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Parvez A, Lee JS, Alam W, Tayara H, Chong KT. Integrated Computational Approaches for Drug Design Targeting Cruzipain. Int J Mol Sci 2024; 25:3747. [PMID: 38612558 PMCID: PMC11011879 DOI: 10.3390/ijms25073747] [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] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Cruzipain inhibitors are required after medications to treat Chagas disease because of the need for safer, more effective treatments. Trypanosoma cruzi is the source of cruzipain, a crucial cysteine protease that has driven interest in using computational methods to create more effective inhibitors. We employed a 3D-QSAR model, using a dataset of 36 known inhibitors, and a pharmacophore model to identify potential inhibitors for cruzipain. We also built a deep learning model using the Deep purpose library, trained on 204 active compounds, and validated it with a specific test set. During a comprehensive screening of the Drug Bank database of 8533 molecules, pharmacophore and deep learning models identified 1012 and 340 drug-like molecules, respectively. These molecules were further evaluated through molecular docking, followed by induced-fit docking. Ultimately, molecular dynamics simulation was performed for the final potent inhibitors that exhibited strong binding interactions. These results present four novel cruzipain inhibitors that can inhibit the cruzipain protein of T. cruzi.
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Affiliation(s)
- Aiman Parvez
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea; (A.P.); (W.A.)
| | - Jeong-Sang Lee
- Department of Functional Food and Biotechnology, College of Medical Sciences, Jeonju University, Jeonju 55069, Republic of Korea;
| | - Waleed Alam
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea; (A.P.); (W.A.)
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea; (A.P.); (W.A.)
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Espinoza-Chávez RM, Oliveira Rezende Júnior CD, de Souza ML, Pauli I, Valli M, Gomes Ferreira LL, Chelucci RC, Michelan-Duarte S, Krogh R, Romualdo da Silva FB, Cruz FC, de Oliveira AS, Andricopulo AD, Dias LC. Structure-activity relationships of novel N-imidazoylpiperazines with potent anti- Trypanosoma cruzi activity. Future Med Chem 2024; 16:253-269. [PMID: 38193294 DOI: 10.4155/fmc-2023-0185] [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: 06/27/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Background: Chagas disease is caused by the parasite Trypanosoma cruzi, and the lack of effective and safe treatments makes identifying new classes of compounds with anti-T. cruzi activity of paramount importance. Methods: Hit-to-lead exploration of a metabolically stable N-imidazoylpiperazine was performed. Results: Compound 2, a piperazine derivative active against T. cruzi, was selected to perform the hit-to-lead exploration, which involved the design, synthesis and biological evaluation of 39 new derivatives. Conclusion: Compounds 6e and 10a were identified as optimized compounds with low micromolar in vitro activity, low cytotoxicity and suitable preliminary absorption, distribution, metabolism and excretion and physicochemical properties. Both compounds reduced parasitemia in mouse models of Chagas disease, providing a promising opportunity for further exploration of new antichagasic compounds.
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Affiliation(s)
- Rocío Marisol Espinoza-Chávez
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas-SP, 13084-971, Brazil
| | - Celso de Oliveira Rezende Júnior
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas-SP, 13084-971, Brazil
- Institute of Chemistry, Federal University of Uberlândia, Uberlândia-MG, 38400-902, Brazil
| | - Mariana Laureano de Souza
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Ivani Pauli
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Marilia Valli
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Leonardo Luiz Gomes Ferreira
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Rafael Consolin Chelucci
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Simone Michelan-Duarte
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Renata Krogh
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | | | - Fábio Cardoso Cruz
- Department of Pharmacology, Federal University of São Paulo - UNIFESP, São Paulo-SP, 04023-062, Brazil
| | - Aldo Sena de Oliveira
- Department of Exact Sciences & Education, Federal University of Santa Catarina, Campus of Blumenau, Santa Catarina-SC, 89036-256, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal & Computational Chemistry, São Carlos Institute of Physics, University of São Paulo, São Carlos-SP, 13563-120, Brazil
| | - Luiz Carlos Dias
- Laboratory of Synthetic Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas-SP, 13084-971, Brazil
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Saha A, Pushpa, Moitra S, Basak D, Brahma S, Mondal D, Molla SH, Samadder A, Nandi S. Targeting Cysteine Proteases and their Inhibitors to Combat Trypanosomiasis. Curr Med Chem 2024; 31:2135-2169. [PMID: 37340748 DOI: 10.2174/0929867330666230619160509] [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] [Received: 01/22/2023] [Revised: 04/21/2023] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Trypanosomiasis, caused by protozoan parasites of the Trypanosoma genus, remains a significant health burden in several regions of the world. Cysteine proteases play a crucial role in the pathogenesis of Trypanosoma parasites and have emerged as potential therapeutic targets for the development of novel antiparasitic drugs. INTRODUCTION This review article aims to provide a comprehensive overview of the role of cysteine proteases in trypanosomiasis and their potential as therapeutic targets. We discuss the biological significance of cysteine proteases in Trypanosoma parasites and their involvement in essential processes, such as host immune evasion, cell invasion, and nutrient acquisition. METHODS A comprehensive literature search was conducted to identify relevant studies and research articles on the role of cysteine proteases and their inhibitors in trypanosomiasis. The selected studies were critically analyzed to extract key findings and provide a comprehensive overview of the topic. RESULTS Cysteine proteases, such as cruzipain, TbCatB and TbCatL, have been identified as promising therapeutic targets due to their essential roles in Trypanosoma pathogenesis. Several small molecule inhibitors and peptidomimetics have been developed to target these proteases and have shown promising activity in preclinical studies. CONCLUSION Targeting cysteine proteases and their inhibitors holds great potential for the development of novel antiparasitic drugs against trypanosomiasis. The identification of potent and selective cysteine protease inhibitors could significantly contribute to the combat against trypanosomiasis and improve the prospects for the treatment of this neglected tropical disease.
