1
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Cardoso Prado Martins F, Dos Reis Rocho F, Bonatto V, Henrique Jatai Batista P, Lameira J, Leitão A, Montanari CA. Novel selective proline-based peptidomimetics for human cathepsin K inhibition. Bioorg Med Chem Lett 2024; 110:129887. [PMID: 39002936 DOI: 10.1016/j.bmcl.2024.129887] [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: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Human cathepsin K (CatK) stands out as a promising target for the treatment of osteoporosis, considering its role in degrading the bone matrix. Given the small and shallow S2 subsite of CatK and considering its preference for proline or hydroxyproline, we now propose the rigidification of the leucine fragment found at the P2 position in a dipeptidyl-based inhibitor, generating rigid proline-based analogs. Accordingly, with these new proline-based peptidomimetics inhibitors, we selectively inhibited CatK against other human cathepsins (B, L and S). Among these new ligands, the most active one exhibited a high affinity (pKi = 7.3 - 50.1 nM) for CatK and no inhibition over the other cathepsins. This specific inhibitor harbors two novel substituents never employed in other CatK inhibitors: the trifluoromethylpyrazole and the 4-methylproline at P3 and P2 positions. These results broaden and advance the path toward new potent and selective inhibitors for CatK.
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Affiliation(s)
- Felipe Cardoso Prado Martins
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Fernanda Dos Reis Rocho
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Vinícius Bonatto
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Jerônimo Lameira
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil; Institute of Biological Science, Federal University of Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos/SP, Brazil.
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2
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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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3
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Alves ETM, Pernichelle FG, Nascimento LA, Ferreira GM, Ferreira EI. Covalent Inhibitors for Neglected Diseases: An Exploration of Novel Therapeutic Options. Pharmaceuticals (Basel) 2023; 16:1028. [PMID: 37513939 PMCID: PMC10385647 DOI: 10.3390/ph16071028] [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: 03/24/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Neglected diseases, primarily found in tropical regions of the world, present a significant challenge for impoverished populations. Currently, there are 20 diseases considered neglected, which greatly impact the health of affected populations and result in difficult-to-control social and economic consequences. Unfortunately, for the majority of these diseases, there are few or no drugs available for patient treatment, and the few drugs that do exist often lack adequate safety and efficacy. As a result, there is a pressing need to discover and design new drugs to address these neglected diseases. This requires the identification of different targets and interactions to be studied. In recent years, there has been a growing focus on studying enzyme covalent inhibitors as a potential treatment for neglected diseases. In this review, we will explore examples of how these inhibitors have been used to target Human African Trypanosomiasis, Chagas disease, and Malaria, highlighting some of the most promising results so far. Ultimately, this review aims to inspire medicinal chemists to pursue the development of new drug candidates for these neglected diseases, and to encourage greater investment in research in this area.
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Affiliation(s)
- Erick Tavares Marcelino Alves
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Filipe Gomes Pernichelle
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Lucas Adriano Nascimento
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
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4
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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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5
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Lameiro RF, Montanari CA. Investigating the Lack of Translation from Cruzain Inhibition to Trypanosoma cruzi Activity with Machine Learning and Chemical Space Analyses. ChemMedChem 2023; 18:e202200434. [PMID: 36692246 DOI: 10.1002/cmdc.202200434] [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: 10/06/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023]
Abstract
Chagas disease is a neglected tropical disease caused by the protozoa Trypanosoma cruzi. Cruzain, its main cysteine protease, is commonly targeted in drug discovery efforts to find new treatments for this disease. Even though the essentiality of this enzyme for the parasite has been established, many cruzain inhibitors fail as trypanocidal agents. This lack of translation from biochemical to biological assays can involve several factors, including suboptimal physicochemical properties. In this work, we aim to rationalize this phenomenon through chemical space analyses of calculated molecular descriptors. These include statistical tests, visualization of projections, scaffold analysis, and creation of machine learning models coupled with interpretability methods. Our results demonstrate a significant difference between the chemical spaces of cruzain and T. cruzi inhibitors, with compounds with more hydrogen bond donors and rotatable bonds being more likely to be good cruzain inhibitors, but less likely to be active on T. cruzi. In addition, cruzain inhibitors seem to occupy specific regions of the chemical space that cannot be easily correlated with T. cruzi activity, which means that using predictive modeling to determine whether cruzain inhibitors will be trypanocidal is not a straightforward task. We believe that the conclusions from this work might be of interest for future projects that aim to develop novel trypanocidal compounds.
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Affiliation(s)
- Rafael F Lameiro
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Trabalhador São-Carlense Avenue 400, São Carlos, Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo, Trabalhador São-Carlense Avenue 400, São Carlos, Brazil
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6
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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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7
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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8
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Ramos RS, Borges RS, de Souza JSN, Araujo IF, Chaves MH, Santos CBR. Identification of Potential Antiviral Inhibitors from Hydroxychloroquine and 1,2,4,5-Tetraoxanes Analogues and Investigation of the Mechanism of Action in SARS-CoV-2. Int J Mol Sci 2022; 23:ijms23031781. [PMID: 35163703 PMCID: PMC8836247 DOI: 10.3390/ijms23031781] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
This study aimed to identify potential inhibitors and investigate the mechanism of action on SARS-CoV-2 ACE2 receptors using a molecular modeling study and theoretical determination of biological activity. Hydroxychloroquine was used as a pivot structure and antimalarial analogues of 1,2,4,5 tetraoxanes were used for the construction and evaluation of pharmacophoric models. The pharmacophore-based virtual screening was performed on the Molport® database (~7.9 million compounds) and obtained 313 structures. Additionally, a pharmacokinetic study was developed, obtaining 174 structures with 99% confidence for human intestinal absorption and penetration into the blood-brain barrier (BBB); posteriorly, a study of toxicological properties was realized. Toxicological predictions showed that the selected molecules do not present a risk of hepatotoxicity, carcinogenicity, mutagenicity, and skin irritation. Only 54 structures were selected for molecular docking studies, and five structures showed binding affinity (ΔG) values satisfactory for ACE2 receptors (PDB 6M0J), in which the molecule MolPort-007-913-111 had the best ΔG value of -8.540 Kcal/mol, followed by MolPort-002-693-933 with ΔG = -8.440 Kcal/mol. Theoretical determination of biological activity was realized for 54 structures, and five molecules showed potential protease inhibitors. Additionally, we investigated the Mpro receptor (6M0K) for the five structures via molecular docking, and we confirmed the possible interaction with the target. In parallel, we selected the TopsHits 9 with antiviral potential that evaluated synthetic accessibility for future synthesis studies and in vivo and in vitro tests.
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Affiliation(s)
- Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Correspondence: (R.S.R.); (C.B.R.S.)
| | - Rosivaldo S. Borges
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Graduate Program on Medicinal Chemistry and Molecular Modeling, Institute of Health Science, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Inana F. Araujo
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Binational Campus, Federal University of Amapá, Oiapoque 68980-000, AP, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
- Correspondence: (R.S.R.); (C.B.R.S.)
