetic properties. Among them, we highlight the nitrogenous heterocyclic compounds, as they are secondary metabolites of many natural products with potential biological activity. The objective of this work was to review studies within a 10-year timeframe (2009- 2019), focusing on the pharmacological application of nitrogen bioprospectives (pyrrole, pyridine, indole, quinoline, acridine, and their respective derivatives) against neglected parasitic infections (malaria, leishmania, trypanosomiases, and schistosomiasis), and their application as a template for semi-synthesis or total synthesis of potential antiparasitic agents. In our studies, it was observed that among the selected articles, there was a higher focus on the attempt to identify and obtain novel antimalarial compounds, in a way that an extensive amount of studies involving all heterocyclic nitrogen nuclei were found. On the other hand, the parasites with the lowest number of publications up until the present date have been trypanosomiasis, especially those caused by Trypanosoma cruzi, and schistosomiasis, where some heterocyclics have not even been cited in recent years. Thus, we conclude that despite the great biodiversity on the planet, little attention has been given to certain neglected tropical diseases, especially those that reach countries with a high poverty rate.
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Affiliation(s)
- Sonaly L Albino
- Universidade Estadual da Paraiba, R. Baraunas, 351, Cidade Universitaria, Campina Grande, Paraiba, 58429-500, Brazil
| | - Jamire M da Silva
- Universidade Federal de Pernambuco, Av. Prof. Moraes Rego 1235, Cidade Universitaria, Recife, Pernambuco, 50670-901, Brazil
| | - Michelangela S de C Nobre
- Universidade Federal de Pernambuco, Av. Prof. Moraes Rego 1235, Cidade Universitaria, Recife, Pernambuco, 50670-901, Brazil
| | - Yvnni M S de M E Silva
- Universidade Estadual da Paraiba, R. Baraunas, 351, Cidade Universitaria, Campina Grande, Paraiba, 58429-500, Brazil
| | - Mirelly B Santos
- Universidade Estadual da Paraiba, R. Baraunas, 351, Cidade Universitaria, Campina Grande, Paraiba, 58429-500, Brazil
| | - Rodrigo S A de Araújo
- Universidade Estadual da Paraiba, R. Baraunas, 351, Cidade Universitaria, Campina Grande, Paraiba, 58429-500, Brazil
| | - Maria do C A de Lima
- Universidade Federal de Pernambuco, Av. Prof. Moraes Rego 1235, Cidade Universitaria, Recife, Pernambuco, 50670-901, Brazil
| | - Martine Schmitt
- Universite de Strasbourg, CNRS, LIT UMR 7200, Laboratoire d'innovation therapeutique, Illkirch, France
| | - Ricardo O de Moura
- Universidade Federal de Pernambuco, Av. Prof. Moraes Rego 1235, Cidade Universitaria, Recife, Pernambuco, 50670-901, Brazil
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Yepes AF, Quintero‐Saumeth J, Cardona‐G W. Chalcone‐Quinoline Conjugates as Potential
T. cruzi
Cruzipain Inhibitors: Docking Studies, Molecular Dynamics and Evaluation of Drug‐Likeness. ChemistrySelect 2020. [DOI: 10.1002/slct.202000777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andrés F. Yepes
- Chemistry of Colombian Plants, Institute of ChemistryFaculty of Exact and Natural Sciences University of Antioquia-UdeA Calle 70 No. 52–21, A.A 1226 Medellín Colombia
| | - Jorge Quintero‐Saumeth
- University of PamplonaFaculty of Basic Sciences Km 1 Vía Bucaramanga Ciudad Universitaria Pamplona Colombia
| | - Wilson Cardona‐G
- Chemistry of Colombian Plants, Institute of ChemistryFaculty of Exact and Natural Sciences University of Antioquia-UdeA Calle 70 No. 52–21, A.A 1226 Medellín Colombia
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24
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Benzimidazole inhibitors of the major cysteine protease of Trypanosoma brucei. Future Med Chem 2020; 11:1537-1551. [PMID: 31469332 DOI: 10.4155/fmc-2018-0523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: Limitations in available therapies for trypanosomiases indicate the need for improved medicines. Cysteine proteases cruzain and rhodesain are validated targets for treatment of Chagas disease and human African trypanosomiasis. Previous studies reported a benzimidazole series as potent cruzain inhibitors. Results & methodology: Considering the high similarity between these proteases, we evaluated 40 benzimidazoles against rhodesain. We describe their structure-activity relationships (SAR), revealing trends similar to those observed for cruzain and features that lead to enzyme selectivity. This series comprises noncovalent competitive inhibitors (best Ki = 0.21 μM against rhodesain) and micromolar activity against Trypanosoma brucei brucei. A cheminformatics analysis confirms scaffold novelty, and the inhibitors described have favorable predicted physicochemical properties. Conclusion: Our results support this series as a starting point for new human African trypanosomiasis medicines.
