1
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Prates JLB, Lopes JR, Chin CM, Ferreira EI, Dos Santos JL, Scarim CB. Discovery of Novel Inhibitors of Cruzain Cysteine Protease of Trypanosoma cruzi. Curr Med Chem 2024; 31:2285-2308. [PMID: 37888814 DOI: 10.2174/0109298673254864230921090519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/11/2023] [Accepted: 08/15/2023] [Indexed: 10/28/2023]
Abstract
Chagas disease (CD) is a parasitic disease endemic in several developing countries. According to the World Health Organization, approximately 6-8 million people worldwide are inflicted by CD. The scarcity of new drugs, mainly for the chronic phase, is the main reason for treatment limitation in CD. Therefore, there is an urgent need to discover new targets for which new therapeutical agents could be developed. Cruzain cysteine protease (CCP) is a promising alternative because this enzyme exhibits pleiotropic effects by acting as a virulence factor, modulating host immune cells, and interacting with host cells. This systematic review was conducted to discover new compounds that act as cruzain inhibitors, and their effects in vitro were studied through enzymatic assays and molecular docking. Additionally, the advances and perspectives of these inhibitors are discussed. These findings are expected to contribute to medicinal chemistry in view of the design of new, safe, and efficacious inhibitors against Trypanosoma cruzi CCP detected in the last decade (2013-2022) to provide scaffolds for further optimization, aiming toward the discovery of new drugs.
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Affiliation(s)
- João Lucas Bruno Prates
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Chemistry Institute Araraquara, São Paulo State University (UNESP), SP, Brazil
| | - Juliana Romano Lopes
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Chung Man Chin
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Union of the Colleges of the Great Lakes (UNILAGO), School of Medicine, Advanced Research Center in Medicine, São José do Rio Preto, SP, Brazil
| | - Elizabeth Igne Ferreira
- LAPEN-Laboratory of Design and Synthesis of Chemotherapeutic Agents Potentially Active on Neglected Diseases, Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Jean Leandro Dos Santos
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
- Chemistry Institute Araraquara, São Paulo State University (UNESP), SP, Brazil
| | - Cauê Benito Scarim
- Department of Drugs and Medicine, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, SP, Brazil
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2
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Ng R, Zhang G, Li JJ. An update on the discovery and development of reversible covalent inhibitors. Med Chem Res 2023; 32:1039-1062. [PMID: 37305209 PMCID: PMC10148018 DOI: 10.1007/s00044-023-03065-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023]
Abstract
Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety. Graphical Abstract
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Affiliation(s)
- Raymond Ng
- Olema Oncology, 512 2nd St., 4th Floor, San Francisco, 94107 CA USA
| | - Guiping Zhang
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
| | - Jie Jack Li
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
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3
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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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4
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Lemke C, Jílková A, Ferber D, Braune A, On A, Johe P, Zíková A, Schirmeister T, Mareš M, Horn M, Gütschow M. Two Tags in One Probe: Combining Fluorescence- and Biotin-based Detection of the Trypanosomal Cysteine Protease Rhodesain. Chemistry 2022; 28:e202201636. [PMID: 35852812 PMCID: PMC9826439 DOI: 10.1002/chem.202201636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Indexed: 01/11/2023]
Abstract
Rhodesain is the major cysteine protease of the protozoan parasite Trypanosoma brucei and a therapeutic target for sleeping sickness, a fatal neglected tropical disease. We designed, synthesized and characterized a bimodal activity-based probe that binds to and inactivates rhodesain. This probe exhibited an irreversible mode of action and extraordinary potency for the target protease with a kinac /Ki value of 37,000 M-1 s-1 . Two reporter tags, a fluorescent coumarin moiety and a biotin affinity label, were incorporated into the probe and enabled highly sensitive detection of rhodesain in a complex proteome by in-gel fluorescence and on-blot chemiluminescence. Furthermore, the probe was employed for microseparation and quantification of rhodesain and for inhibitor screening using a competition assay. The developed bimodal rhodesain probe represents a new proteomic tool for studying Trypanosoma pathobiochemistry and antitrypanosomal drug discovery.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Adéla Jílková
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Dominic Ferber
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Annett Braune
- Research Group Intestinal MicrobiologyGerman Institute of Human Nutrition Potsdam-RehbrueckeArthur-Scheunert-Allee 114–11614558NuthetalGermany
| | - Anja On
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Alena Zíková
- Biology Centre CASInstitute of ParasitologyUniversity of South BohemiaFaculty of ScienceBranišovská 1160/3137005České BudějoviceCzech Republic
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Michael Mareš
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Martin Horn
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Michael Gütschow
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
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5
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Brogi S, Ibba R, Rossi S, Butini S, Calderone V, Gemma S, Campiani G. Covalent Reversible Inhibitors of Cysteine Proteases Containing the Nitrile Warhead: Recent Advancement in the Field of Viral and Parasitic Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082561. [PMID: 35458759 PMCID: PMC9029279 DOI: 10.3390/molecules27082561] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/29/2022]
Abstract
In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.