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9
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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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10
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Xiong X, Tang N, Lai X, Zhang J, Wen W, Li X, Li A, Wu Y, Liu Z. Insights Into Amentoflavone: A Natural Multifunctional Biflavonoid. Front Pharmacol 2022; 12:768708. [PMID: 35002708 PMCID: PMC8727548 DOI: 10.3389/fphar.2021.768708] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Amentoflavone is an active phenolic compound isolated from Selaginella tamariscina over 40 years. Amentoflavone has been extensively recorded as a molecule which displays multifunctional biological activities. Especially, amentoflavone involves in anti-cancer activity by mediating various signaling pathways such as extracellular signal-regulated kinase (ERK), nuclear factor kappa-B (NF-κB) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), and emerges anti-SARS-CoV-2 effect via binding towards the main protease (Mpro/3CLpro), spike protein receptor binding domain (RBD) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Therefore, amentoflavone is considered to be a promising therapeutic agent for clinical research. Considering the multifunction of amentoflavone, the current review comprehensively discuss the chemistry, the progress in its diverse biological activities, including anti-inflammatory, anti-oxidation, anti-microorganism, metabolism regulation, neuroprotection, radioprotection, musculoskeletal protection and antidepressant, specially the fascinating role against various types of cancers. In addition, the bioavailability and drug delivery of amentoflavone, the molecular mechanisms underlying the activities of amentoflavone, the molecular docking simulation of amentoflavone through in silico approach and anti-SARS-CoV-2 effect of amentoflavone are discussed.
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Affiliation(s)
- Xifeng Xiong
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Nan Tang
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Xudong Lai
- Department of Infectious Disease, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Jinli Zhang
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Weilun Wen
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Xiaojian Li
- Department of Burn and Plastic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Aiguo Li
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Yanhua Wu
- Department of Traditional Chinese Medicine, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
| | - Zhihe Liu
- Guangzhou Institute of Traumatic Surgery, Guangzhou Red Cross Hospital, Jinan University, Guangzhou, China
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11
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Bonatto V, Shamim A, Rocho FDR, Leitão A, Luque FJ, Lameira J, Montanari CA. Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations. J Chem Inf Model 2021; 61:4733-4744. [PMID: 34460252 DOI: 10.1021/acs.jcim.1c00515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covalent inhibitors are assuming central importance in drug discovery projects, especially in this pandemic scenario. Many research groups have focused their attention on inhibiting viral proteases or human proteases such as cathepsin L (hCatL). The inhibition of these critical enzymes may impair viral replication. However, molecular modeling of covalent ligands is challenging since covalent and noncovalent ligand-bound states must be considered in the binding process. In this work, we evaluated the suitability of free energy perturbation (FEP) calculations as a tool for predicting the binding affinity of reversible covalent inhibitors of hCatL. Our strategy relies on the relative free energy calculated for both covalent and noncovalent complexes and the free energy changes have been compared with experimental data for eight nitrile-based inhibitors, including three new inhibitors of hCatL. Our results demonstrate that the covalent complex can be employed to properly rank the inhibitors. Nevertheless, a comparison of the free energy changes in both noncovalent and covalent states is valuable to interpret the effect triggered by the formation of the covalent bond on the interactions played by functional groups distant from the warhead. Overall, FEP can be employed as a powerful predictor tool in developing and understanding the activity of reversible covalent inhibitors.
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Affiliation(s)
- Vinícius Bonatto
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Anwar Shamim
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Fernanda Dos R Rocho
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain
| | - Jerônimo Lameira
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil.,Institute of Biological Science, Federal University of Pará, Rua Augusto Correa S/N, 66075-110 Belém, Pará, Brazil
| | - Carlos A Montanari
- Medicinal & Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
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12
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Alves L, Santos DA, Cendron R, Rocho FR, Matos TKB, Leitão A, Montanari CA. Nitrile-based peptoids as cysteine protease inhibitors. Bioorg Med Chem 2021; 41:116211. [PMID: 33991733 DOI: 10.1016/j.bmc.2021.116211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
Peptidomimetics of the class of dipeptidyl nitrile analog peptoids were synthesized as inhibitors of mammalian cysteine proteases of the papain superfamily. The dipeptidyl nitrile side chains were attached to the peptide backbone's nitrogen atom, not to the α-carbons. Synthesized nitrile-based peptoid analogs that lack the hydrogen amide at P2-P3 are responsible for many of the secondary structure elements in peptides and proteins, making them resistant to proteolysis. The designed peptoids would lose a hydrogen bond with cruzain Asp161 decreasing the affinity toward the enzyme. A structure-activity relationship and matched molecular pair-based analysis between the dipeptidyl nitrile Neq0409 and its peptoid 4a yielded the following cruzain affinities: pKiNeq0409 = 6.5 and pKi4a = 5.2. respectively. A retrosynthetic matched molecular pair cliff (RMMP-cliff) analysis with a ΔpKiNeq0409-4a of 1.3 log is found for this transformation. These novel peptoids were then optimized, leading to compound 4i, with high cruzain inhibition (pKi = 6.8). Cross-class cathepsin activity was observed for some of these novel compounds against cathepsins K, L and S, while other compounds presented a selective inhibition of cathepsin K (4b, 4c, 4k) over ten times higher than the other enzymes. The putative mode of binding was determined by using covalent docking, which also aided to describe the structure-activity relationship (SAR). Interestingly, none of the peptoids inhibited CatB to any appreciable extent. These results provide guidance to identify novel bioactive nitrile-based peptoids.
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Affiliation(s)
- Luana Alves
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Deborah A Santos
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil.
| | - Rodrigo Cendron
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Fernanda R Rocho
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Thiago K B Matos
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil.
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
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13
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Marinho MM, Almeida-Neto FWQ, Marinho EM, da Silva LP, Menezes RR, dos Santos RP, Marinho ES, de Lima-Neto P, Martins AM. Quantum computational investigations and molecular docking studies on amentoflavone. Heliyon 2021; 7:e06079. [PMID: 33553750 PMCID: PMC7851790 DOI: 10.1016/j.heliyon.2021.e06079] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 01/02/2023] Open
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, with approximately 6-7 million people infected worldwide, becoming a public health problem in tropical countries, thus generating an increasing demand for the development of more effective drugs, due to the low efficiency of the existing drugs. Aiming at the development of a new antichagasic pharmacological tool, the density functional theory was used to calculate the reactivity descriptors of amentoflavone, a biflavonoid with proven anti-trypanosomal activity in vitro, as well as to perform a study of interactions with the enzyme cruzain, an enzyme key in the evolutionary process of T-cruzi. Structural properties (in solvents with different values of dielectric constant), the infrared spectrum, the frontier orbitals, Fukui analysis, thermodynamic properties were the parameters calculated from DFT method with the monomeric structure of the apigenin used for comparison. Furthermore, molecular docking studies were performed to assess the potential use of this biflavonoid as a pharmacological antichagasic tool. The frontier orbitals (HOMO-LUMO) study to find the band gap of compound has been extended to calculate electron affinity, ionization energy, electronegativity electrophilicity index, chemical potential, global chemical hardness and global chemical softness to study the chemical behaviour of compound. The optimized structure was subjected to molecular Docking to characterize the interaction between amentoflavone and cruzain enzyme, a classic pharmacological target for substances with anti-gas activity, where significant interactions were observed with amino acid residues from each one's catalytic sites enzyme. These results suggest that amentoflavone has the potential to interfere with the enzymatic activity of cruzain, thus being an indicative of being a promising antichagasic agent.
