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Adeoye AO, Lobb KA. Malaria parasite cysteine and aspartic proteases as key drug targets for antimalarial therapy. J Mol Model 2025; 31:78. [PMID: 39920505 DOI: 10.1007/s00894-025-06303-0] [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: 10/12/2024] [Accepted: 01/27/2025] [Indexed: 02/09/2025]
Abstract
CONTEXT Cysteine and aspartic proteases are enzyme families that play crucial roles in the life cycle of Plasmodium, the parasite responsible for malaria. These proteases are involved in vital biological processes, such as hemoglobin degradation within the host's red blood cells, protein turnover, and regulation of parasite development. Inhibiting these proteases with small molecule drugs can block the parasite's growth and survival. Chemically, these enzymes have specific active sites where inhibitors can bind, preventing the breakdown of key proteins, making them attractive targets for the design of novel antimalarial compounds. Understanding the structure and catalytic mechanisms of these proteases is critical for developing selective and potent inhibitors. The degradation of hemoglobin occurs in the parasite's digestive vacuole, and disruption of this process by targeting these proteases can inhibit parasite development, leading to the death of the parasite. Hence, these proteases are critical for maintaining the parasite's metabolic functions, and inhibiting them can disrupt the parasite's life cycle. Malaria remains a major global health problem, particularly in tropical and subtropical regions, where resistance to existing antimalarial drugs, such as chloroquine and artemisinin-based therapies, is an escalating issue. The emergence of drug-resistant Plasmodium strains highlights the urgent need for new therapeutic strategies. Targeting cysteine and aspartic proteases offers a novel approach to antimalarial drug development, as these enzymes are crucial for parasite survival and have not been widely exploited in current therapies. By inhibiting these proteases, researchers aim to develop new antimalarial treatments that could overcome resistance mechanisms and provide more effective options for malaria control and eradication. METHODS The application of computational methods such as molecular docking, dynamics simulations, and quantum mechanical calculations, combined with powerful molecular modeling tools, provides a comprehensive framework for discovering and optimizing inhibitors targeting Plasmodium cysteine and aspartic proteases. These methods facilitate the rational design of novel antimalarial drugs, offering a pathway to overcome drug resistance and improve therapeutic outcomes.
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Affiliation(s)
- Akinwunmi O Adeoye
- Biomembrane and Toxicology Unit, Department of Biochemistry, Federal University Oye-Ekiti, Ekiti State, Nigeria.
- Department of Chemistry, Rhodes University, Grahamstown, South Africa.
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
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2
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Uddin A, Gupta S, Shoaib R, Aneja B, Irfan I, Gupta K, Rawat N, Combrinck J, Kumar B, Aleem M, Hasan P, Joshi MC, Chhonker YS, Zahid M, Hussain A, Pandey K, Alajmi MF, Murry DJ, Egan TJ, Singh S, Abid M. Blood-stage antimalarial activity, favourable metabolic stability and in vivo toxicity of novel piperazine linked 7-chloroquinoline-triazole conjugates. Eur J Med Chem 2024; 264:115969. [PMID: 38039787 DOI: 10.1016/j.ejmech.2023.115969] [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: 08/04/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
The persistence of drug resistance poses a significant obstacle to the advancement of efficacious malaria treatments. The remarkable efficacy displayed by 1,2,3-triazole-based compounds against Plasmodium falciparum highlights the potential of triazole conjugates, with diverse pharmacologically active structures, as potential antimalarial agents. We aimed to synthesize 7-dichloroquinoline-triazole conjugates and their structure-activity relationship (SAR) derivatives to investigate their anti-plasmodial activity. Among them, QP11, featuring a m-NO2 substitution, demonstrated efficacy against both chloroquine-sensitive and -resistant parasite strains. QP11 selectively inhibited FP2, a cysteine protease involved in hemoglobin degradation, and showed synergistic effects when combined with chloroquine. Additionally, QP11 hindered hemoglobin degradation and hemozoin formation within the parasite. Metabolic stability studies indicated high stability of QP11, making it a promising antimalarial candidate. In vivo evaluation using a murine malaria model demonstrated QP11's efficacy in eradicating parasite growth without neurotoxicity, presenting it as a promising compound for novel antimalarial development.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sonal Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rumaisha Shoaib
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Babita Aneja
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Iram Irfan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Kanika Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Rawat
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jill Combrinck
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Bhumika Kumar
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India; National Institute of Malaria Research, New Delhi, 110077, India
| | - Mohd Aleem
- Division of Behavioral Neuroscience, Institute of Nuclear Medicine and Allied Sciences, Delhi, 110054, India
| | - Phool Hasan
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mukesh C Joshi
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi, 110007, India