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Affiliation(s)
- Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Roberta Ibba
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Sara Rossi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
- Correspondence:
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
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6
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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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7
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Barbosa da Silva E, Rocha DA, Fortes IS, Yang W, Monti L, Siqueira-Neto JL, Caffrey CR, McKerrow J, Andrade SF, Ferreira RS. Structure-Based Optimization of Quinazolines as Cruzain and TbrCATL Inhibitors. J Med Chem 2021; 64:13054-13071. [PMID: 34461718 DOI: 10.1021/acs.jmedchem.1c01151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cysteine proteases, cruzain and TbrCATL (rhodesain), are therapeutic targets for Chagas disease and Human African Trypanosomiasis, respectively. Among the known inhibitors for these proteases, we have described N4-benzyl-N2-phenylquinazoline-2,4-diamine (compound 7 in the original publication, 1a in this study), as a competitive cruzain inhibitor (Ki = 1.4 μM). Here, we describe the synthesis and biological evaluation of 22 analogs of 1a, containing modifications in the quinazoline core, and in the substituents in positions 2 and 4 of this ring. The analogs demonstrate low micromolar inhibition of the target proteases and cidal activity against Trypanosoma cruzi with up to two log selectivity indices in counterscreens with myoblasts. Fourteen compounds were active against Trypanosoma brucei at low to mid micromolar concentrations. During the optimization of 1a, structure-based design and prediction of physicochemical properties were employed to maintain potency against the enzymes while removing colloidal aggregator characteristics observed for some molecules in this series.
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Affiliation(s)
- Elany Barbosa da Silva
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil.,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Débora A Rocha
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Isadora S Fortes
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Wenqian Yang
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Ludovica Monti
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Jair L Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - James McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0657, United States
| | - Saulo F Andrade
- Pharmaceutical Synthesis Group (PHARSG), Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Pharmaceutical Sciences Graduate Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil.,Graduate Program in Agricultural and Environmental Microbiology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul 90040-060, Brazil
| | - Rafaela S Ferreira
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31270-901, Brazil
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8
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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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9
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Update on relevant trypanosome peptidases: Validated targets and future challenges. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140577. [PMID: 33271348 DOI: 10.1016/j.bbapap.2020.140577] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Trypanosoma cruzi, the agent of the American Trypanosomiasis, Chagas disease, and Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, the agents of Sleeping sickness (Human African Trypanosomiasis, HAT), as well as Trypanosoma brucei brucei, the agent of the cattle disease nagana, contain cysteine, serine, threonine, aspartyl and metallo peptidases. The most abundant among these enzymes are the cysteine proteases from the Clan CA, the Cathepsin L-like cruzipain and rhodesain, and the Cathepsin B-like enzymes, which have essential roles in the parasites and thus are potential targets for chemotherapy. In addition, several other proteases, present in one or both parasites, have been characterized, and some of them are also promising candidates for the developing of new drugs. Recently, new inhibitors, with good selectivity for the parasite proteasomes, have been described and are very promising as lead compounds for the development of new therapies for these neglected diseases. This article is part of a Special Issue entitled: "Play and interplay of proteases in health and disease".
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10
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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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11
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Lemke C, Cianni L, Feldmann C, Gilberg E, Yin J, Dos Reis Rocho F, de Vita D, Bartz U, Bajorath J, Montanari CA, Gütschow M. N-Sulfonyl dipeptide nitriles as inhibitors of human cathepsin S: In silico design, synthesis and biochemical characterization. Bioorg Med Chem Lett 2020; 30:127420. [PMID: 32763808 DOI: 10.1016/j.bmcl.2020.127420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 11/27/2022]
Abstract
A library of cathepsin S inhibitors of the dipeptide nitrile chemotype, bearing a bioisosteric sulfonamide moiety, was synthesized. Kinetic investigations were performed at four human cysteine proteases, i.e. cathepsins S, B, K and L. Compound 12 with a terminal 3-biphenyl sulfonamide substituent was the most potent (Ki = 4.02 nM; selectivity ratio cathepsin S/K = 5.8; S/L = 67) and 24 with a 4'-fluoro-4-biphenyl sulfonamide substituent the most selective cathepsin S inhibitor (Ki = 35.5 nM; selectivity ratio cathepsin S/K = 57; S/L = 31). In silico design and biochemical evaluation emphasized the impact of the sulfonamide linkage on selectivity and a possible switch of P2 and P3 substituents with respect to the occupation of the corresponding binding sites of cathepsin S.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Lorenzo Cianni
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany; Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Christian Feldmann
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Erik Gilberg
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jiafei Yin
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Fernanda Dos Reis Rocho
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Daniela de Vita
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, D-53359 Rheinbach, Germany
| | - Jürgen Bajorath
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany.
| | - Carlos A Montanari
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil.
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany.
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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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