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Affiliation(s)
- Márcia M. Marinho
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
| | - Francisco Wagner Q. Almeida-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Emanuelle M. Marinho
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Leonardo P. da Silva
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Ramon R.P.P.B. Menezes
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
| | - Ricardo P. dos Santos
- Engenharia de Computação / Biotecnologia, Universidade Federal do Ceará, Campus de Sobral, 62010-560, Sobral Ceará, Brazil
| | - Emmanuel S. Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, 62930-000, Limoeiro do Norte, Ceará, Brazil
| | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Centro de Ciências, Universidade Federal do Ceará, Campus do Pici, Bloco 940, 60440-900, Fortaleza, Ceará, Brazil
| | - Alice M.C. Martins
- Departamento de Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Federal do Ceará, Campus Porangabussu, 60430-370, Fortaleza, Ceará, Brazil
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14
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Design, synthesis and stepwise optimization of nitrile-based inhibitors of cathepsins B and L. Bioorg Med Chem 2021; 29:115827. [PMID: 33254069 DOI: 10.1016/j.bmc.2020.115827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Human cathepsin B (CatB) is an important biological target in cancer therapy. In this work, we performed a knowledge-based design approach and the synthesis of a new set of 19 peptide-like nitrile-based cathepsin inhibitors. Reported compounds were assayed against a panel of human cysteine proteases: CatB, CatL, CatK, and CatS. Three compounds (7h, 7i, and 7j) displayed nanomolar inhibition of CatB and selectivity over CatK and CatL. The selectivity was achieved by using the combination of a para biphenyl ring at P3, halogenated phenylalanine in P2 and Thr-O-Bz group at P1. Likewise, compounds 7i and 7j showed selective CatB inhibition among the panel of enzymes studied. We have also described a successful example of bioisosteric replacement of the amide bond for a sulfonamide one [7e → 6b], where we observed an increase in affinity and selectivity for CatB while lowering the compound lipophilicity (ilogP). Our knowledge-based design approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cathepsins.
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15
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Ribeiro JFR, Cianni L, Li C, Warwick TG, de Vita D, Rosini F, Dos Reis Rocho F, Martins FCP, Kenny PW, Lameira J, Leitão A, Emsley J, Montanari CA. Crystal structure of Leishmania mexicana cysteine protease B in complex with a high-affinity azadipeptide nitrile inhibitor. Bioorg Med Chem 2020; 28:115743. [PMID: 33038787 DOI: 10.1016/j.bmc.2020.115743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 11/19/2022]
Abstract
Leishmania mexicana is an obligate intracellular protozoan parasite that causes the cutaneous form of leishmaniasis affecting South America and Mexico. The cysteine protease LmCPB is essential for the virulence of the parasite and therefore, it is an appealing target for antiparasitic therapy. A library of nitrile-based cysteine protease inhibitors was screened against LmCPB to develop a treatment of cutaneous leishmaniasis. Several compounds are sufficiently high-affinity LmCPB inhibitors to serve both as starting points for drug discovery projects and as probes for target validation. A 1.4 Å X ray crystal structure, the first to be reported for LmCPB, was determined for the complex of this enzyme covalently bound to an azadipeptide nitrile ligand. Mapping the structure-activity relationships for LmCPB inhibition revealed superadditive effects for two pairs of structural transformations. Therefore, this work advances our understanding of azadipeptidyl and dipeptidyl nitrile structure-activity relationships for LmCPB structure-based inhibitor design. We also tested the same series of inhibitors on related cysteine proteases cathepsin L and Trypanosoma cruzi cruzain. The modulation of these mammalian and protozoan proteases represents a new framework for targeting papain-like cysteine proteases.
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Affiliation(s)
- Jean F R Ribeiro
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Lorenzo Cianni
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Chan Li
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Thomas G Warwick
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Daniela de Vita
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Fabiana Rosini
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Fernanda Dos Reis Rocho
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Felipe C P Martins
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Peter W Kenny
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Jeronimo Lameira
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil; Laboratory of Design and Development of Pharmaceuticals, Federal University of Pará, Belém, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil
| | - Jonas Emsley
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, Brazil.
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16
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Quilles JC, Shamim A, Tezuka DY, Batista PHJ, Lopes CD, de Albuquerque S, Montanari CA, Leitão A. Dipeptidyl nitrile derivatives suppress the Trypanosoma cruzi in vitro infection. Exp Parasitol 2020; 219:108032. [PMID: 33137308 DOI: 10.1016/j.exppara.2020.108032] [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] [Received: 01/12/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022]
Abstract
Chagas disease affects several countries around the world with health and sanitation problems. Cysteine proteases are essential for the virulence and replication of the Trypanosoma cruzi, being modulated by dipeptidyl nitriles and derivatives. Here, four dipeptidyl nitrile derivatives were assayed in three T. cruzi morphologies and two strains (Tulahuen and Y) using a set of assays: (i) analysis of the inhibitory activity against cysteine proteases; (ii) determination of the cytotoxic activity and selectivity index; (iii) verification of the inhibition of the trypomastigote invasion in the host cell. These compounds could inhibit the activity of cysteine proteases using the selective substrate Z-FR-MCA for the trypomastigote lysate and extracellular amastigotes. Interestingly, these compounds did not present relevant enzymatic inhibition for the epimastigote lysate. Most of the substances were also cytotoxic and selective against the trypomastigotes and intracellular amastigotes. The best compound of the series (Neq0662) could reduce the enzymatic activity of the cysteine proteases for the trypomastigotes and amastigotes. It was equipotent to the benznidazole drug in the cytotoxic studies using these two parasite forms. Neq0662 was also selective for the parasite, and it inhibited the invasion of the mammalian host cell in all conditions tested at 10 μM. The stereochemistry of the trifluoromethyl group was an important factor for the bioactivity when the two diastereomers (Neq0662 and Neq0663) were compared. All-in-all, these results indicate that these compounds could move further in the drug development stage because of its promising bioactive profile.
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Affiliation(s)
- José C Quilles
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil.
| | - Anwar Shamim
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil.
| | - Daiane Y Tezuka
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Interunidades em Bioengenharia - PPGIB-USP, Brazil.
| | - Pedro H J Batista
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil.
| | - Carla D Lopes
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil; Programa de Pós-Graduação Interunidades em Bioengenharia - PPGIB-USP, Brazil.
| | - Sérgio de Albuquerque
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.
| | - Carlos A Montanari
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil.