| | - Yashpal S Chhonker
- Department of Pharmacy Practice and Science College of Pharmacy, University of Nebraska Medical Center, 986145, Nebraska Medical Center, Omaha, NE, 68198-6145, USA
| | - Muhammad Zahid
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska Medical Center, 986145, Nebraska Medical Center, Omaha, NE, 68198-6145, USA
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Kailash Pandey
- National Institute of Malaria Research, New Delhi, 110077, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Daryl J Murry
- Department of Pharmacy Practice and Science College of Pharmacy, University of Nebraska Medical Center, 986145, Nebraska Medical Center, Omaha, NE, 68198-6145, USA
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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3
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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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4
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Strumfs B, Velikijs K, Uljanovs R, Sinkarevs S, Strumfa I. Non-Aziridination Approaches to 3-Arylaziridine-2-carboxylic Acid Derivatives and 3-Aryl-(aziridin-2-yl)ketones. Int J Mol Sci 2022; 23:ijms23115919. [PMID: 35682596 PMCID: PMC9180376 DOI: 10.3390/ijms23115919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/14/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Highly functionalized aziridines, including compounds with aromatic moieties, are attractive substrates both in synthetic and medical areas of chemistry. There is a broad and interesting set of synthetic methods for reaching these compounds. Aziridination represents the most explored tool, but there are several other more specific, less well-known, but highly promising approaches. Therefore, the current review focuses on recently described or updated ways to obtain 3-arylated aziridines via different non-aziridination-based synthetic methods, reported mainly since 2000. The presented methods belong to two main directions of synthesis, namely, cyclization of open-chain substrates and rearrangement of other heterocycles. Cyclization of open-chain substrates includes the classic Gabriel-Cromwell type cyclization of halogenated substrates with amines, base-promoted cyclization of activated aminoalcohols (or its analogues), and the oxidative cyclization of β-dicarbonyls. Rearrangements of other heterocycles are presented as the Baldwin rearrangement of 4-isoxazolines, the cycloaddition of 1.3-dipoles or dienes to 2H-azirines, and the addition of C- and N-nucleophiles to the double bond of azirines.
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Affiliation(s)
- Boriss Strumfs
- Latvian Institute of Organic Synthesis, 21 Aizkraukles Street, LV-1006 Riga, Latvia; or
- Department of Pathology, Riga Stradins University, 16 Dzirciema Street, LV-1007 Riga, Latvia; (K.V.); (R.U.); (S.S.)
| | - Kirils Velikijs
- Department of Pathology, Riga Stradins University, 16 Dzirciema Street, LV-1007 Riga, Latvia; (K.V.); (R.U.); (S.S.)
| | - Romans Uljanovs
- Department of Pathology, Riga Stradins University, 16 Dzirciema Street, LV-1007 Riga, Latvia; (K.V.); (R.U.); (S.S.)
| | - Stanislavs Sinkarevs
- Department of Pathology, Riga Stradins University, 16 Dzirciema Street, LV-1007 Riga, Latvia; (K.V.); (R.U.); (S.S.)
| | - Ilze Strumfa
- Department of Pathology, Riga Stradins University, 16 Dzirciema Street, LV-1007 Riga, Latvia; (K.V.); (R.U.); (S.S.)
- Correspondence:
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5
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Singh MK, Lakshman MK. Recent developments in the utility of saturated azaheterocycles in peptidomimetics. Org Biomol Chem 2022; 20:963-979. [PMID: 35018952 DOI: 10.1039/d1ob01329g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To a large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules to modulate conformational flexibility, improve bioavailability, and fine-tune electronics, and in order to achieve potency similar to or better than that of the natural peptide ligand. This mini-review delineates recent developments, limited to the past five years, in the utility of selected saturated 3- to 6-membered heterocyclic moieties in peptidomimetic design. Also discussed is the chemistry involved in the synthesis of the azaheterocyclic scaffolds and the structural implications of the introduction of these azaheterocycles in peptide backbones as well as side chains of the peptide mimics.
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Affiliation(s)
- Manish K Singh
- Department of Science, Technology, and Mathematics, Lincoln University, 820 Chestnut Street, Jefferson City, Missouri 65101, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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6
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Identification of promising inhibitors for Plasmodium haemoglobinase Falcipain-2, using virtual screening, molecular docking, and MD Simulation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Nowak MG, Skwarecki AS, Milewska MJ. Amino Acid Based Antimicrobial Agents - Synthesis and Properties. ChemMedChem 2021; 16:3513-3544. [PMID: 34596961 PMCID: PMC9293202 DOI: 10.1002/cmdc.202100503] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/02/2021] [Indexed: 12/20/2022]
Abstract
Structures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are effective enzyme inhibitors, as structural mimics of tetrahedral transition state intermediates. Synthesis of amino acid antimicrobials is a particular challenge, especially in terms of the need for enantioselective methods, including the asymmetric synthesis. All these issues are addressed in this review, summing up the current state‐of‐the‐art and presenting perspectives fur further progress.