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Affiliation(s)
- Aloke Saha
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Pushpa
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Susmita Moitra
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Deblina Basak
- Endocrinology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sayandeep Brahma
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Dipu Mondal
- Cell and Developmental Biology Special, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sabir Hossen Molla
- Parasitology Laboratory, Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Sisir Nandi
- Global Institute of Pharmaceutical Education and Research (Affiliated to Veer Madho Singh Bhandari Uttarakhand Technical University), Kashipur, 244713, India
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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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Giroud M, Kuhn B, Haap W. Drug Discovery Efforts to Identify Novel Treatments for Neglected Tropical Diseases - Cysteine Protease Inhibitors. Curr Med Chem 2024; 31:2170-2194. [PMID: 37916489 DOI: 10.2174/0109298673249097231017051733] [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] [Received: 02/14/2023] [Revised: 06/19/2023] [Accepted: 09/14/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Neglected tropical diseases are a severe burden for mankind, affecting an increasing number of people around the globe. Many of those diseases are caused by protozoan parasites in which cysteine proteases play a key role in the parasite's pathogenesis. OBJECTIVE In this review article, we summarize the drug discovery efforts of the research community from 2017 - 2022 with a special focus on the optimization of small molecule cysteine protease inhibitors in terms of selectivity profiles or drug-like properties as well as in vivo studies. The cysteine proteases evaluated by this methodology include Cathepsin B1 from Schistosoma mansoni, papain, cruzain, falcipain, and rhodesain. METHODS Exhaustive literature searches were performed using the keywords "Cysteine Proteases" and "Neglected Tropical Diseases" including the years 2017 - 2022. Overall, approximately 3'000 scientific papers were retrieved, which were filtered using specific keywords enabling the focus on drug discovery efforts. RESULTS AND CONCLUSION Potent and selective cysteine protease inhibitors to treat neglected tropical diseases were identified, which progressed to pharmacokinetic and in vivo efficacy studies. As far as the authors are aware of, none of those inhibitors reached the stage of active clinical development. Either the inhibitor's potency or pharmacokinetic properties or safety profile or a combination thereof prevented further development of the compounds. More efforts with particular emphasis on optimizing pharmacokinetic and safety properties are needed, potentially by collaborations of academic and industrial research groups with complementary expertise. Furthermore, new warheads reacting with the catalytic cysteine should be exploited to advance the research field in order to make a meaningful impact on society.
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Affiliation(s)
- Maude Giroud
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Bernd Kuhn
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Wolfgang Haap
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
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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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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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8
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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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Synthesis and investigation of the trypanocidal potential of novel 1,2,3-triazole-selenide hybrids. Eur J Med Chem 2022; 243:114687. [DOI: 10.1016/j.ejmech.2022.114687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022]
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Valli M, Souza JM, Chelucci RC, Biasetto CR, Araujo AR, Bolzani VDS, Andricopulo AD. Identification of natural cytochalasins as leads for neglected tropical diseases drug discovery. PLoS One 2022; 17:e0275002. [PMID: 36190979 PMCID: PMC9529094 DOI: 10.1371/journal.pone.0275002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Investigating the chemical diversity of natural products from tropical environments is an inspiring approach to developing new drug candidates for neglected tropical diseases (NTDs). In the present study, phenotypic screenings for antiprotozoal activity and a combination of computational and biological approaches enabled the identification and characterization of four cytochalasins, which are fungal metabolites from Brazilian biodiversity sources. Cytochalasins A-D exhibited IC50 values ranging from 2 to 20 μM against intracellular Trypanosoma cruzi and Leishmania infantum amastigotes, values comparable to those of the standard drugs benznidazole and miltefosine for Chagas disease and leishmaniasis, respectively. Furthermore, cytochalasins A-D reduced L. infantum infections by more than 80% in THP-1 cells, most likely due to the inhibition of phagocytosis by interactions with actin. Molecular modelling studies have provided useful insights into the mechanism of action of this class of compounds. Furthermore, cytochalasins A-D showed moderate cytotoxicity against normal cell lines (HFF-1, THP-1, and HepG2) and a good overall profile for oral bioavailability assessed in vitro. The results of this study support the use of natural products from Brazilian biodiversity sources to find potential drug candidates for two of the most important NTDs.
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Affiliation(s)
- Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
| | - Julia Medeiros Souza
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Rafael Consolin Chelucci
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Carolina Rabal Biasetto
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Angela Regina Araujo
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
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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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Alzain AA, Elbadwi FA. De Novo Design of Cathepsin B1 Inhibitors as Potential Anti-Schistosomal Agents Using Computational Studies. ADVANCES AND APPLICATIONS IN BIOINFORMATICS AND CHEMISTRY 2022; 15:29-41. [PMID: 35935393 PMCID: PMC9355347 DOI: 10.2147/aabc.s361626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022]
Abstract
Background Schistosomiasis is the world’s second most devastating disease after malaria and the leading cause of disease and mortality for more than 200 million people in developing countries. Cysteine proteases, in particular SmCB1, are the most well-researched biological targets for this disorder. Objective To apply computational techniques to design new antischistosomal agents against SmCB1 protein with favorable pharmacokinetic properties. Methods The smCB1 receptor-based pharmacophore model was created and used to screen 567,000 fragments from the Enamine library. The best scoring fragments have been linked to build novel compounds that were subjected to molecular docking, MM-GBSA free energy estimation, ADME prediction, and molecular dynamics. Results A seven-point pharmacophore hypothesis ADDDRRR was created. The developed hypothesis was used to screen 1.3 M fragment conformations. Among them, 23,732 fragments matched the hypothesis and screened against the protein. The top 50 fragments were used to design new 7745 compounds using the Breed ligand panel which were subjected to docking and MMGBSA binding energy. This led to the identification of 10 compounds with better docking scores (−8.033– −7.483 kcal/mol) and lower-bound free energies (−58.49 – −40.02 kcal/mol) compared to the reference bound ligand. Most of the designed compounds demonstrated good drug-like properties. Concerning Molecular dynamics (MD) simulation results, a low root mean square deviation (RMSD) range (0.25–1.2 Å) was found for the top 3 complexes which indicated their stability. Conclusion We identified compounds that could be potential candidates in the search for novel Schistosoma mansoni inhibitors by targeting SmCB1 utilizing various computational tools. Three newly designed compounds namely breed 1, 2, and 3 showed promising affinity to the target as well as favorable drug-like properties which might be considered potential anti-schistosomal agents.
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Affiliation(s)
- Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
- Correspondence: Abdulrahim A Alzain, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan, Tel +249-511854501, Fax +249-511861180, Email
| | - Fatima A Elbadwi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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13
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Novel trypanocidal thiophen-chalcone cruzain inhibitors: structure- and ligand-based studies. Future Med Chem 2022; 14:795-808. [PMID: 35543430 DOI: 10.4155/fmc-2022-0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Chagas disease is a neglected tropical disease that affects millions of people worldwide and for which no effective treatment is available. Materials & methods: 17 chalcones were synthesized, for which the inhibition of cruzain and trypanocidal activity were investigated. Results: Chalcone C8 showed the highest cruzain inhibitory (IC50 = 0.536 μM) and trypanocidal activity (IC50 = 0.990 μM). Molecular docking studies showed interactions involving Asp161 and the thiophen group interacting with the S2 subsite. Furthermore, quantitative structure-activity relationship (q2 = 0.786; r2 = 0.953) and density functional theory studies were carried out, and a correlation between the lowest unoccupied molecular orbital surface and trypanocidal activity was observed. Conclusion: These results demonstrate that these chalcones are worthwhile hits to be further optimized in Chagas disease drug discovery programs.