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), São Carlos, São Paulo, Brazil.
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17
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de Albuquerque S, Cianni L, de Vita D, Duque C, Gomes ASM, Gomes P, Laughton C, Leitão A, Montanari CA, Montanari R, Ribeiro JFR, da Silva JS, Teixeira C. Molecular design aided by random forests and synthesis of potent trypanocidal agents as cruzain inhibitors for Chagas disease treatment. Chem Biol Drug Des 2020; 96:948-960. [PMID: 33058457 DOI: 10.1111/cbdd.13663] [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: 09/30/2019] [Revised: 12/13/2019] [Accepted: 12/23/2019] [Indexed: 11/30/2022]
Abstract
Cruzain is an established target for the identification of novel trypanocidal agents, but how good are in vitro/in vivo correlations? This work describes the development of a random forests model for the prediction of the bioavailability of cruzain inhibitors that are Trypanosoma cruzi killers. Some common properties that characterize drug-likeness are poorly represented in many established cruzain inhibitors. This correlates with the evidence that many high-affinity cruzain inhibitors are not trypanocidal agents against T. cruzi. On the other hand, T. cruzi killers that present typical drug-like characteristics are likely to show better trypanocidal action than those without such features. The random forests model was not outperformed by other machine learning methods (such as artificial neural networks and support vector machines), and it was validated with the synthesis of two new trypanocidal agents. Specifically, we report a new lead compound, Neq0565, which was tested on T. cruzi Tulahuen (β-galactosidase) with a pEC50 of 4.9. It is inactive in the host cell line showing a selectivity index (SI = EC50 cyto /EC50 T. cruzi ) higher than 50.
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Affiliation(s)
- Sérgio de Albuquerque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Lorenzo Cianni
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Daniela de Vita
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Carla Duque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ana S M Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Andrei Leitão
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Carlos A Montanari
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - Raphael Montanari
- Centro de Robótica de São Carlos, EESC-ICMC, Universidade de São Paulo, São Paulo, Brazil
| | - Jean F R Ribeiro
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos/SP, Brazil
| | - João Santana da Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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18
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Matos TKB, Batista PHJ, Dos Reis Rocho F, de Vita D, Pearce N, Kellam B, Montanari CA, Leitão A. Synthesis and matched molecular pair analysis of covalent reversible inhibitors of the cysteine protease CPB. Bioorg Med Chem Lett 2020; 30:127439. [PMID: 32717373 DOI: 10.1016/j.bmcl.2020.127439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/30/2023]
Abstract
Cysteine protease B (CPB) can be targeted by reversible covalent inhibitors that could serve as antileishmanial compounds. Here, sixteen dipeptidyl nitrile derivatives were synthesized, tested against CPB, and analyzed using matched molecular pairs to determine the effects of stereochemistry and p-phenyl substitution on enzyme inhibition. The compound (S)-2-(((S)-1-(4-bromophenyl)-2,2,2-trifluoroethyl)amino)-N-(1-cyanocyclopropyl)-3-phenylpropanamide (5) was the most potent CPB inhibitor (pKi = 6.82), which was also selective for human cathepsin B (pKi < 5). The inversion of the stereochemistry from S to R was more detrimental to potency when placed at the P2 position than at P3. The p-Br derivatives were more potent than the p-CH3 and p-OCH3 derivatives, probably due to intermolecular interactions with the S3 subsite.
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Affiliation(s)
- Thiago Kelvin Brito Matos
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil
| | - Fernanda Dos Reis Rocho
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil
| | - Daniela de Vita
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil
| | - Nicholas Pearce
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Barrie Kellam
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Carlos Alberto Montanari
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry-University of São Paulo (IQSC-USP), São Carlos, SP, Brazil.
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19
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Bonatto V, Batista PHJ, Cianni L, De Vita D, Silva DG, Cedron R, Tezuka DY, de Albuquerque S, Moraes CB, Franco CH, Lameira J, Leitão A, Montanari CA. On the intrinsic reactivity of highly potent trypanocidal cruzain inhibitors. RSC Med Chem 2020; 11:1275-1284. [PMID: 34095840 DOI: 10.1039/d0md00097c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. Hence, peptidomimetic cruzipain inhibitors having a reactive group (known as warhead) are subject to continuous studies to discover novel antichagasic compounds. Here, we evaluated how different warheads for a set of structurally similar related compounds could inhibit the activity of cruzipain and, ultimately, their trypanocidal effect. We first investigated in silico the intrinsic reactivity of these compounds by applying the Fukui index to correlate it with the enzymatic affinity. Then, we evaluated their potency against T. cruzi (Y and Tulahuen strains), which revealed the reversible cruzain inhibitor Neq0656 as a better trypanocidal agent (ECY.strain 50 = 0.1 μM; SI = 58.4) than the current drug benznidazole (ECY.strain 50 = 5.1 μM; SI > 19.6). We also measured the half-life time by HPLC analysis of three lead compounds in the presence of glutathione and cysteine to experimentally assess their intrinsic reactivity. Results clearly illustrated the reactivity trend for the warheads (azanitrile > aldehyde > nitrile), where the aldehyde displayed an intermediate intrinsic reactivity. Therefore, the aldehyde bearing peptidomimetic compounds should be subject for in-depth evaluation in the drug discovery process.
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Affiliation(s)
- Vinicius Bonatto
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Lorenzo Cianni
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daniela De Vita
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daniel G Silva
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Rodrigo Cedron
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Daiane Y Tezuka
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil .,Ribeirão Preto School of Pharmaceutical Sciences, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - Sérgio de Albuquerque
- Ribeirão Preto School of Pharmaceutical Sciences, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - Carolina Borsoi Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brazil
| | - Caio Haddad Franco
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brazil
| | - Jerônimo Lameira
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil .,Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará Rua Augusto Corrêa 01 CP 66075-110 Belém-PA Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
| | - Carlos A Montanari
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo Avenue Trabalhador Sancarlense, 400 23566-590 São Carlos/SP Brazil
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20
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Optimization strategy of single-digit nanomolar cross-class inhibitors of mammalian and protozoa cysteine proteases. Bioorg Chem 2020; 101:104039. [PMID: 32629285 DOI: 10.1016/j.bioorg.2020.104039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 01/04/2023]
Abstract
Cysteine proteases (CPs) are involved in a myriad of actions that include not only protein degradation, but also play an essential biological role in infectious and systemic diseases such as cancer. CPs also act as biomarkers and can be reached by active-based probes for diagnostic and mechanistic purposes that are critical in health and disease. In this paper, we present the modulation of a CP panel of parasites and mammals (Trypanosoma cruzi cruzain, LmCPB, CatK, CatL and CatS), whose inhibition by nitrile peptidomimetics allowed the identification of specificity and selectivity for a given CP. The activity cliffs identified at the CP inhibition level are useful for retrieving trends through multiple structure-activity relationships. For two of the cruzain inhibitors (10g and 4e), both enthalpy and entropy are favourable to Gibbs binding energy, thus overcoming enthalpy-entropy compensation (EEC). Group contribution of individual molecular modification through changes in enthalpy and entropy results in a separate partition on the relative differences of Gibbs binding energy (ΔΔG). Overall, this study highlights the role of CPs in polypharmacology and multi-target screening, which represents an imperative trend in the actual drug discovery effort.