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Affiliation(s)
- Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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8
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Zhu L, Shan L, Zhu J, Li L, Li S, Wang L, Wang J, Zhang S, Zhou H, Zhang W, Li H. Discovery of a natural fluorescent probe targeting the Plasmodium falciparum cysteine protease falcipain-2. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1016-1025. [PMID: 32048162 DOI: 10.1007/s11427-019-1581-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/26/2019] [Indexed: 01/19/2023]
Abstract
The Plasmodium falciparum cysteine protease falcipain-2 (FP-2) is an attractive antimalarial target. Here, we discovered that the natural compound NP1024 is a nonpeptidic inhibitor of FP-2 with an IC50 value of 0.44 μmol L-1. The most exciting finding is that both in vitro and in vivo, NP1024 directly targets FP-2 in malaria parasite-infected erythrocytes as a natural fluorescent probe, thereby paving the way for an integration of malaria diagnosis and treatment.
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Affiliation(s)
- Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lei Shan
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Junsheng Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Li Li
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Liyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiawei Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Shoude Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Hongchang Zhou
- School of Medicine, Huzhou University, Huzhou Central Hospital, Huzhou, 313000, China
| | - Weidong Zhang
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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9
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Design, synthesis and evaluation of 2-(4-(substituted benzoyl)-1,4-diazepan-1-yl)-N-phenylacetamide derivatives as a new class of falcipain-2 inhibitors. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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10
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Asymmetric synthesis and evaluation of epoxy-α-acyloxycarboxamides as selective inhibitors of cathepsin L. Bioorg Med Chem 2017; 25:4620-4627. [DOI: 10.1016/j.bmc.2017.06.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 01/01/2023]
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11
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Roy KK. Targeting the active sites of malarial proteases for antimalarial drug discovery: approaches, progress and challenges. Int J Antimicrob Agents 2017; 50:287-302. [PMID: 28668681 DOI: 10.1016/j.ijantimicag.2017.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/12/2017] [Accepted: 04/27/2017] [Indexed: 02/08/2023]
Abstract
Malaria is an infectious disease causing vast mortality and morbidity worldwide. Although antimalarial drugs are effective in several parts of the world, there is a serious threat to malaria control as malaria parasites are continuously developing widespread resistance against currently available antimalarial drugs, including artemisinin. Such widespread antimalarial drug resistance confirms the need to improve the efficacy of existing or new drugs as well as to develop alternative treatments through the identification of novel drug targets and the development of candidate drugs. Similar to proteases in other parasitic diseases such as leishmaniasis, schistosomiasis, Chagas disease and African sleeping sickness, malarial proteases constitute the major virulence factors in malaria. Malarial proteases belong to several classes and many of them have been targeted for the design and discovery of antimalarial agents. This review summarises the approaches, progress and challenges in the design of small-molecule inhibitors as antimalarial drugs targeting the inhibition of various malarial proteases.
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Affiliation(s)
- Kuldeep K Roy
- National Institute of Pharmaceutical Education and Research (NIPER), 4 Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.
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12
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Musyoka TM, Kanzi AM, Lobb KA, Bishop ÖT. Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow. J Biomol Struct Dyn 2016; 34:2084-101. [PMID: 26471975 PMCID: PMC5035544 DOI: 10.1080/07391102.2015.1108231] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Falcipain-2 (FP-2) and falcipain-3 (FP-3), haemoglobin-degrading enzymes in Plasmodium falciparum, are validated drug targets for the development of effective inhibitors against malaria. However, no commercial drug-targeting falcipains has been developed despite their central role in the life cycle of the parasites. In this work, in silico approaches are used to identify key structural elements that control the binding and selectivity of a diverse set of non-peptidic compounds onto FP-2, FP-3 and homologues from other Plasmodium species as well as human cathepsins. Hotspot residues and the underlying non-covalent interactions, important for the binding of ligands, are identified by interaction fingerprint analysis between the proteases and 2-cyanopyridine derivatives (best hits). It is observed that the size and chemical type of substituent groups within 2-cyanopyridine derivatives determine the strength of protein-ligand interactions. This research presents novel results that can further be exploited in the structure-based molecular-guided design of more potent antimalarial drugs.