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14
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A copper-catalyzed three-component reaction of alkenes, cycloketone oximes and DABCO·(SO2)2: Direct C(sp2)-H cyanoalkylsulfonylation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Reis CRCD, Souza HVCMD, Leme RPP, Castelo-Branco FS, Fernandes TVA, Boechat N, Dias LRS, Hoelz LVB. Study of the dynamic behavior of the cruzain enzyme in free and complexed forms with competitive and noncovalent benzimidazole inhibitors. J Biomol Struct Dyn 2022:1-15. [PMID: 35475501 DOI: 10.1080/07391102.2022.2067238] [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: 10/18/2022]
Abstract
There are only two drugs for the treatment of Chagas disease, namely, nifurtimox and benznidazole, that can cause several adverse effects. Despite the effectiveness of these drugs in the disease's acute phase, they are not recognized as curative in the chronic phase, establishing the need for more effective treatment in all stages of the disease. Cruzain is an enzyme that plays a vital role in the life cycle of the etiologic agent, the protozoan Trypanosoma cruzi, being relevant as a therapeutic target in the planning of new drugs. Using molecular docking and dynamics simulations, we have investigated the structural and dynamic factors that can be involved in the enzyme inhibition process at the atomic-molecular level by benzimidazole compounds that are potent cruzain inhibitors with in vitro trypanocidal activity. The study suggests that these inhibitors bind cruzain through steric and hydrogen bonding interactions without altering its secondary structure content and protein compaction. Besides, we observed that these inhibitors decrease the correlation of movements between Cα-atoms of cruzain, increasing the number of atomic communities, mainly in the α-helix that presents the catalytic Cys25 residue. As expected, we also observed a correlation between the inhibitory activity of each inhibitor and their respective binding-free energies, reinforcing that the affinity of the complexes seems to be a relevant factor for enzymatic inhibition. Hence, the results presented in this work contribute to a better understanding of the cruzain enzyme inhibition mechanism through competitive and non-covalent inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Caroline Rodrigues Chaves Dos Reis
- Programa de Pós-Graduação em Ciências Aplicadas a Produtos Para Saúde (PPG-CAPS), Faculdade de Farmácia, Universidade Federal Fluminense, Rua Mário Viana, Niterói, RJ, Brazil.,Faculdade de Farmácia, Laboratório de Química Medicinal - LQMed, Universidade Federal Fluminense (UFF), Santa Rosa, Niterói, RJ, Brazil.,Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
| | - Hellen Valério Chaves Moura de Souza
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
| | - Rennan Papaleo Paes Leme
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal - Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, UFRJ, Centro de Ciências da Saúde (CCS), Bloco J - Ilha do Fundão, Rio de Janeiro, RJ, Brazil
| | - Frederico Silva Castelo-Branco
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
| | - Tácio Vinício Amorim Fernandes
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
| | - Núbia Boechat
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
| | - Luiza Rosaria Sousa Dias
- Faculdade de Farmácia, Laboratório de Química Medicinal - LQMed, Universidade Federal Fluminense (UFF), Santa Rosa, Niterói, RJ, Brazil
| | - Lucas Villas Bôas Hoelz
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos, Farmanguinhos - Fiocruz, Laboratório de Síntese Fármacos - LASFAR, Manguinhos Rio de Janeiro, RJ, Brazil
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16
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Approaches to advance drug discovery for neglected tropical diseases. Drug Discov Today 2022; 27:2278-2287. [DOI: 10.1016/j.drudis.2022.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/21/2022] [Accepted: 04/02/2022] [Indexed: 12/19/2022]
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17
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Pauli I, Rezende CDO, Slafer BW, Dessoy MA, de Souza ML, Ferreira LLG, Adjanohun ALM, Ferreira RS, Magalhães LG, Krogh R, Michelan-Duarte S, Del Pintor RV, da Silva FBR, Cruz FC, Dias LC, Andricopulo AD. Multiparameter Optimization of Trypanocidal Cruzain Inhibitors With In Vivo Activity and Favorable Pharmacokinetics. Front Pharmacol 2022; 12:774069. [PMID: 35069198 PMCID: PMC8767159 DOI: 10.3389/fphar.2021.774069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cruzain, the main cysteine protease of Trypanosoma cruzi, plays key roles in all stages of the parasite's life cycle, including nutrition acquisition, differentiation, evasion of the host immune system, and invasion of host cells. Thus, inhibition of this validated target may lead to the development of novel drugs for the treatment of Chagas disease. In this study, a multiparameter optimization (MPO) approach, molecular modeling, and structure-activity relationships (SARs) were employed for the identification of new benzimidazole derivatives as potent competitive inhibitors of cruzain with trypanocidal activity and suitable pharmacokinetics. Extensive pharmacokinetic studies enabled the identification of metabolically stable and permeable compounds with high selectivity indices. CYP3A4 was found to be involved in the main metabolic pathway, and the identification of metabolic soft spots provided insights into molecular optimization. Compound 28, which showed a promising trade-off between pharmacodynamics and pharmacokinetics, caused no acute toxicity and reduced parasite burden both in vitro and in vivo.
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Affiliation(s)
- Ivani Pauli
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Celso de O Rezende
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Brian W Slafer
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marco A Dessoy
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Mariana L de Souza
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Leonardo L G Ferreira
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Abraham L M Adjanohun
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafaela S Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luma G Magalhães
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Renata Krogh
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Simone Michelan-Duarte
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | | | | | - Fabio C Cruz
- Departamento de Farmacologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Adriano D Andricopulo
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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18
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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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19
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Diaminomaleonitrile derivatives as new potential antichagasic compounds: a study of structure-activity relationships. Future Med Chem 2021; 13:2167-2183. [PMID: 34708659 DOI: 10.4155/fmc-2021-0194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Schiff bases are synthetically accessible compounds that have been used in medicinal chemistry. Methods & results: In this work, 27 Schiff bases derived from diaminomaleonitrile were synthesized in high yields (80-98%). Molecular docking studies suggested that the Schiff bases interact with the catalytic site of cruzain. The most active cruzain inhibitor, analog 13 (IC50 = 263 nM), was predicted to form an additional hydrophobic contact with Met68 in the binding site of the enzyme. A strong correlation between the IC50 values and ChemScore binding energies was observed (R = 0.99). Kernel-based 2D quantitative structure-activity relationship models for the whole dataset yielded sound correlation coefficients (R2 = 0.844; Q2 = 0.719). Conclusion: These novel and potent cruzain inhibitors are worthwhile starting points in further Chagas disease drug discovery programs.