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21
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Kaur G, Shamim M, Bhardwaj V, Gupta VK, Banerjee B. Mandelic acid catalyzed one-pot three-component synthesis of α-aminonitriles and α-aminophosphonates under solvent-free conditions at room temperature. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1745844] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Gurpreet Kaur
- Department of Chemistry, Indus International University, Una, Himachal Pradesh, India
| | - Mussarat Shamim
- Department of Chemistry, Indus International University, Una, Himachal Pradesh, India
| | - Vaishali Bhardwaj
- Department of Chemistry, Indus International University, Una, Himachal Pradesh, India
| | - Vivek Kumar Gupta
- Post-Graduate Department of Physics, University of Jammu, Jammu, India
| | - Bubun Banerjee
- Department of Chemistry, Indus International University, Una, Himachal Pradesh, India
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22
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Mapping the S1 and S1' subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents. PLoS Negl Trop Dis 2020; 14:e0007755. [PMID: 32163418 PMCID: PMC7067379 DOI: 10.1371/journal.pntd.0007755] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/30/2020] [Indexed: 12/24/2022] Open
Abstract
The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds were designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1´ subsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a Ki smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. Three inhibitors had an EC50 value of ca. 4.0 μM, thus being equipotent to benznidazole according to the antitrypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases.
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23
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da Silva Lima CH, de Araujo Vanelis Soares JC, de Sousa Ribeiro JL, Muri EMF, de Albuquerque S, Dias LRS. Anti-Trypanosoma cruzi Activity and Molecular Docking Studies of 1Hpyrazolo[ 3, 4-b]pyridine Derivatives. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190305141733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Untargeted studies led to the development of some pyrazolopyridine
derivatives for the antiparasitic profile, particularly the derivatives containing the structural
carbohydrazide subunit. In this work, we proceeded in the biological screening of 27 N’- (substitutedphenylmethylene)-
4-carbohydrazide-3-methyl-1-phenyl-1H-pyrazolo[3, 4-b]pyridine derivatives against
T. cruzi as well as the cytotoxic evaluation. To obtain more information about the trypanocidal
activity of this class of compounds, we carried out molecular docking simulations to get an insight
into putative targets in T. cruzi.
Methods:
The assays were evaluated against both trypomastigote and amastigote forms of T. cruzi
and cytotoxicity assays on LLCMK2 cells. The predominant conformational compounds were
analyzed and molecular docking simulations performed.
Results:
The results from trypanocidal activity screening of this series showed that just the
compounds with phenyl group at C-6 position exhibited activity and the N’-4-hydroxyphenylmethylene
derivative presented the best profile against both trypomastigote and amastigote
forms of T. cruzi. Docking simulation results showed that this compound has a binding affinity with
both CYP51 and cruzain targets of T. cruzi.
Conclusion:
Our results indicate that the hydroxyl substituent at the N’-substituted-phenylmethylene
moiety and the phenyl ring at C-6 of 1H-pyrazolo[3,4-b]pyridine system are relevant for the
trypanocidal activity of this class of compounds. Also, docking simulations showed that activity
presented can be related to more than one target of the parasite.
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Affiliation(s)
- Camilo Henrique da Silva Lima
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | | | - Joana Lucius de Sousa Ribeiro
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | - Estela Maris Freitas Muri
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
| | - Sérgio de Albuquerque
- Universidade de Sao Paulo, Departamento de Analises Clinicas, Toxicologicas e Bromatologicas, Av. do Cafe s/n, Ribeirao Preto, SP, 14040-903, Brazil
| | - Luiza Rosaria Sousa Dias
- Laboratório de Quimica Medicinal, Universidade Federal Fluminense, Faculdade de Farmacia, Niteroi, Rio de Janeiro, Brazil
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24
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Arafet K, González FV, Moliner V. Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes. Chemistry 2020; 26:2002-2012. [PMID: 31692123 DOI: 10.1002/chem.201904513] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Indexed: 11/10/2022]
Abstract
In this work a computational study of the mechanism of inhibition of cruzain, rhodesain, and cathepsin L cysteine proteases by the dipeptidyl nitroalkene Cbz-Phe-Ala-CH=CH-NO2 has been carried out by means of molecular dynamics simulations with hybrid QM/MM potentials. The free-energy surfaces confirmed that the inhibition takes place by the formation of a covalent bond between the protein and the β-carbon atom of the inhibitor. According to the results, the tested inhibitor should be a much more efficient inhibitor of cruzain than of rhodesain, and little activity would be expected against cathepsin L, in total correspondence with the available experimental data. The origin of these differences may lie in the different stabilizing electrostatic interactions established between the inhibitor and the residues of the active site and S2 pocket of these enzymes. These results may be useful for the rational design of new dipeptidyl nitroalkenes with higher and more selective inhibitory activity against cysteine proteases.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain
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25
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Nasser AA, Eissa IH, Oun MR, El-Zahabi MA, Taghour MS, Belal A, Saleh AM, Mehany ABM, Luesch H, Mostafa AE, Afifi WM, Rocca JR, Mahdy HA. Discovery of new pyrimidine-5-carbonitrile derivatives as anticancer agents targeting EGFRWT and EGFRT790M. Org Biomol Chem 2020; 18:7608-7634. [DOI: 10.1039/d0ob01557a] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new series of pyrimidine-5-carbonitrile derivatives has been designed as ATP mimicking tyrosine kinase inhibitors of the epidermal growth factor receptor (EGFR).
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26
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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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27
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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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28
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Lameira J, Bonatto V, Cianni L, Dos Reis Rocho F, Leitão A, Montanari CA. Predicting the affinity of halogenated reversible covalent inhibitors through relative binding free energy. Phys Chem Chem Phys 2019; 21:24723-24730. [PMID: 31680132 DOI: 10.1039/c9cp04820k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nitrile reversible covalent inhibitors of human cathepsin L (hCatL) bind covalently to the side chain of the catalytic Cys25 residue in the S1 pocket to form thioimidates. Predicting the binding of reversible covalent inhibitors is essential for their practical application in drug design. In this report, five nitrile-based inhibitors coded Neq0570, Neq0710, Neq0802, Neq0803 and Neq0804 had their hCatL inhibition constants, Ki, determined. These analogs of the prototypical Neq0570 are halogenated reversible covalent inhibitors of hCatL, which bear a halogen atom in the meta position of the P3 benzyl ring that can form a halogen bond with the Gly61 of the hCatL. To describe halogen bonding interaction in an inhibitor-hCatL complex, we applied an extra point (EP) of charge to represent the anisotropic distribution of charge on the iodine, bromine and chlorine atoms. Besides, we have used alchemical free energy calculations for evaluating the overall relative binding free energies of these inhibitors using a two-state binding model: noncovalent and covalent bond states. Our results show that free energy perturbation (FEP) can predict the hCatL binding affinities of halogenated reversible covalent inhibitors in close agreement with experiments.