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Affiliation(s)
- Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Aquillah M. Kanzi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Kevin A. Lobb
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Department of Chemistry, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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Development of a New Antileishmanial Aziridine-2,3-Dicarboxylate-Based Inhibitor with High Selectivity for Parasite Cysteine Proteases. Antimicrob Agents Chemother 2015; 60:797-805. [PMID: 26596939 DOI: 10.1128/aac.00426-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 11/13/2015] [Indexed: 11/20/2022] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases of the world. Druggable targets are the parasite cysteine proteases (CPs) of clan CA, family C1 (CAC1). In previous studies, we identified two peptidomimetic compounds, the aziridine-2,3-dicarboxylate compounds 13b and 13e, in a series of inhibitors of the cathepsin L (CL) subfamily of the papain clan CAC1. Both displayed antileishmanial activity in vitro while not showing cytotoxicity against host cells. In further investigations, the mode of action was characterized in Leishmania major. It was demonstrated that aziridines 13b and 13e mainly inhibited the parasitic cathepsin B (CB)-like CPC enzyme and, additionally, mammalian CL. Although these compounds induced cell death of Leishmania promastigotes and amastigotes in vitro, the induction of a proleishmanial T helper type 2 (Th2) response caused by host CL inhibition was observed in vivo. Therefore, we describe here the synthesis of a new library of more selective peptidomimetic aziridine-2,3-dicarboxylates discriminating between host and parasite CPs. The new compounds are based on 13b and 13e as lead structures. One of the most promising compounds of this series is compound s9, showing selective inhibition of the parasite CPs LmaCatB (a CB-like enzyme of L. major; also named L. major CPC) and LmCPB2.8 (a CL-like enzyme of Leishmania mexicana) while not affecting mammalian CL and CB. It displayed excellent leishmanicidal activities against L. major promastigotes (50% inhibitory concentration [IC50] = 37.4 μM) and amastigotes (IC50 = 2.3 μM). In summary, we demonstrate a new selective aziridine-2,3-dicarboxylate, compound s9, which might be a good candidate for future in vivo studies.
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14
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Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR. A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection. Antimicrob Agents Chemother 2013; 57:6063-73. [PMID: 24060869 PMCID: PMC3837922 DOI: 10.1128/aac.00734-13] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/16/2013] [Indexed: 02/06/2023] Open
Abstract
Cryptosporidiosis, caused by the protozoan parasite Cryptosporidium parvum, can stunt infant growth and can be lethal in immunocompromised individuals. The most widely used drugs for treating cryptosporidiosis are nitazoxanide and paromomycin, although both exhibit limited efficacy. To investigate an alternative approach to therapy, we demonstrate that the clan CA cysteine protease inhibitor N-methyl piperazine-Phe-homoPhe-vinylsulfone phenyl (K11777) inhibits C. parvum growth in mammalian cell lines in a concentration-dependent manner. Further, using the C57BL/6 gamma interferon receptor knockout (IFN-γR-KO) mouse model, which is highly susceptible to C. parvum, oral or intraperitoneal treatment with K11777 for 10 days rescued mice from otherwise lethal infections. Histologic examination of untreated mice showed intestinal inflammation, villous blunting, and abundant intracellular parasite stages. In contrast, K11777-treated mice (210 mg/kg of body weight/day) showed only minimal inflammation and no epithelial changes. Three putative protease targets (termed cryptopains 1 to 3, or CpaCATL-1, -2, and -3) were identified in the C. parvum genome, but only two are transcribed in infected mammals. A homology model predicted that K11777 would bind to cryptopain 1. Recombinant enzymatically active cryptopain 1 was successfully targeted by K11777 in a competition assay with a labeled active-site-directed probe. K11777 exhibited no toxicity in vitro and in vivo, and surviving animals remained free of parasites 3 weeks after treatment. The discovery that a cysteine protease inhibitor provides potent anticryptosporidial activity in an animal model of infection encourages the investigation and development of this biocide class as a new, and urgently needed, chemotherapy for cryptosporidiosis.
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Affiliation(s)
- Momar Ndao
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Milli Nath-Chowdhury
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Mohammed Sajid
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Leiden University Medical Center, Leiden, Netherlands
| | - Victoria Marcus
- Department of Pathology, McGill University Health Centre, Montreal General Hospital, Montreal, Canada
| | - Susan T. Mashiyama
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Judy Sakanari
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Eric Chow
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Zachary Mackey
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Kirkwood M. Land
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Department of Biological Sciences, University of the Pacific, Stockton, California, USA
| | - Matthew P. Jacobson
- Departments of Pharmaceutical Sciences
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Chakrapani Kalyanaraman
- Departments of Pharmaceutical Sciences
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael J. Arrowood
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases and Department of Pathology, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
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15
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Mugumbate G, Newton AS, Rosenthal PJ, Gut J, Moreira R, Chibale K, Guedes RC. Novel anti-plasmodial hits identified by virtual screening of the ZINC database. J Comput Aided Mol Des 2013; 27:859-71. [PMID: 24158745 DOI: 10.1007/s10822-013-9685-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/12/2013] [Indexed: 01/16/2023]
Abstract
Increased resistance of Plasmodium falciparum to most available drugs challenges the control of malaria. Studies with protease inhibitors have suggested important roles for the falcipain family of cysteine proteases. These enzymes act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. In order to find potential new antimalarial drugs, we screened in silico the ZINC database using two different protocols involving structure- and ligand-based methodologies. Our search identified 19 novel low micromolar inhibitors of cultured chloroquine resistant P. falciparum. The most active compound presented an IC50 value of 0.5 μM against cultured parasites and it also inhibited the cysteine protease falcipain-2 (IC50 = 25.5 μM). These results identify novel classes of antimalarials that are structurally different from those currently in use and which can be further derivatized to deliver leads suitable for optimisation.