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20
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Santos VC, Oliveira AER, Campos ACB, Reis-Cunha JL, Bartholomeu DC, Teixeira SMR, Lima APCA, Ferreira RS. The gene repertoire of the main cysteine protease of Trypanosoma cruzi, cruzipain, reveals four sub-types with distinct active sites. Sci Rep 2021; 11:18231. [PMID: 34521898 PMCID: PMC8440672 DOI: 10.1038/s41598-021-97490-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cruzipains are the main papain-like cysteine proteases of Trypanosoma cruzi, the protozoan parasite that causes Chagas disease. Encoded by a multigenic family, previous studies have estimated the presence of dozens of copies spread over multiple chromosomes in different parasite strains. Here, we describe the complete gene repertoire of cruzipain in three parasite strains, their genomic organization, and expression pattern throughout the parasite life cycle. Furthermore, we have analyzed primary sequence variations among distinct family members as well as structural differences between the main groups of cruzipains. Based on phylogenetic inferences and residue positions crucial for enzyme function and specificity, we propose the classification of cruzipains into two families (I and II), whose genes are distributed in two or three separate clusters in the parasite genome, according with the strain. Family I comprises nearly identical copies to the previously characterized cruzipain 1/cruzain, whereas Family II encompasses three structurally distinct sub-types, named cruzipain 2, cruzipain 3, and cruzipain 4. RNA-seq data derived from the CL Brener strain indicates that Family I genes are mainly expressed by epimastigotes, whereas trypomastigotes mainly express Family II genes. Significant differences in the active sites among the enzyme sub-types were also identified, which may play a role in their substrate selectivity and impact their inhibition by small molecules.
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Affiliation(s)
- Viviane Corrêa Santos
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - Antonio Edson Rocha Oliveira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil ,grid.11899.380000 0004 1937 0722Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Augusto César Broilo Campos
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - João Luís Reis-Cunha
- grid.8430.f0000 0001 2181 4888Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil ,grid.8430.f0000 0001 2181 4888Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | | | - Santuza Maria Ribeiro Teixeira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - Ana Paula C. A. Lima
- grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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21
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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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23
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Medeiros AR, Ferreira LLG, de Souza ML, de Oliveira Rezende Junior C, Espinoza-Chávez RM, Dias LC, Andricopulo AD. Chemoinformatics Studies on a Series of Imidazoles as Cruzain Inhibitors. Biomolecules 2021; 11:biom11040579. [PMID: 33920961 PMCID: PMC8071344 DOI: 10.3390/biom11040579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022] Open
Abstract
Natural products based on imidazole scaffolds have inspired the discovery of a wide variety of bioactive compounds. Herein, a series of imidazoles that act as competitive and potent cruzain inhibitors was investigated using a combination of ligand- and structure-based drug design strategies. Quantitative structure-activity relationships (QSARs) were generated along with the investigation of enzyme-inhibitor molecular interactions. Predictive hologram QSAR (HQSAR, r2pred = 0.80) and AutoQSAR (q2 = 0.90) models were built, and key structural properties that underpin cruzain inhibition were identified. Moreover, comparative molecular field analysis (CoMFA, r2pred = 0.81) and comparative molecular similarity indices analysis (CoMSIA, r2pred = 0.73) revealed 3D molecular features that strongly affect the activity of the inhibitors. These findings were examined along with molecular docking studies and were highly compatible with the intermolecular contacts that take place between cruzain and the inhibitors. The results gathered herein revealed the main factors that determine the activity of the imidazoles studied and provide novel knowledge for the design of improved cruzain inhibitors.
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Affiliation(s)
- Alex R. Medeiros
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos, SP 13563-120, Brazil; (A.R.M.); (L.L.G.F.); (M.L.d.S.)
| | - Leonardo L. G. Ferreira
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos, SP 13563-120, Brazil; (A.R.M.); (L.L.G.F.); (M.L.d.S.)
| | - Mariana L. de Souza
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos, SP 13563-120, Brazil; (A.R.M.); (L.L.G.F.); (M.L.d.S.)
| | | | - Rocío Marisol Espinoza-Chávez
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP 13084-971, Brazil; (C.d.O.R.J.); (R.M.E.-C.); (L.C.D.)
| | - Luiz Carlos Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP 13084-971, Brazil; (C.d.O.R.J.); (R.M.E.-C.); (L.C.D.)
| | - Adriano D. Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos, SP 13563-120, Brazil; (A.R.M.); (L.L.G.F.); (M.L.d.S.)
- Correspondence: ; Tel.: +55-16-33739844
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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: 3] [Impact Index Per Article: 1.0] [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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25
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Mondal A, Sen U, Roy N, Muthukumar V, Sahoo SK, Bose B, Paira P. DNA targeting half sandwich Ru(ii)-p-cymene-N^N complexes as cancer cell imaging and terminating agents: influence of regioisomers in cytotoxicity. Dalton Trans 2021; 50:979-997. [DOI: 10.1039/d0dt03107k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One pot green synthesis and isolation of regioisomers of a library of DNA targeting anticancer Ru(ii)-p-cymene complexes to bringforth as cancer cell imaging as well as terminating agents.
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Affiliation(s)
- Ashaparna Mondal
- Department of Chemistry
- School of advanced sciences
- Vellore Institute of Technology Vellore
- India
| | - Utsav Sen
- Department Stem Cells and Regenerative Medicine Centre
- Institution Yenepoya Research Centre
- Yenepoya University
- Mangalore 575018
- India
| | - Nilmadhab Roy
- Department of Chemistry
- School of advanced sciences
- Vellore Institute of Technology Vellore
- India
| | - Venkatesan Muthukumar
- Department of Chemistry
- School of advanced sciences
- Vellore Institute of Technology Vellore
- India
| | - Suban Kumar Sahoo
- Department of Applied Chemistry
- S.V. National Institute of Technology (SVNIT)
- Surat
- India
| | - Bipasha Bose
- Department Stem Cells and Regenerative Medicine Centre
- Institution Yenepoya Research Centre
- Yenepoya University
- Mangalore 575018
- India
| | - Priyankar Paira
- Department of Chemistry
- School of advanced sciences
- Vellore Institute of Technology Vellore
- India
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26
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Synthesis, biochemical evaluation and molecular modeling studies of nonpeptidic nitrile-based fluorinated compounds. Future Med Chem 2020; 13:25-43. [PMID: 33289603 DOI: 10.4155/fmc-2020-0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: Compounds that block enzyme activity can kill pathogens and help develop effective and safe drugs for Chagas disease and leishmaniasis. Materials & methods: A library of nonpeptidic nitrile-based compounds was synthesized and had their inhibitory affinity tested against cruzain, Leishmania mexicana cysteine protease B and cathepsin L. Isothermal titration calorimetry experiments and molecular simulations were performed for selected compounds to obtain thermodynamic fingerprints and identify main interactions and putative modes of binding with cruzain. Results: The derivatives provided increased affinity against all enzymes compared with the lead, and thermodynamic and computational studies showed improved thermodynamic properties and a possible different mode of binding. Conclusion: Our studies culminated in 1b, a compound 60-fold more potent in cruzain than its lead that also showed entropic and enthalpic contributions favorable to Gibbs binding energy.