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Affiliation(s)
- Jerônimo Lameira
- On leave from Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, 66075-110, Belém, PA, Brazil.
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29
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Synthesis and structure-activity relationship of nitrile-based cruzain inhibitors incorporating a trifluoroethylamine-based P2 amide replacement. Bioorg Med Chem 2019; 27:115083. [PMID: 31561938 DOI: 10.1016/j.bmc.2019.115083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 02/02/2023]
Abstract
The structure-activity relationship for nitrile-based cruzain inhibitors incorporating a P2 amide replacement based on trifluoroethylamine was explored by deconstruction of a published series of inhibitors. It was demonstrated that the P3 biphenyl substituent present in the published inhibitor structures could be truncated to phenyl with only a small loss of affinity. The effects of inverting the configuration of the P2 amide replacement and linking a benzyl substituent at P1 were observed to be strongly nonadditive. We show that plotting affinity against molecular size provides a means to visualize both the molecular size efficiency of structural transformations and the nonadditivity in the structure-activity relationship. We also show how the relationship between affinity and lipophilicity, measured by high-performance liquid chromatography with an immobilized artificial membrane stationary phase, may be used to normalize affinity with respect to lipophilicity.
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30
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Quilles JC, Tezuka DY, Lopes CD, Ribeiro FL, Laughton CA, de Albuquerque S, Montanari CA, Leitão A. Dipeptidyl nitrile derivatives have cytostatic effects against Leishmania spp. promastigotes. Exp Parasitol 2019; 200:84-91. [PMID: 30954455 DOI: 10.1016/j.exppara.2019.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 02/14/2019] [Accepted: 04/01/2019] [Indexed: 12/28/2022]
Abstract
Cysteine proteases are involved in critical cell processes to the protozoa from Leishmania genus, and their inhibition is a therapeutic alternative to treat the disease. In this work, derivatives of dipeptidyl nitriles acting as reversible covalent inhibitors of cysteine proteases were studied as cytostatic agents. The proteolytic activity inside the living and lysed parasite cells was quantified using a selective substrate for cysteine proteases (Z-FR-MCA) from Leishmania amazonensis and L. infantum. The overall proteolytic activity of intact cells and even cell extracts was only marginally affected at high concentrations, with the observation of cytostatic activity and cell cycle arrest of promastigotes. However, the cytotoxic effects were only observed for infected J774 macrophages, which impaired further analysis of the amastigote infection. Therefore, the proteolytic inhibition in intact L. amazonensis and L. infantum promastigotes had no relationship to the cytostatic activity, which emphasizes that these dipeptidyl nitriles act through another mechanism of action.
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Affiliation(s)
- José C Quilles
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil.
| | - Daiane Y Tezuka
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil; Programa de Pós-graduação em Bioengenharia, University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, Brazil.
| | - Carla D Lopes
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil; Programa de Pós-graduação em Bioengenharia, University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, Brazil.
| | - Fernanda L Ribeiro
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil.
| | - Charles A Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Sérgio de Albuquerque
- Laboratório de Parasitologia, Falculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP-USP), Ribeirão Preto, SP, Brazil.
| | - Carlos A Montanari
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil.
| | - Andrei Leitão
- Medicinal Chemistry Group (NEQUIMED), São Carlos Institute of Chemistry (IQSC), University of São Paulo (USP), Av. Trabalhador São-carlense, 400, São Carlos, SP, 13.566-590, Brazil.
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31
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Dos Santos AM, Cianni L, De Vita D, Rosini F, Leitão A, Laughton CA, Lameira J, Montanari CA. Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles. Phys Chem Chem Phys 2019; 20:24317-24328. [PMID: 30211406 DOI: 10.1039/c8cp03320j] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chagas disease affects millions of people in Latin America. This disease is caused by the protozoan parasite Trypanossoma cruzi. The cysteine protease cruzain is a key enzyme for the survival and propagation of this parasite lifecycle. Nitrile-based inhibitors are efficient inhibitors of cruzain that bind by forming a covalent bond with this enzyme. Here, three nitrile-based inhibitors dubbed Neq0409, Neq0410 and Neq0570 were synthesized, and the thermodynamic profile of the bimolecular interaction with cruzain was determined using isothermal titration calorimetry (ITC). The result suggests the inhibition process is enthalpy driven, with a detrimental contribution of entropy. In addition, we have used hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) and Molecular Dynamics (MD) simulations to investigate the reaction mechanism of reversible covalent modification of cruzain by Neq0409, Neq0410 and Neq0570. The computed free energy profile shows that the nucleophilic attack of Cys25 on the carbon C1 of inhibitiors and the proton transfer from His162 to N1 of the dipeptidyl nitrile inhibitor take place in a single step. The calculated free energy of the inhibiton reaction is in agreement with covalent experimental binding. Altogether, the results reported here suggests that nitrile-based inhibitors are good candidates for the development of reversible covalent inhibitors of cruzain and other cysteine proteases.
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Affiliation(s)
- Alberto Monteiro Dos Santos
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Cidade Universitária Prof. José da Silveira Netto, Rua Augusto Correa S/N, Belém-PA, Brazil.