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Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
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16
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Batista R, García PA, Castro MA, Miguel Del Corral JM, Speziali NL, de P Varotti F, de Paula RC, García-Fernández LF, Francesch A, San Feliciano A, de Oliveira AB. Synthesis, cytotoxicity and antiplasmodial activity of novel ent-kaurane derivatives. Eur J Med Chem 2012; 62:168-76. [PMID: 23353738 DOI: 10.1016/j.ejmech.2012.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/06/2012] [Accepted: 12/07/2012] [Indexed: 10/27/2022]
Abstract
This paper reports on the syntheses and spectrometric characterisation of eleven novel ent-kaurane diterpenoids, including a complete set of (1)H, (13)C NMR and crystallographic data for two novel ent-kaurane diepoxides. Moreover, the antineoplastic cytotoxicity for kaurenoic acid and the majority of ent-kaurane derivatives were assessed in vitro against a panel of fourteen cancer cell lines, of which allylic alcohols were shown to be the most active compounds. The good in vitro antimalarial activity and the higher selectivity index values observed for some ent-kaurane epoxides against the chloroquine-resistant W2 clone of Plasmodium falciparum indicate that this class of natural products may provide new hits for the development of antimalarial drugs.
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Affiliation(s)
- Ronan Batista
- Departamento de Estudos Básicos e Instrumentais, Universidade Estadual do Sudoeste da Bahia, BR 415, Km 03, s/n°, 45.700-000 Itapetinga, Bahia, Brazil
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17
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On the evolutionary significance of the size and planarity of the proline ring. Naturwissenschaften 2012; 99:789-99. [DOI: 10.1007/s00114-012-0960-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/04/2012] [Accepted: 08/08/2012] [Indexed: 10/27/2022]
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18
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Grazioso G, Legnani L, Toma L, Ettari R, Micale N, De Micheli C. Mechanism of falcipain-2 inhibition by α,β-unsaturated benzo[1,4]diazepin-2-one methyl ester. J Comput Aided Mol Des 2012; 26:1035-43. [PMID: 22965332 PMCID: PMC7088093 DOI: 10.1007/s10822-012-9596-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/27/2012] [Indexed: 01/11/2023]
Abstract
Falcipain-2 (FP-2) is a papain-family cysteine protease of Plasmodium falciparum whose primary function is to degrade the host red cell hemoglobin, within the food vacuole, in order to provide free amino acids for parasite protein synthesis. Additionally it promotes host cell rupture by cleaving the skeletal proteins of the erythrocyte membrane. Therefore, the inhibition of FP-2 represents a promising target in the search of novel anti-malarial drugs. A potent FP-2 inhibitor, characterized by the presence in its structure of the 1,4-benzodiazepine scaffold and an α,β-unsaturated methyl ester moiety capable to react with the Cys42 thiol group located in the active site of FP-2, has been recently reported in literature. In order to study in depth the inhibition mechanism triggered by this interesting compound, we carried out, through ONIOM hybrid calculations, a computational investigation of the processes occurring when the inhibitor targets the enzyme and eventually leads to an irreversible covalent Michael adduct. Each step of the reaction mechanism has been accurately characterized and a detailed description of each possible intermediate and transition state along the pathway has been reported.
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Affiliation(s)
- Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Farmaceutica Pietro Pratesi, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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19
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Langolf S, Machon U, Ehlers M, Sicking W, Schirmeister T, Büchhold C, Gelhaus C, Rosenthal PJ, Schmuck C. Development of Antitrypanosomal and Antiplasmodial Nonpeptidic Cysteine Protease Inhibitors based on N-Protected-Guanidino-Furan and -Pyrrole Building Blocks. ChemMedChem 2011; 6:1581-6. [DOI: 10.1002/cmdc.201100189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Indexed: 11/08/2022]
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20
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Peptidomimetics containing a vinyl ketone warhead as falcipain-2 inhibitors. Eur J Med Chem 2011; 46:2058-65. [DOI: 10.1016/j.ejmech.2011.02.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 02/21/2011] [Accepted: 02/23/2011] [Indexed: 11/23/2022]
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21
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Grabowsky S, Schirmeister T, Paulmann C, Pfeuffer T, Luger P. Effect of electron-withdrawing substituents on the epoxide ring: an experimental and theoretical electron density analysis of a series of epoxide derivatives. J Org Chem 2011; 76:1305-18. [PMID: 21250719 DOI: 10.1021/jo102125n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of acceptor-substituted epoxide derivatives is scrutinized by means of experimental and theoretical electron-density investigations. Due to the possibility of nucleophilic ring-opening, the epoxide ring is not only a very useful functional group in organic synthesis, but acceptor-substituted epoxides are valuable building blocks for the design of protease inhibitors. Therefore, the electron-density analysis in this work focuses on two main aspects that can contribute to rational drug design: (i) the quantification of the electron-withdrawing substituent effects on the epoxide ring and (ii) the intermolecular interactions involving the epoxide ring in combination with different substituents. It can be shown that the electron-withdrawing properties of the substituents cause an elongation of the C-C bonds in the epoxide rings and the loss of electron density can be measured by an analysis of critical points, atomic charges, and the source function. The different strengths of the substituents are reflected in these properties. Covalent and electrostatic contributions to the intermolecular interactions and thus the lattice energies are depicted on different molecular surfaces.