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27
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Kaur R, Raghav N. Some thiocarbamoyl based novel anticathepsin agents. Bioorg Chem 2020; 104:104174. [DOI: 10.1016/j.bioorg.2020.104174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/18/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022]
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28
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The role of imidazole and benzimidazole heterocycles in Chagas disease: A review. Eur J Med Chem 2020; 206:112692. [PMID: 32818869 DOI: 10.1016/j.ejmech.2020.112692] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/02/2023]
Abstract
The haemoflagellate protozoan Trypanosoma cruzi (T. cruzi) is the causative agent of Chagas disease (CD), a potentially life-threatening disease. Little by little, remarkable progress has been achieved against CD, although it is still not enough. In the absence of effective chemotherapy, many research groups, organizations and pharmaceutical companies have focused their efforts on the search for compounds that could become viable drugs against CD. Within the wide variety of reported derivatives, this review summarizes and provides a global vision of the situation of those compounds that include broadly studied heterocycles in their structures due to their applications in medicinal chemistry: imidazole and benzimidazole rings. Therefore, the intention of this work is to present a compilation, as much as possible, of all the reported information, regarding these imidazole and benzimidazole derivatives against T. cruzi, as a starting point for future researchers in this field.
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29
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Francisco AF, Jayawardhana S, Olmo F, Lewis MD, Wilkinson SR, Taylor MC, Kelly JM. Challenges in Chagas Disease Drug Development. Molecules 2020; 25:E2799. [PMID: 32560454 PMCID: PMC7355550 DOI: 10.3390/molecules25122799] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 02/08/2023] Open
Abstract
The protozoan parasite Trypanosoma cruzi causes Chagas disease, an important public health problem throughout Latin America. Current therapeutic options are characterised by limited efficacy, long treatment regimens and frequent toxic side-effects. Advances in this area have been compromised by gaps in our knowledge of disease pathogenesis, parasite biology and drug activity. Nevertheless, several factors have come together to create a more optimistic scenario. Drug-based research has become more systematic, with increased collaborations between the academic and commercial sectors, often within the framework of not-for-profit consortia. High-throughput screening of compound libraries is being widely applied, and new technical advances are helping to streamline the drug development pipeline. In addition, drug repurposing and optimisation of current treatment regimens, informed by laboratory research, are providing a basis for new clinical trials. Here, we will provide an overview of the current status of Chagas disease drug development, highlight those areas where progress can be expected, and describe how fundamental research is helping to underpin the process.
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Affiliation(s)
- Amanda F. Francisco
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Shiromani Jayawardhana
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Francisco Olmo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Michael D. Lewis
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - Shane R. Wilkinson
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road, London E1 4NS, UK;
| | - Martin C. Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine Keppel Street, London WC1E 7HT, UK; (A.F.F.); (S.J.); (F.O.); (M.D.L.); (M.C.T.)
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30
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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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31
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de Souza ML, de Oliveira Rezende Junior C, Ferreira RS, Espinoza Chávez RM, Ferreira LLG, Slafer BW, Magalhães LG, Krogh R, Oliva G, Cruz FC, Dias LC, Andricopulo AD. Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach. J Chem Inf Model 2019; 60:1028-1041. [PMID: 31765144 DOI: 10.1021/acs.jcim.9b00802] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A virtual screening conducted with nearly 4 000 000 compounds from lead-like and fragment-like subsets enabled the identification of a small-molecule inhibitor (1) of the Trypanosoma cruzi cruzain enzyme, a validated drug target for Chagas disease. Subsequent comprehensive structure-based drug design and structure-activity relationship studies led to the discovery of carbamoyl imidazoles as potent, reversible, and competitive cruzain inhibitors. The most potent carbamoyl imidazole inhibitor (45) exhibited high affinity with a Ki value of 20 nM, presenting both in vitro and in vivo activity against T. cruzi. Furthermore, the most promising compounds reduced parasite burden in vivo and showed no toxicity at a dose of 100 mg/kg. These carbamoyl imidazoles are structurally attractive, nonpeptidic, and easy to prepare and synthetically modify. Finally, these results further advance our understanding of the noncovalent mode of inhibition of this pharmaceutically relevant enzyme, building strong foundations for drug discovery efforts.
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Affiliation(s)
- Mariana L de Souza
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
| | | | - Rafaela S Ferreira
- Department of Biochemistry and Immunology , Federal University of Minas Gerais , Belo Horizonte - MG 31270-901 , Brazil
| | | | - Leonardo L G Ferreira
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
| | - Brian W Slafer
- Institute of Chemistry , State University of Campinas , Campinas - SP 13084-971 , Brazil
| | - Luma G Magalhães
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
| | - Renata Krogh
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
| | - Glaucius Oliva
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
| | - Fabio Cardoso Cruz
- Department of Pharmacology , Federal University of Sao Paulo , Sao Paulo - SP 04023-062 , Brazil
| | - Luiz Carlos Dias
- Institute of Chemistry , State University of Campinas , Campinas - SP 13084-971 , Brazil
| | - Adriano D Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of Sao Carlos , University of Sao Paulo , Sao Carlos - SP 13563-120 , Brazil
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32
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Ferreira RAA, Pauli I, Sampaio TS, de Souza ML, Ferreira LLG, Magalhães LG, Rezende CDO, Ferreira RS, Krogh R, Dias LC, Andricopulo AD. Structure-Based and Molecular Modeling Studies for the Discovery of Cyclic Imides as Reversible Cruzain Inhibitors With Potent Anti- Trypanosoma cruzi Activity. Front Chem 2019; 7:798. [PMID: 31824926 PMCID: PMC6886403 DOI: 10.3389/fchem.2019.00798] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
Abstract
Chagas disease causes ~10,000 deaths each year, mainly in Latin America, where it is endemic. The currently available chemotherapeutic agents are ineffective in the chronic stage of the disease, and the lack of pharmaceutical innovation for Chagas disease highlights the urgent need for the development of new drugs. The enzyme cruzain, the main cysteine protease of Trypanosoma cruzi, has been explored as a validated molecular target for drug discovery. Herein, the design, molecular modeling studies, synthesis, and biological evaluation of cyclic imides as cruzain inhibitors are described. Starting with a micromolar-range cruzain inhibitor (3a, IC50 = 2.2 μM), this molecular optimization strategy resulted in the nanomolar-range inhibitor 10j (IC50 = 0.6 μM), which is highly active against T. cruzi intracellular amastigotes (IC50 = 1.0 μM). Moreover, most compounds were selective toward T. cruzi over human fibroblasts, which were used as host cells, and are less toxic to hepatic cells than the marketed drug benznidazole. This study enabled the discovery of novel chemical diversity and established robust structure-activity relationships to guide the design of optimized cruzain inhibitors as new trypanocidal agents.