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32
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Quilles Junior JC, Carlos FDRR, Montanari A, Leitão A, Mignone VW, Arruda MA, Turyanska L, Bradshaw TD. Apoferritin encapsulation of cysteine protease inhibitors for cathepsin L inhibition in cancer cells. RSC Adv 2019; 9:36699-36706. [PMID: 35539052 PMCID: PMC9075514 DOI: 10.1039/c9ra07161j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/04/2019] [Indexed: 11/21/2022] Open
Abstract
Cysteine proteases play a key role in tumorigenesis causing protein degradation and promoting invasive tumour growth. Cathepsin L is overexpressed in cancer cells and could provide a specific target for delivery of anticancer agents. We encapsulated novel dipeptidyl nitrile based cysteine protease inhibitors (Neq0551, Neq0554 and Neq0568) into biocompatible apoferritin (AFt) protein nanocages to achieve specific delivery to tumours and pH-induced drug release. AFt-encapsulated Neq0554 demonstrated ∼3-fold enhanced in vitro activity (GI50 = 79 μM) compared to naked agent against MiaPaCa-2 pancreatic carcinoma cells. Selectivity for cancer cells was confirmed by comparing their activity to non-tumourigenic human fibroblasts (GI50 > 200 μM). Transferrin receptor (TfR-1) expression, detected only in lysates prepared from carcinoma cells, may contribute to the cancer-selectivity. The G1 cell cycle arrest caused by AFt-Neq0554 resulting in cytostasis was corroborated by clonogenic assays. Superior and more persistent inhibition of cathepsin L up to 80% was achieved with AFt-encapsulated agent in HCT-116 cells following 6 h exposure to 50 μM agent. The selective anticancer activity of AFt-encapsulated cysteine protease inhibitor Neq0554 reported here warrants further preclinical in vivo evaluation. Novel apoferritin encapsulated cysteine protease inhibitors are developed with enhanced and selective uptake by cancer cells, and sustained pH-induced release of the agent. The persistent inhibition of cathepsin L is demonstrated in vitro.![]()
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Affiliation(s)
- José C. Quilles Junior
- Centre for Biomolecular Sciences
- School of Pharmacy
- University of Nottingham
- UK
- Medicinal Chemistry Group (NEQUIMED)
| | | | - A. Montanari
- Medicinal Chemistry Group (NEQUIMED)
- São Carlos Institute of Chemistry (IQSC)
- University of São Paulo
- Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group (NEQUIMED)
- São Carlos Institute of Chemistry (IQSC)
- University of São Paulo
- Brazil
| | | | | | | | - Tracey D. Bradshaw
- Centre for Biomolecular Sciences
- School of Pharmacy
- University of Nottingham
- UK
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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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Cathepsin B: Active site mapping with peptidic substrates and inhibitors. Bioorg Med Chem 2018; 27:1-15. [PMID: 30473362 DOI: 10.1016/j.bmc.2018.10.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 12/11/2022]
Abstract
The potential of papain-like cysteine proteases, such as cathepsin B, as drug discovery targets for systemic human diseases has prevailed over the past years. The development of potent and selective low-molecular cathepsin B inhibitors relies on the detailed expertise on preferred amino acid and inhibitor residues interacting with the corresponding specificity pockets of cathepsin B. Such knowledge might be obtained by mapping the active site of the protease with combinatorial libraries of peptidic substrates and peptidomimetic inhibitors. This review, for the first time, summarizes a wide spectrum of active site mapping approaches. It considers relevant X-ray crystallographic data and discloses propensities towards favorable protein-ligand interactions in case of the therapeutically relevant protease cathepsin B.
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35
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Leveraging the cruzain S3 subsite to increase affinity for reversible covalent inhibitors. Bioorg Chem 2018; 79:285-292. [DOI: 10.1016/j.bioorg.2018.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 01/06/2023]
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36
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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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37
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Hiller NDJ, Silva NAAE, Faria RX, Souza ALA, Resende JALC, Borges Farias A, Correia Romeiro N, de Luna Martins D. Synthesis and Evaluation of the Anticancer and Trypanocidal Activities of Boronic Tyrphostins. ChemMedChem 2018; 13:1395-1404. [PMID: 29856519 DOI: 10.1002/cmdc.201800206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Molecules containing an (cyanovinyl)arene moiety are known as tyrphostins because of their ability to inhibit proteins from the tyrosine kinase family, an interesting target for the development of anticancer and trypanocidal drugs. In the present work, (E)-(cyanovinyl)benzeneboronic acids were synthesized by Knoevenagel condensations without the use of any catalysts in water through a simple protocol that completely avoided the use of organic solvents in the synthesis and workup process. The in vitro anticancer and trypanocidal activities of the synthesized boronic acids were also evaluated, and it was discovered that the introduction of the boronic acid functionality improved the activity of the boronic tyrphostins. In silico target fishing with the use of a chemogenomic approach suggested that tyrosine-phosphorylation-regulated kinase 1a (DYRK1A) was a potential target for some of the designed compounds.
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Affiliation(s)
- Noemi de J Hiller
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
| | - Nayane A A E Silva
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
| | - Robson X Faria
- Laboratory of Toxoplasmosis and other Protozoan Diseases, Oswaldo Cruz Institute (Fiocruz), Brasil
| | - André Luís A Souza
- Laboratory of Biochemistry of Peptides, Oswaldo Cruz Institute (Fiocruz), Brazil
| | - Jackson A L C Resende
- Laboratory of Solid-State Chemistry, Universidade Federal do Mato Grosso, Instituto de Ciências Exatas e da Terra, Campus Universitário do Araguaia, Barra do Garças, MT, 78600-000, Brazil
| | - André Borges Farias
- Núcleo de Pesquisas em Ecologia e Desenvolvimento Social (NUPEM), Universidade Federal do Rio de Janeiro, Campus de Macaé, Av. Rotary Club s/n; São José do Barreto, Macaé, RJ, 27901-000, Brazil
| | - Nelilma Correia Romeiro
- Núcleo de Pesquisas em Ecologia e Desenvolvimento Social (NUPEM), Universidade Federal do Rio de Janeiro, Campus de Macaé, Av. Rotary Club s/n; São José do Barreto, Macaé, RJ, 27901-000, Brazil
| | - Daniela de Luna Martins
- Research Group on Catalysis and Synthesis (CSI), Universidade Federal Fluminense, Laboratório 413, Instituto de Química, Campus do Valonguinho, Centro, Niterói, RJ, 24020-141, Brazil
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Giroud M, Dietzel U, Anselm L, Banner D, Kuglstatter A, Benz J, Blanc JB, Gaufreteau D, Liu H, Lin X, Stich A, Kuhn B, Schuler F, Kaiser M, Brun R, Schirmeister T, Kisker C, Diederich F, Haap W. Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors. J Med Chem 2018; 61:3350-3369. [DOI: 10.1021/acs.jmedchem.7b01869] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Uwe Dietzel
- Rudolf-Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Lilli Anselm
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jörg Benz
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jean-Baptiste Blanc
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Delphine Gaufreteau
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Haixia Liu
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, 720 Cailun Road, Pudong, Shanghai 201203, China
| | - Xianfeng Lin
- Roche Pharma Research and Early Development, Roche Innovation Center Shanghai, 720 Cailun Road, Pudong, Shanghai 201203, China
| | - August Stich
- Department of Tropical Medicine, Medical Mission Institute, Salvatorstrasse 7, 97074 Würzburg, Germany
| | - Bernd Kuhn
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Caroline Kisker
- Rudolf-Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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Giroud M, Kuhn B, Saint-Auret S, Kuratli C, Martin RE, Schuler F, Diederich F, Kaiser M, Brun R, Schirmeister T, Haap W. 2H-1,2,3-Triazole-Based Dipeptidyl Nitriles: Potent, Selective, and Trypanocidal Rhodesain Inhibitors by Structure-Based Design. J Med Chem 2018; 61:3370-3388. [DOI: 10.1021/acs.jmedchem.7b01870] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sarah Saint-Auret
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christoph Kuratli
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Rainer E. Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Wolfgang Haap
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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40
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Kouznetsov VV, Galvis CEP. Strecker reaction and α-amino nitriles: Recent advances in their chemistry, synthesis, and biological properties. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Silva DG, Ribeiro JF, De Vita D, Cianni L, Franco CH, Freitas-Junior LH, Moraes CB, Rocha JR, Burtoloso AC, Kenny PW, Leitão A, Montanari CA. A comparative study of warheads for design of cysteine protease inhibitors. Bioorg Med Chem Lett 2017; 27:5031-5035. [DOI: 10.1016/j.bmcl.2017.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 02/07/2023]
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42
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Brand S, Ko EJ, Viayna E, Thompson S, Spinks D, Thomas M, Sandberg L, Francisco AF, Jayawardhana S, Smith VC, Jansen C, De Rycker M, Thomas J, MacLean L, Osuna-Cabello M, Riley J, Scullion P, Stojanovski L, Simeons FRC, Epemolu O, Shishikura Y, Crouch SD, Bakshi TS, Nixon CJ, Reid IH, Hill AP, Underwood TZ, Hindley SJ, Robinson SA, Kelly JM, Fiandor JM, Wyatt PG, Marco M, Miles TJ, Read KD, Gilbert IH. Discovery and Optimization of 5-Amino-1,2,3-triazole-4-carboxamide Series against Trypanosoma cruzi. J Med Chem 2017; 60:7284-7299. [PMID: 28844141 PMCID: PMC5601362 DOI: 10.1021/acs.jmedchem.7b00463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Chagas’
disease, caused by the protozoan parasite Trypanosoma
cruzi, is the most common cause of cardiac-related
deaths in endemic regions of Latin America. There is an urgent need
for new safer treatments because current standard therapeutic options,
benznidazole and nifurtimox, have significant side effects and are
only effective in the acute phase of the infection with limited efficacy
in the chronic phase. Phenotypic high content screening against the
intracellular parasite in infected VERO cells was used to identify
a novel hit series of 5-amino-1,2,3-triazole-4-carboxamides (ATC).