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Affiliation(s)
- Simon Grabowsky
- Freie Universität Berlin, Institut für Chemie und Biochemie/Anorganische Chemie, Fabeckstr. 36a, 14195 Berlin, Germany.
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22
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Ehmke V, Kilchmann F, Heindl C, Cui K, Huang J, Schirmeister T, Diederich F. Peptidomimetic nitriles as selective inhibitors for the malarial cysteine protease falcipain-2. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00115a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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23
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Ehmke V, Heindl C, Rottmann M, Freymond C, Schweizer WB, Brun R, Stich A, Schirmeister T, Diederich F. Potent and selective inhibition of cysteine proteases from Plasmodium falciparum and Trypanosoma brucei. ChemMedChem 2010; 6:273-8. [PMID: 21275051 PMCID: PMC7162187 DOI: 10.1002/cmdc.201000449] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Veronika Ehmke
- Laboratory of Organic Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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24
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Aziridine-2,3-dicarboxylate-based cysteine cathepsin inhibitors induce cell death in Leishmania major associated with accumulation of debris in autophagy-related lysosome-like vacuoles. Antimicrob Agents Chemother 2010; 54:5028-41. [PMID: 20855728 DOI: 10.1128/aac.00327-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The papain-like cysteine cathepsins expressed by Leishmania play a key role in the life cycle of these parasites, turning them into attractive targets for the development of new drugs. We previously demonstrated that two compounds of a series of peptidomimetic aziridine-2,3-dicarboxylate [Azi(OBn)(2)]-based inhibitors, Boc-(S)-Leu-(R)-Pro-(S,S)-Azi(OBn)(2) (compound 13b) and Boc-(R)-Leu-(S)-Pro-(S,S)-Azi(OBn)(2) (compound 13e), reduced the growth and viability of Leishmania major and the infection rate of macrophages while not showing cytotoxicity against host cells. In the present study, we characterized the mode of action of inhibitors 13b and 13e in L. major. Both compounds targeted leishmanial cathepsin B-like cysteine cathepsin cysteine proteinase C, as shown by fluorescence proteinase activity assays and active-site labeling with biotin-tagged inhibitors. Furthermore, compounds 13b and 13e were potent inducers of cell death in promastigotes, characterized by cell shrinkage, reduction of mitochondrial transmembrane potential, and increased DNA fragmentation. Transmission electron microscopic studies revealed the enrichment of undigested debris in lysosome-like organelles participating in micro- and macroautophagy-like processes. The release of digestive enzymes into the cytoplasm after rupture of membranes of lysosome-like vacuoles resulted in the significant digestion of intracellular compartments. However, the plasma membrane integrity of compound-treated promastigotes was maintained for several hours. Taken together, our results suggest that the induction of cell death in Leishmania by cysteine cathepsin inhibitors 13b and 13e is different from mammalian apoptosis and is caused by incomplete digestion in autophagy-related lysosome-like vacuoles.
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25
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Abstract
Malaria, particularly that one caused by Plasmodium falciparum, remains a serious health problem in Africa, South America, and many parts of Asia where it afflicts about 500 million people and is responsible for the death of more than one million children each year. The main reasons for the persistence of malaria are the emergence of resistance to common antimalarial drugs, inadequate control of mosquito vectors, and the lack of effective vaccines. Therefore, the identification and characterization of new targets for antimalarial chemotherapy are of urgent priority. This review is focused on inhibitors of falcipain-2, a cysteine protease from P. falciparum, which represents one of the most promising targets for antimalarial drug design. Falcipain-2 is a key enzyme in the life cycle of P. falciparum since it degrades hemoglobin, at the early trophozoite stage, and cleaves ankyrin and protein 4.1, the cytoskeletal elements vital to the stability of red cell membrane, at the schizont stage. The main classes of falcipain-2 inhibitors are peptides or peptidomimetics bearing the most popular pharmacophores of cysteine protease inhibitors, such as vinyl sulfones, halomethyl ketones, and aldehydes. Furthermore, many other chemotypes have been identified as inhibitors of falcipain-2, such as isoquinolines, thiosemicarbazones, and chalcones. These inhibitors represent all classes, which, to the best of our knowledge, have been disclosed in journal articles to date.