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Affiliation(s)
| | - Ivani Pauli
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Thiago S Sampaio
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Mariana L de Souza
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Leonardo L G Ferreira
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Luma G Magalhães
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Celso de O Rezende
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Rafaela S Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Renata Krogh
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Adriano D Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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33
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Vieira RP, Santos VC, Ferreira RS. Structure-based Approaches Targeting Parasite Cysteine Proteases. Curr Med Chem 2019; 26:4435-4453. [PMID: 28799498 DOI: 10.2174/0929867324666170810165302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 12/17/2022]
Abstract
Cysteine proteases are essential hydrolytic enzymes present in the majority of organisms, including viruses and unicellular parasites. Despite the high sequence identity displayed among these proteins, specific structural features across different species grant distinct functions to these biomolecules, frequently related to pathological conditions. Consequently, their relevance as promising targets for potential specific inhibitors has been highlighted and occasionally validated in recent decades. In this review, we discuss the recent outcomes of structure-based campaigns aiming the discovery of new inhibitor prototypes against cruzain and falcipain, as alternative therapeutic tools for Chagas disease and malaria treatments, respectively. Computational and synthetic approaches have been combined on hit optimization strategies and are also discussed herein. These rationales are extended to additional tropical infectious and neglected pathologies, such as schistosomiasis, leishmaniasis and babesiosis, and also to Alzheimer's Disease, a widespread neurodegenerative disease poorly managed by currently available drugs and recently linked to particular physiopathological roles of human cysteine proteases.
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Affiliation(s)
- Rafael Pinto Vieira
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.,CAPES Foundation, Ministry of Education of Brazil, 70040-020 Brasília, DF, Brazil
| | - Viviane Corrêa Santos
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquimica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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34
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Zhang L, Li Z, Takimoto M, Hou Z. Carboxylation Reactions with Carbon Dioxide Using N-Heterocyclic Carbene-Copper Catalysts. CHEM REC 2019; 20:494-512. [PMID: 31573147 DOI: 10.1002/tcr.201900060] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/26/2019] [Indexed: 12/16/2022]
Abstract
The development of versatile catalyst systems and new transformations for the utilization of carbon dioxide (CO2 ) is of great interest and significance. This Personal Account reviews our studies on the exploration of the reactions of CO2 with various substrates by the use of N-heterocyclic carbene (NHC)-copper catalysts. The carboxylation of organoboron compounds gave access to a wide range of carboxylic acids with excellent functional group tolerance. The C-H bond carboxylation with CO2 emerged as a straightforward protocol for the preparation of a series of aromatic carboxylic esters and butenoates from simple substrates. The hydrosilylation of CO2 with hydrosilanes provided an efficient method for the synthesis of silyl formate on gram scale. The hydrogenative or alkylative carboxylation of alkynes, ynamides and allenamides yielded useful α,β-unsaturated carboxylic acids and α,β-dehydro amino acid esters. The boracarboxylation of alkynes or aldehydes afforded the novel lithium cyclic boralactone or boracarbonate products, respectively. The NHC-copper catalysts generally featured excellent functional group compatibility, broad substrate scope, high efficiency, and high regio- and stereoselectivity. The unique electronic and steric properties of the NHC-copper units also enabled the isolation and structural characterization of some key intermediates for better understanding of the catalytic reaction mechanisms.
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Affiliation(s)
- Liang Zhang
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Zhenghua Li
- Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masanori Takimoto
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Zhaomin Hou
- Organometallic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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35
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Lei K, Li P, Yang XF, Wang SB, Wang XK, Hua XW, Sun B, Ji LS, Xu XH. Design and Synthesis of Novel 4-Hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one Derivatives for Use as Herbicides and Evaluation of Their Mode of Action. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10489-10497. [PMID: 31452371 DOI: 10.1021/acs.jafc.9b03109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In order to develop a novel herbicide containing the β-triketone motif, a series of 4-hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one derivatives were designed and synthesized. The bioassay results showed that compound II15 had good pre-emergent herbicidal activity even at a dosage of 187.5 g ha-1. Moreover, compound II15 showed a broader spectrum of weed control when compared with a commercial herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and displayed good crop safety to Triticum aestivum L. and Zea mays Linn. when applied at 375 g ha-1 under pre-emergence conditions, which indicated its great potential as a herbicide. More importantly, studying the molecular mode of action of compound II15 revealed that the novel triketone structure is a proherbicide of its corresponding phenoxyacetic acid auxin herbicide, which has a herbicidal mechanism similar to that of 2,4-D. The present work indicates that the 4-hydroxyl-3-(2-phenoxyacetyl)-pyran-2-one motif may be a potential lead structure for further development of novel auxin-type herbicides.
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Affiliation(s)
- Kang Lei
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Pan Li
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
| | - Xue-Fang Yang
- College of Agriculture , Shanxi Agricultural University , Jinzhong , Shanxi 030800 , China
| | - Shi-Ben Wang
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
| | - Xue-Kun Wang
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
| | - Xue-Wen Hua
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Bin Sun
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Lu-Sha Ji
- School of Pharmacy , Liaocheng University , Liaocheng 252059 , China
| | - Xiao-Hua Xu
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
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36
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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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Sartori GR, Leitão A, Montanari CA, Laughton CA. Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors. PLoS One 2019; 14:e0222055. [PMID: 31856175 PMCID: PMC6922342 DOI: 10.1371/journal.pone.0222055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/19/2019] [Indexed: 11/25/2022] Open
Abstract
Cruzain, a cysteine protease of Trypanosoma cruzi, is a validated target for the treatment of Chagas disease. Due to its high similarity in three-dimensional structure with human cathepsins and their sequence identity above 70% in the active site regions, identifying potent but selective cruzain inhibitors with low side effects on the host organism represents a significant challenge. Here a panel of nitrile ligands with varying potencies against cathepsin K, cathepsin L and cruzain, are studied by molecular dynamics simulations as both non-covalent and covalent complexes. Principal component analysis (PCA), identifies and quantifies patterns of ligand-induced conformational selection that enable the construction of a decision tree which can predict with high confidence a low-nanomolar inhibitor of each of three proteins, and determine the selectivity for one against others.
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Affiliation(s)
- Geraldo Rodrigues Sartori
- Grupo de Química Medicinal do IQSC/USP, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Andrei Leitão
- Grupo de Química Medicinal do IQSC/USP, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Carlos A. Montanari
- Grupo de Química Medicinal do IQSC/USP, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Charles A. Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, England, United Kingdom
- * E-mail:
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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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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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Bilsland E, Tavella TA, Krogh R, Stokes JE, Roberts A, Ajioka J, Spring DR, Andricopulo AD, Costa FTM, Oliver SG. Antiplasmodial and trypanocidal activity of violacein and deoxyviolacein produced from synthetic operons. BMC Biotechnol 2018; 18:22. [PMID: 29642881 PMCID: PMC5896143 DOI: 10.1186/s12896-018-0428-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 03/15/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Violacein is a deep violet compound that is produced by a number of bacterial species. It is synthesized from tryptophan by a pathway that involves the sequential action of 5 different enzymes (encoded by genes vioA to vioE). Violacein has antibacterial, antiparasitic, and antiviral activities, and also has the potential of inducing apoptosis in certain cancer cells. RESULTS Here, we describe the construction of a series of plasmids harboring the complete or partial violacein biosynthesis operon and their use to enable production of violacein and deoxyviolacein in E.coli. We performed in vitro assays to determine the biological activity of these compounds against Plasmodium, Trypanosoma, and mammalian cells. We found that, while deoxyviolacein has a lower activity against parasites than violacein, its toxicity to mammalian cells is insignificant compared to that of violacein. CONCLUSIONS We constructed E. coli strains capable of producing biologically active violacein and related compounds, and propose that deoxyviolacein might be a useful starting compound for the development of antiparasite drugs.