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Abstract
Aim: Cysteine proteases are important molecular targets involved in the replication, virulence and survival of parasitic organisms, including Trypanosoma and Leishmania species. Methodology & results: Analogs of the 7-chloro-N-[3-(morpholin-4-yl)propyl]quinolin-4-amine were synthesized and their inhibitory activity against the enzymes cruzain and rhodesain as well as against promastigotes forms of Leishmania species and epimastigotes forms of Trypanosoma cruzi were evaluated. Five compounds showed activity against both enzymes with half maximal inhibitory concentration (IC50) values ranging from 23 to 123 μM. Among these, compounds 3 and 4 displayed leishmanicidal activity; compound 4 was the most promising with IC50 values <10 μM and no cytotoxicity for uninfected cells. Conclusion: The results obtained indicate that cysteine proteases are likely to be the molecular target of compounds 3 and 4.
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26
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Santos SS, de Araújo RV, Giarolla J, Seoud OE, Ferreira EI. Searching for drugs for Chagas disease, leishmaniasis and schistosomiasis: a review. Int J Antimicrob Agents 2020; 55:105906. [PMID: 31987883 DOI: 10.1016/j.ijantimicag.2020.105906] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/16/2022]
Abstract
Chagas disease, leishmaniasis and schistosomiasis are neglected diseases (NDs) and are a considerable global challenge. Despite the huge number of people infected, NDs do not create interest from pharmaceutical companies because the associated revenue is generally low. Most of the research on these diseases has been conducted in academic institutions. The chemotherapeutic armamentarium for NDs is scarce and inefficient and better drugs are needed. Researchers have found some promising potential drug candidates using medicinal chemistry and computational approaches. Most of these compounds are synthetic but some are from natural sources or are semi-synthetic. Drug repurposing or repositioning has also been greatly stimulated for NDs. This review considers some potential drug candidates and provides details of their design, discovery and activity.
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Affiliation(s)
- Soraya Silva Santos
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil
| | - Renan Vinicius de Araújo
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil
| | - Jeanine Giarolla
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil
| | - Omar El Seoud
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil
| | - Elizabeth Igne Ferreira
- Laboratory of Design and Synthesis of Chemotherapeutics Potentially Active in Neglected Diseases (LAPEN), Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo-USP, Avenue Professor Lineu Prestes, 580-Building 13, São Paulo SP, 05508-900, Brazil.
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27
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Conceição RA, Ascari LM, Ferreira NC, Goes CF, Matos CO, Pinheiro AS, Alves MA, Souza AMT, Maia RC, Caughey B, Cordeiro Y, Barbosa MLC. Synthesis and in silico and in vitro evaluation of trimethoxy-benzamides designed as anti-prion derivatives. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02441-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Virtual screening of antibacterial compounds by similarity search of Enoyl-ACP reductase (FabI) inhibitors. Future Med Chem 2019; 12:51-68. [PMID: 31729258 DOI: 10.4155/fmc-2019-0158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Aim: Antibiotic resistance is an alarming issue, as multidrug-resistant bacteria are growing worldwide, hence the decrease of therapeutic potential of available antibiotic arsenal. Among these bacteria, Staphylococcus aureus was pointed by the WHO in the pathogens list to be prioritized in drug development. Methods: We report the use of chemical similarity models for the virtual screening of new antibacterial with structural similarity to known inhibitors of FabI. The potential inhibitors were experimentally evaluated for antibacterial activity and membrane disrupting capabilities. Results & conclusion: These models led to the finding of four new compounds with antibacterial activity, one of which having antimicrobial activity already reported in the literature.
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29
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Wang S, Dong G, Sheng C. Structural simplification: an efficient strategy in lead optimization. Acta Pharm Sin B 2019; 9:880-901. [PMID: 31649841 PMCID: PMC6804494 DOI: 10.1016/j.apsb.2019.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/04/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
The trend toward designing large hydrophobic molecules for lead optimization is often associated with poor drug-likeness and high attrition rates in drug discovery and development. Structural simplification is a powerful strategy for improving the efficiency and success rate of drug design by avoiding "molecular obesity". The structural simplification of large or complex lead compounds by truncating unnecessary groups can not only improve their synthetic accessibility but also improve their pharmacokinetic profiles, reduce side effects and so on. This review will summarize the application of structural simplification in lead optimization. Numerous case studies, particularly those involving successful examples leading to marketed drugs or drug-like candidates, will be introduced and analyzed to illustrate the design strategies and guidelines for structural simplification.