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Affiliation(s)
- Roberta Ettari
- Dipartimento Farmaco-Chimico, University of Messina, Messina, Italy.
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26
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Breuning A, Degel B, Schulz F, Büchold C, Stempka M, Machon U, Heppner S, Gelhaus C, Leippe M, Leyh M, Kisker C, Rath J, Stich A, Gut J, Rosenthal PJ, Schmuck C, Schirmeister T. Michael Acceptor Based Antiplasmodial and Antitrypanosomal Cysteine Protease Inhibitors with Unusual Amino Acids. J Med Chem 2010; 53:1951-63. [DOI: 10.1021/jm900946n] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Breuning
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Björn Degel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Franziska Schulz
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christian Büchold
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Stempka
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Rudolf-Virchow-Zentrum, DFG-Forschungszentrum für Experimentelle Biomedizin, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Uwe Machon
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141 Essen, Germany
| | - Saskia Heppner
- Institute of Zoology, University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
| | - Christoph Gelhaus
- Institute of Zoology, University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
| | - Matthias Leippe
- Institute of Zoology, University of Kiel, Olshausenstrasse 40, 24098 Kiel, Germany
| | - Matthias Leyh
- Rudolf-Virchow-Zentrum, DFG-Forschungszentrum für Experimentelle Biomedizin, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Zentrum, DFG-Forschungszentrum für Experimentelle Biomedizin, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jennifer Rath
- Department of Tropical Medicine, Medical Mission Institute, Salvatorstrasse 7, 97074 Würzburg, Germany
| | - August Stich
- Department of Tropical Medicine, Medical Mission Institute, Salvatorstrasse 7, 97074 Würzburg, Germany
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, Box 0811, San Francisco, California 94143
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, Box 0811, San Francisco, California 94143
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141 Essen, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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27
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Machon U, Büchold C, Stempka M, Schirmeister T, Gelhaus C, Leippe M, Gut J, Rosenthal PJ, Kisker C, Leyh M, Schmuck C. On-bead screening of a combinatorial fumaric acid derived peptide library yields antiplasmodial cysteine protease inhibitors with unusual peptide sequences. J Med Chem 2009; 52:5662-72. [PMID: 19715342 DOI: 10.1021/jm900629w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A new class of cysteine protease inhibitors based on fumaric acid derived oligopeptides was successfully identified from a high-throughput screening of a solid-phase bound combinatorial library. As target enzymes falcipain and rhodesain were used, which play important roles in the life cycles of the parasites which cause malaria (Plasmodium falciparum) and African sleeping sickness (Trypanosoma brucei rhodesiense). The best inhibitors with unusual amino acid sequences not reported before for this type of enzyme were also fully analyzed in detail in solution. K(i) values in the lower micromolar and even nanomolar region were found. Some inhibitors are even active against plasmodia and show good selectivity relative to other enzymes. Also the mechanism of action was studied and could be shown to be irreversible inhibition.
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Affiliation(s)
- Uwe Machon
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatstrasse 7, 45141 Essen, Germany
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28
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Kerr ID, Lee JH, Farady CJ, Marion R, Rickert M, Sajid M, Pandey KC, Caffrey CR, Legac J, Hansell E, McKerrow JH, Craik CS, Rosenthal PJ, Brinen LS. Vinyl sulfones as antiparasitic agents and a structural basis for drug design. J Biol Chem 2009; 284:25697-703. [PMID: 19620707 DOI: 10.1074/jbc.m109.014340] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine proteases of the papain superfamily are implicated in a number of cellular processes and are important virulence factors in the pathogenesis of parasitic disease. These enzymes have therefore emerged as promising targets for antiparasitic drugs. We report the crystal structures of three major parasite cysteine proteases, cruzain, falcipain-3, and the first reported structure of rhodesain, in complex with a class of potent, small molecule, cysteine protease inhibitors, the vinyl sulfones. These data, in conjunction with comparative inhibition kinetics, provide insight into the molecular mechanisms that drive cysteine protease inhibition by vinyl sulfones, the binding specificity of these important proteases and the potential of vinyl sulfones as antiparasitic drugs.
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Affiliation(s)
- Iain D Kerr
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2550, USA
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29
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Mallari JP, Guiguemde WA, Guy RK. Antimalarial activity of thiosemicarbazones and purine derived nitriles. Bioorg Med Chem Lett 2009; 19:3546-9. [PMID: 19447616 DOI: 10.1016/j.bmcl.2009.04.142] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 04/29/2009] [Accepted: 04/30/2009] [Indexed: 11/19/2022]
Abstract
Malaria is a devastating illness caused by multiple species of the Plasmodium genus. The parasite's falcipain proteases have been extensively studied as potential drug targets. Here we report the testing of two established cysteine protease inhibitor scaffolds against both chloroquine sensitive and chloroquine resistant parasites. A subset of purine derived nitriles killed the parasite with moderate potency, and these inhibitors do not seem to exert their antiproliferative effects as cysteine protease inhibitors. Compound potency was determined to be similar against both parasite strains, indicating a low probability of cross resistance with chloroquine. These compounds represent a novel antimalarial scaffold, and a potential starting point for the development new inhibitors.