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Affiliation(s)
- Elizabeth Bilsland
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK ,0000 0001 0723 2494grid.411087.bDepartment of Structural and Functional Biology, Institute of Biology, UNICAMP, Campinas, SP Brazil ,0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Tatyana A. Tavella
- 0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Renata Krogh
- 0000 0004 1937 0722grid.11899.38Laboratory of Medicinal and Computational Chemistry, University of São Paulo, São Carlos, SP Brazil
| | - Jamie E. Stokes
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annabelle Roberts
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - James Ajioka
- 0000000121885934grid.5335.0Department of Pathology, University of Cambridge, Cambridge, UK
| | - David R. Spring
- 0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Adriano D. Andricopulo
- 0000 0004 1937 0722grid.11899.38Laboratory of Medicinal and Computational Chemistry, University of São Paulo, São Carlos, SP Brazil
| | - Fabio T. M. Costa
- 0000 0001 0723 2494grid.411087.bLaboratory of Tropical Diseases – Prof. Dr. Luiz Jacintho da Silva - Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, SP Brazil
| | - Stephen G. Oliver
- 0000000121885934grid.5335.0Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK
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FERREIRA LEONARDOG, OLIVA GLAUCIUS, ANDRICOPULO ADRIANOD. From Medicinal Chemistry to Human Health: Current Approaches to Drug Discovery for Cancer and Neglected Tropical Diseases. ACTA ACUST UNITED AC 2018; 90:645-661. [DOI: 10.1590/0001-3765201820170505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022]
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Naveja JJ, Oviedo-Osornio CI, Trujillo-Minero NN, Medina-Franco JL. Chemoinformatics: a perspective from an academic setting in Latin America. Mol Divers 2017; 22:247-258. [PMID: 29204824 DOI: 10.1007/s11030-017-9802-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/26/2017] [Indexed: 12/13/2022]
Abstract
This perspective discusses the current progress of a chemoinformatics group in a major university in Latin America. Three major aspects are discussed in a critical manner: research, education, and collaboration with industry and other public research networks. It is also presented an overview of the progress in applied research and development of research concepts. Efforts to teach chemoinformatics at the undergraduate and graduate levels are discussed. It is addressed how the partnership with industry and other not-for-profit research institutions not only brings additional sources of funding but, more importantly, increases the impact of the multidisciplinary work and offers the students to be exposed to other research environments. We also discuss the main perspectives and challenges that remain to be addressed in these settings.
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Affiliation(s)
- J Jesús Naveja
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico.,PECEM, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico
| | - C Iluhí Oviedo-Osornio
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico
| | - Nicole N Trujillo-Minero
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico
| | - José L Medina-Franco
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510, Mexico City, Mexico.
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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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Ferreira LG, Andricopulo AD. Targeting cysteine proteases in trypanosomatid disease drug discovery. Pharmacol Ther 2017; 180:49-61. [PMID: 28579388 DOI: 10.1016/j.pharmthera.2017.06.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Chagas disease and human African trypanosomiasis are endemic conditions in Latin America and Africa, respectively, for which no effective and safe therapy is available. Efforts in drug discovery have focused on several enzymes from these protozoans, among which cysteine proteases have been validated as molecular targets for pharmacological intervention. These enzymes are expressed during the entire life cycle of trypanosomatid parasites and are essential to many biological processes, including infectivity to the human host. As a result of advances in the knowledge of the structural aspects of cysteine proteases and their role in disease physiopathology, inhibition of these enzymes by small molecules has been demonstrated to be a worthwhile approach to trypanosomatid drug research. This review provides an update on drug discovery strategies targeting the cysteine peptidases cruzain from Trypanosoma cruzi and rhodesain and cathepsin B from Trypanosoma brucei. Given that current chemotherapy for Chagas disease and human African trypanosomiasis has several drawbacks, cysteine proteases will continue to be actively pursued as valuable molecular targets in trypanosomatid disease drug discovery efforts.
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Affiliation(s)
- Leonardo G Ferreira
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil
| | - Adriano D Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Avenida João Dagnone 1100, São Carlos, SP 13563-120, Brazil.
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45
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Molecular modeling and structure-activity relationships for a series of benzimidazole derivatives as cruzain inhibitors. Future Med Chem 2017; 9:641-657. [PMID: 28509592 DOI: 10.4155/fmc-2016-0236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIM Chagas disease is endemic in Latin America and no effective treatment is available. Efforts in drug research have focused on several enzymes from Trypanosoma cruzi, among which cruzain is a validated pharmacological target. METHODOLOGY Chemometric analyses were performed on the data set using the hologram quantitative structure-activity relationship, comparative molecular field analysis and comparative molecular similarity index analysis methods. Docking simulations were executed using the crystallographic structure of cruzain in complex with a benzimidazole inhibitor. The top-scoring enzyme-inhibitor complexes were selected for the development of the 3D quantitative structure-activity relationship (QSAR) models and to assess the inhibitor binding modes and intermolecular interactions. RESULTS Benzimidazole derivatives as cruzain inhibitors were used in molecular docking and QSAR studies. Significant statistical indicators were obtained, and the best models demonstrated high predictive ability for an external test set (r 2pred = 0.65, 0.94 and 0.82 for hologram QSAR, comparative molecular field analysis and comparative molecular similarity index analysis, respectively). Additionally, the graphical information of the chemometric analyses demonstrated substantial complementarity with the enzyme-binding site. CONCLUSION These results demonstrate the relevance of the QSAR models to guide the design of structurally related benzimidazole derivatives with improved potency.