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Key Words
- 11β-HSD, 11β-hydroxysteroid dehydrogenase
- 3D, three-dimensional
- ADMET, absorption, distribution, metabolism, excretion and toxicity
- AM2, adrenomedullin-2 receptor
- BIOS, biology-oriented synthesis
- CCK, cholecystokinin receptor
- CGRP, calcitonin gene-related peptide
- Drug design
- Drug discovery
- GlyT1, glycine transport 1
- HBV, hepatitis B virus
- HDAC, histone deacetylase
- HLM, human liver microsome
- JAKs, Janus tyrosine kinases
- LE, ligand efficiency
- Lead optimization
- LeuRS, leucyl-tRNA synthetase
- MCRs, multicomponent reactions
- MDR-TB, multidrug-resistant tuberculosis
- MW, molecular weight
- NP, natural product
- NPM, nucleophosmin
- PD, pharmacodynamic
- PK, pharmacokinetic
- PKC, protein kinase C
- Pharmacophore-based simplification
- Reducing chiral centers
- Reducing rings number
- SAHA, vorinostat
- SAR, structure‒activity relationship
- SCONP, structural classification of natural product
- Structural simplification
- Structure-based simplification
- TSA, trichostatin A
- TbLeuRS, T. brucei LeuRS
- ThrRS, threonyl-tRNA synthetase
- VANGL1, van-Gogh-like receptor protein 1
- aa-AMP, aminoacyl-AMP
- aa-AMS, aminoacylsulfa-moyladenosine
- aaRSs, aminoacyl-tRNA synthetases
- hA3 AR, human A3 adenosine receptor
- mTORC1, mammalian target of rapamycin complex 1
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Affiliation(s)
- Shengzheng Wang
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Department of Medicinal Chemistry and Pharmaceutical Analysis, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Guoqiang Dong
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chunquan Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
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30
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Silva ACC, Brelaz-de-Castro MCA, Leite ACL, Pereira VRA, Hernandes MZ. Chagas Disease Treatment and Rational Drug Discovery: A Challenge That Remains. Front Pharmacol 2019; 10:873. [PMID: 31427977 PMCID: PMC6690016 DOI: 10.3389/fphar.2019.00873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ana Catarina Cristovão Silva
- Laboratório de Imunopatologia e Biologia Molecular, Departamento de Imunologia, Instituto Aggeu Magalhães, Recife, Brazil.,Programa de Pós-graduação em Inovação Terapêutica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Maria Carolina Accioly Brelaz-de-Castro
- Laboratório de Imunopatologia e Biologia Molecular, Departamento de Imunologia, Instituto Aggeu Magalhães, Recife, Brazil.,Laboratório de Parasitologia, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, Brazil
| | | | - Valéria Rêgo Alves Pereira
- Laboratório de Imunopatologia e Biologia Molecular, Departamento de Imunologia, Instituto Aggeu Magalhães, Recife, Brazil
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31
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Pereira GAN, da Silva EB, Braga SFP, Leite PG, Martins LC, Vieira RP, Soh WT, Villela FS, Costa FMR, Ray D, de Andrade SF, Brandstetter H, Oliveira RB, Caffrey CR, Machado FS, Ferreira RS. Discovery and characterization of trypanocidal cysteine protease inhibitors from the 'malaria box'. Eur J Med Chem 2019; 179:765-778. [PMID: 31284086 DOI: 10.1016/j.ejmech.2019.06.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 02/04/2023]
Abstract
Chagas disease, Human African Trypanosomiasis, and schistosomiasis are neglected parasitic diseases for which new treatments are urgently needed. To identify new chemical leads, we screened the 400 compounds of the Open Access Malaria Box against the cysteine proteases, cruzain (Trypanosoma cruzi), rhodesain (Trypanosoma brucei) and SmCB1 (Schistosoma mansoni), which are therapeutic targets for these diseases. Whereas just three hits were observed for SmCB1, 70 compounds inhibited cruzain or rhodesain by at least 50% at 5 μM. Among those, 15 commercially available compounds were selected for confirmatory assays, given their potency, time-dependent inhibition profile and reported activity against parasites. Additional assays led to the confirmation of four novel classes of cruzain and rhodesain inhibitors, with potency in the low-to mid-micromolar range against enzymes and T. cruzi. Assays against mammalian cathepsins S and B revealed inhibitor selectivity for parasitic proteases. For the two competitive inhibitors identified (compounds 7 and 12), their binding mode was predicted by docking, providing a basis for structure-based optimization efforts. Compound 12 also acted directly against the trypomastigote and the intracellular amastigote forms of T. cruzi at 3 μM. Therefore, through a combination of experimental and computational approaches, we report promising hits for optimization in the development of new trypanocidal drugs.