Optimization of the ATC series gave improvements in potency, aqueous
solubility, and metabolic stability, which combined to give significant
improvements in oral exposure. Mitigation of a potential Ames and hERG liability ultimately led to two promising compounds, one of which demonstrated significant suppression of parasite burden in a mouse model of Chagas’ disease.
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Affiliation(s)
- Stephen Brand
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Eun Jung Ko
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Elisabet Viayna
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Stephen Thompson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Daniel Spinks
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Michael Thomas
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Lars Sandberg
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Amanda F Francisco
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Shiromani Jayawardhana
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Victoria C Smith
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Chimed Jansen
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Manu De Rycker
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - John Thomas
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Lorna MacLean
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Laste Stojanovski
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Frederick R C Simeons
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Yoko Shishikura
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Sabrinia D Crouch
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Tania S Bakshi
- GlaxoSmithKline , 1250 South Collegeville Road, PO Box 5089, Collegeville, Pennsylvania 19426-0989, United States
| | - Christopher J Nixon
- GlaxoSmithKline , 1250 South Collegeville Road, PO Box 5089, Collegeville, Pennsylvania 19426-0989, United States
| | - Iain H Reid
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alan P Hill
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Tim Z Underwood
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sean J Hindley
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sharon A Robinson
- David Jack Centre for R&D, GlaxoSmithKline , Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
| | - John M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Jose M Fiandor
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Paul G Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Maria Marco
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Timothy J Miles
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Kevin D Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Ian H Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
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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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Burtoloso ACB, de Albuquerque S, Furber M, Gomes JC, Gonçalez C, Kenny PW, Leitão A, Montanari CA, Quilles JC, Ribeiro JFR, Rocha JR. Anti-trypanosomal activity of non-peptidic nitrile-based cysteine protease inhibitors. PLoS Negl Trop Dis 2017; 11:e0005343. [PMID: 28222138 PMCID: PMC5344518 DOI: 10.1371/journal.pntd.0005343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 03/09/2017] [Accepted: 01/21/2017] [Indexed: 11/22/2022] Open
Abstract
The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. Anti-trypanosomal activity against the CL Brener strain of T. cruzi was observed in the 0.1 μM to 1 μM range for three nitrile-based cysteine protease inhibitors based on two scaffolds known to be associated with cathepsin K inhibition. The two compounds showing the greatest potency against the trypanosome were characterized by EC50 values (0.12 μM and 0.25 μM) that were an order of magnitude lower than the corresponding Ki values measured against cruzain, a recombinant form of cruzipain, in an enzyme inhibition assay. This implies that the anti-trypanosomal activity of these two compounds may not be explained only by the inhibition of the cruzain enzyme, thereby triggering a putative polypharmacological profile towards cysteine proteases.
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Affiliation(s)
- Antonio C. B. Burtoloso
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil
| | - Sérgio de Albuquerque
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Juliana C. Gomes
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil
| | - Cristiana Gonçalez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Peter W. Kenny
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Andrei Leitão
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Carlos A. Montanari
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brasil
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - José Carlos Quilles
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Jean F. R. Ribeiro
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Josmar R. Rocha
- Grupo de Estudos em Química Medicinal – NEQUIMED, Instituto de Química de São Carlos – Universidade de São Paulo, São Carlos, São Paulo, Brazil
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Silva DG, Rocha JR, Sartori GR, Montanari CA. Highly predictive hologram QSAR models of nitrile-containing cruzain inhibitors. J Biomol Struct Dyn 2016; 35:3232-3249. [DOI: 10.1080/07391102.2016.1252282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Daniel Gedder Silva
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Josmar Rodrigues Rocha
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
| | - Carlos Alberto Montanari
- Grupo de Química Medicinal, Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP 13566-590, Brazil
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Gold(III) complexes with ONS-Tridentate thiosemicarbazones: Toward selective trypanocidal drugs. Eur J Med Chem 2016; 120:217-26. [PMID: 27191616 DOI: 10.1016/j.ejmech.2016.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 12/11/2022]
Abstract
Tridentate thiosemicarbazone ligands with an ONS donor set, H2L(R) (R = Me and Et) were prepared by reactions of 1-phenyl-1,3-butanedione with 4-R-3-thiosemicarbazides. H2L(R) reacts with Na[AuCl4]·2H2O in MeOH in a 1:1 M ratio under formation of green gold(III) complexes of composition [AuCl(L(R))]. These compounds represent the first examples of gold(III) complexes with ONS chelate-bonded thiosemicarbazones. The in vitro anti-Trypanosoma cruzi activity against both trypomastigote and amastigote forms (IC50try/ama) of CL Brener strains as well as the cytotoxicity against LLC-MK2 cells of the free ligands and complexes was evaluated. The complex [AuCl(L(Me))] was found to be more active and more selective than its precursor ligand and the standard drug benznidazole with a SItry/ama value higher than 200, being considered as a lead candidate for Chagas disease treatment. Moreover the in vitro activity against the replicative amastigote form (IC50ama) of T. cruzi was additionally investigated revealing that [AuCl(L(Me))] was also more potent than benznidazole still with a similar selectivity index. Finally, docking studies showed that free ligands and complexes interact with the same residues of the parasite protease cruzain but with different intensities, suggesting that this protease could be a possible target for the trypanocidal action of the obtained compounds.
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