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da Silva EB, Oliveira E Silva DA, Oliveira AR, da Silva Mendes CH, Dos Santos TAR, da Silva AC, de Castro MCA, Ferreira RS, Moreira DRM, Cardoso MVDO, de Simone CA, Pereira VRA, Leite ACL. Desing and synthesis of potent anti-Trypanosoma cruzi agents new thiazoles derivatives which induce apoptotic parasite death. Eur J Med Chem 2017; 130:39-50. [PMID: 28242550 DOI: 10.1016/j.ejmech.2017.02.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/28/2022]
Abstract
Chagas disease, caused by the kinetoplastid protozoan parasite Trypanosoma cruzi, remains a relevant cause of illness and premature death and it is estimated that 6 million to 7 million people are infected worldwide. Although chemotherapy options are limited presenting serious problems, such as low efficacy and high toxicity. T. cruzi is susceptible to thiazoles, making this class of compounds appealing for drug development. Previously, thiazoles resulted in an increase in anti-T. cruzi activity in comparison to thiosemicarbazones. Here, we report the structural planning, synthesis and anti-T. cruzi evaluation of new thiazoles derivatives (3a-m and 4a-m), designed from molecular hybridization associated with non-classical bioisosterism. By varying substituents attached to the phenyl and thiazole rings, substituents were observed to retain, enhance or greatly increase their anti-T. cruzi activity, in comparison to the corresponding thiosemicarbazones. In most cases, electron-withdrawing substituents, such as bromine, 3,4-dichloro and nitro groups, greatly increased antiparasitic activity. Specifically, new thiazoles were identified that inhibit the epimastigote proliferation and were toxic for trypomastigotes without affecting macrophages viability. These compounds were also evaluated against cruzain. However, inhibition of this enzyme was not observed, suggesting that the compounds work through another mechanism. In addition, examination of T. cruzi cell death showed that these molecules induce apoptosis. In conclusion, except for compounds 3h and 3k, all thiazoles derivatives evaluated exhibited higher cytotoxic activity against the trypomastigote forms than the reference medicament benznidazole, without affecting macrophages viability. Compounds 4d and 4k were highlights, CC50 = 1.2 e 1.6 μM, respectively. Mechanistically, these compounds do not inhibit the cruzain, but induce T. cruzi cell death by an apoptotic process, being considered a good starting point for the development of new anti-Chagas drug candidates.
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Affiliation(s)
- Elany Barbosa da Silva
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil; Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | | | - Arsênio Rodrigues Oliveira
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil
| | - Carlos Henrique da Silva Mendes
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil
| | | | | | - Maria Carolina Acioly de Castro
- Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, 50670-420, Recife, PE, Brazil; Laboratório de Parasitologia, Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, 55608-680, Vitória de Santo Antão, PE, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | | | | | - Carlos Alberto de Simone
- Departamento de Física e Informática, Instituto de Física, Universidade de São Paulo, CEP 13560-970, São Carlos, SP, Brazil
| | | | - Ana Cristina Lima Leite
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil.
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Ueno A, Takimoto M, Hou Z. Synthesis of 2-aryloxy butenoates by copper-catalysed allylic C–H carboxylation of allyl aryl ethers with carbon dioxide. Org Biomol Chem 2017; 15:2370-2375. [DOI: 10.1039/c7ob00341b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
2-Aryloxy butenoates were efficiently synthesized by deprotonative alumination of ally aryl ethers and subsequent Cu-catalysed carboxylation with CO2.
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Affiliation(s)
- Atsushi Ueno
- Advanced Catalysis Research Group
- RIKEN Center for Sustainable Resource Science
- Wako
- Japan
| | - Masanori Takimoto
- Advanced Catalysis Research Group
- RIKEN Center for Sustainable Resource Science
- Wako
- Japan
- Organometallic Chemistry Laboratory
| | - Zhaomin Hou
- Advanced Catalysis Research Group
- RIKEN Center for Sustainable Resource Science
- Wako
- Japan
- Organometallic Chemistry Laboratory
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48
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Abou-Elkhair RAI, Hassan AEA, Boykin DW, Wilson WD. Lithium Hexamethyldisilazane Transformation of Transiently Protected 4-Aza/Benzimidazole Nitriles to Amidines and their Dimethyl Sulfoxide Mediated Imidazole Ring Formation. Org Lett 2016; 18:4714-7. [PMID: 27607538 DOI: 10.1021/acs.orglett.6b02359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Trimethylsilyl-transient protection successfully allowed the use of lithium hexamethyldisilazane to prepare benzimidazole (BI) and 4-azabenzimidazole (azaBI) amidines from nitriles in 58-88% yields. This strategy offers a much better choice to prepare BI/azaBI amidines than the lengthy, low-yielding Pinner reaction. Synthesis of aza/benzimidazole rings from aromatic diamines and aldehydes was affected in dimethyl sulfoxide in 10-15 min, while known procedures require long time and purification. These methods are important for the BI/azaBI-based drug industry and for developing specific DNA binders for expanded therapeutic applications.
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Affiliation(s)
- Reham A I Abou-Elkhair
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States.,Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Sciences, Zagazig University , Zagazig 44519, Egypt
| | - Abdalla E A Hassan
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Sciences, Zagazig University , Zagazig 44519, Egypt
| | - David W Boykin
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
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Rodriguez JB, Falcone BN, Szajnman SH. Detection and treatment ofTrypanosoma cruzi: a patent review (2011-2015). Expert Opin Ther Pat 2016; 26:993-1015. [DOI: 10.1080/13543776.2016.1209487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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50
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Conti R, Chagas FO, Caraballo-Rodriguez AM, Melo WGDP, do Nascimento AM, Cavalcanti BC, de Moraes MO, Pessoa C, Costa-Lotufo LV, Krogh R, Andricopulo AD, Lopes NP, Pupo MT. Endophytic Actinobacteria from the Brazilian Medicinal Plant Lychnophora ericoides Mart. and the Biological Potential of Their Secondary Metabolites. Chem Biodivers 2016; 13:727-36. [PMID: 27128202 DOI: 10.1002/cbdv.201500225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/14/2016] [Indexed: 12/25/2022]
Abstract
Endophytic actinobacteria from the Brazilian medicinal plant Lychnophora ericoides were isolated for the first time, and the biological potential of their secondary metabolites was evaluated. A phylogenic analysis of isolated actinobacteria was accomplished with 16S rRNA gene sequencing, and the predominance of the genus Streptomyces was observed. All strains were cultured on solid rice medium, and ethanol extracts were evaluated with antimicrobial and cytotoxic assays against cancer cell lines. As a result, 92% of the extracts showed a high or moderate activity against at least one pathogenic microbial strain or cancer cell line. Based on the biological and chemical analyses of crude extracts, three endophytic strains were selected for further investigation of their chemical profiles. Sixteen compounds were isolated, and 3-hydroxy-4-methoxybenzamide (9) and 2,3-dihydro-2,2-dimethyl-4(1H)-quinazolinone (15) are reported as natural products for the first time in this study. The biological activity of the pure compounds was also assessed. Compound 15 displayed potent cytotoxic activity against all four tested cancer cell lines. Nocardamine (2) was only moderately active against two cancer cell lines but showed strong activity against Trypanosoma cruzi. Our results show that endophytic actinobacteria from L. ericoides are a promising source of bioactive compounds.
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Affiliation(s)
- Raphael Conti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Andrés Mauricio Caraballo-Rodriguez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Weilan Gomes da Paixão Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | | | | | | | - Cláudia Pessoa
- Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Fortaleza, CE, Brazil
| | | | - Renata Krogh
- CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Adriano Defini Andricopulo
- CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Norberto Peporine Lopes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil. .,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.
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