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Affiliation(s)
- Glaécia A N Pereira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Elany B da Silva
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Saulo F P Braga
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Paulo Gaio Leite
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Luan C Martins
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafael P Vieira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Wai Tuck Soh
- Structural Biology Group By Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Filipe S Villela
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Francielly M R Costa
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Debalina Ray
- University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Saulo F de Andrade
- Pharmaceutical Synthesis Group (PHARSG), Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Hans Brandstetter
- Structural Biology Group By Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Renata B Oliveira
- Faculdade de Farmácia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Fabiana S Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafaela S Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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32
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Santos LH, Waldner BJ, Fuchs JE, Pereira GAN, Liedl KR, Caffarena ER, Ferreira RS. Understanding Structure–Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. J Chem Inf Model 2018; 59:137-148. [DOI: 10.1021/acs.jcim.8b00557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lucianna H. Santos
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, RJ 21040-360, Brazil
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Birgit J. Waldner
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 82, Innsbruck, Tyrol 6020, Austria
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 82, Innsbruck, Tyrol 6020, Austria
| | - Glaécia A. N. Pereira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 31270-901, Brazil
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF Brazil
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 82, Innsbruck, Tyrol 6020, Austria
| | - Ernesto R. Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Rafaela S. Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 31270-901, Brazil
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33
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Synthesis, antitrypanosomal activity and molecular docking studies of pyrimidine derivatives. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2253-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Rocha DA, Silva EB, Fortes IS, Lopes MS, Ferreira RS, Andrade SF. Synthesis and structure-activity relationship studies of cruzain and rhodesain inhibitors. Eur J Med Chem 2018; 157:1426-1459. [DOI: 10.1016/j.ejmech.2018.08.079] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 08/13/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
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Scarim CB, Jornada DH, Chelucci RC, de Almeida L, Dos Santos JL, Chung MC. Current advances in drug discovery for Chagas disease. Eur J Med Chem 2018; 155:824-838. [PMID: 30033393 DOI: 10.1016/j.ejmech.2018.06.040] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 12/29/2022]
Abstract
Chagas disease, also known as American trypanosomiasis, is one of the 17 neglected tropical diseases (NTDs) according to World Health Organization. It is estimated that 8-10 million people are infected worldwide, mainly in Latin America. Chagas disease is caused by the parasite Trypanosoma cruzi and is characterized by two phases: acute and chronic. The current therapy for Chagas disease is limited to drugs such as nifurtimox and benznidazole, which are effective in treating only the acute phase of the disease. In addition, several side effects ranging from hypersensitivity to bone marrow depression and peripheral polyneuropathy have been associated with these drugs. Therefore, the current challenge is to find new effective and safe drugs against this NTD. The aim of this review is to describe the advances in the medicinal chemistry of new anti-chagasic compounds reported in the literature in the last five years. We report promising prototypes for drug discovery identified through target-based and phenotype-based strategies and present some important targets for the development of new synthetic compounds.
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Affiliation(s)
- Cauê Benito Scarim
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Araraquara, SP, Brazil.
| | - Daniela Hartmann Jornada
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Araraquara, SP, Brazil
| | - Rafael Consolin Chelucci
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Araraquara, SP, Brazil
| | - Leticia de Almeida
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, USP, Brazil
| | - Jean Leandro Dos Santos
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Araraquara, SP, Brazil
| | - Man Chin Chung
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho", UNESP, Araraquara, SP, Brazil
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Martins LC, Torres PHM, de Oliveira RB, Pascutti PG, Cino EA, Ferreira RS. Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations. J Comput Aided Mol Des 2018; 32:591-605. [PMID: 29564808 DOI: 10.1007/s10822-018-0112-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/14/2018] [Indexed: 12/24/2022]
Abstract
Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.
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Affiliation(s)
- Luan Carvalho Martins
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, CEP 31270-901, Brazil.,Laboratório de Química Farmacêutica, Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Pedro Henrique Monteiro Torres
- Programa de Computação Científica, Fundação Oswaldo Cruz - FIOCRUZ, Av. Brasil, 4365, Rio de Janeiro, RJ, CEP 21040-900, Brazil
| | - Renata Barbosa de Oliveira
- Laboratório de Química Farmacêutica, Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, CEP 21944-970, Brazil
| | - Elio A Cino
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Rafaela Salgado Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG, CEP 31270-901, Brazil.
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de Souza AS, de Oliveira MT, Andricopulo AD. Development of a pharmacophore for cruzain using oxadiazoles as virtual molecular probes: quantitative structure–activity relationship studies. J Comput Aided Mol Des 2017; 31:801-816. [DOI: 10.1007/s10822-017-0039-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
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