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Affiliation(s)
- Jeremy P Mallari
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, CA 94143-2280, USA
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30
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Buback V, Mladenovic M, Engels B, Schirmeister T. Rational Design of Improved Aziridine-Based Inhibitors of Cysteine Proteases. J Phys Chem B 2009; 113:5282-9. [DOI: 10.1021/jp810549n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Verena Buback
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Milena Mladenovic
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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31
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Evers A, Heppner S, Leippe M, Gelhaus C. An efficient fluorimetric method to measure the viability of intraerythrocytic Plasmodium falciparum. Biol Chem 2009; 389:1523-5. [PMID: 18844447 DOI: 10.1515/bc.2008.167] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A range of various assays to measure chemosusceptibility of Plasmodium falciparum have been described in the literature. As the screening of a plethora of compounds for antiplasmodial activity is urgently needed and becomes a constantly increasing routine analysis, a test system has to fulfill the following requirements: sensitivity, reliability, simplicity of performance, high-throughput compatibility, and cost-effectiveness. Here, we describe an assay that fulfills all criteria and in which the fluorescent SYTOX Green dye is introduced to determine growth inhibition of Plasmodia in in vitro cultures.
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Affiliation(s)
- Astrid Evers
- 1Department of Zoophysiology, Zoological Institute, University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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32
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Dude MA, Kaeppler U, Herb M, Schiller M, Schulz F, Vedder B, Heppner S, Pradel G, Gut J, Rosenthal PJ, Schirmeister T, Leippe M, Gelhaus C. Synthesis and evaluation of non-peptidic cysteine protease inhibitors of P. falciparum derived from etacrynic acid. Molecules 2008; 14:19-35. [PMID: 19104483 PMCID: PMC6253875 DOI: 10.3390/molecules14010019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 12/12/2008] [Accepted: 12/19/2008] [Indexed: 11/28/2022] Open
Abstract
A series of etacrynic acid derivatives was synthesized and screened for their in vitro activity against Plasmodium falciparum, as well as their activity against recombinantly expressed falcipain-2 and -3. The two most active compounds of the series displayed IC50 values of 9.0 and 18.8 μM against Plasmodia.
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Affiliation(s)
- Marie-Adrienne Dude
- Research Center for Infectious Diseases, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany; E-mail: (M-A. D.), (G. P.)
| | - Ulrich Kaeppler
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, Germany E-mail: (T. S.)
| | - Monika Herb
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, Germany E-mail: (T. S.)
| | - Markus Schiller
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, Germany E-mail: (T. S.)
| | - Franziska Schulz
- Zoological Institute, University of Kiel, Olshausenstr. 40, D-24098 Kiel, GermanyE-mail: (M. L.)
| | - Birgit Vedder
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, Germany E-mail: (T. S.)
| | - Saskia Heppner
- Zoological Institute, University of Kiel, Olshausenstr. 40, D-24098 Kiel, GermanyE-mail: (M. L.)
| | - Gabriele Pradel
- Research Center for Infectious Diseases, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany; E-mail: (M-A. D.), (G. P.)
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA; E-mail: (P-J. R.)
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA; E-mail: (P-J. R.)
| | - Tanja Schirmeister
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, Germany E-mail: (T. S.)
| | - Matthias Leippe
- Zoological Institute, University of Kiel, Olshausenstr. 40, D-24098 Kiel, GermanyE-mail: (M. L.)
| | - Christoph Gelhaus
- Zoological Institute, University of Kiel, Olshausenstr. 40, D-24098 Kiel, GermanyE-mail: (M. L.)
- Author to whom correspondence should be addressed; E-mail:
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Dolle RE, Bourdonnec BL, Goodman AJ, Morales GA, Thomas CJ, Zhang W. Comprehensive Survey of Chemical Libraries for Drug Discovery and Chemical Biology: 2007. ACTA ACUST UNITED AC 2008; 10:753-802. [PMID: 18991466 DOI: 10.1021/cc800119z] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roland E. Dolle
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Bertrand Le Bourdonnec
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Allan J. Goodman
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Guillermo A. Morales
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Craig J. Thomas
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
| | - Wei Zhang
- Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341, Semafore Pharmaceuticals Inc., 8496 Georgetown Road, Indianapolis, Indiana 46268, NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, and Department of Chemistry, University of Massachusetts, 100 Morrissey Boulevard, Boston, Massachusetts 02125
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Hodgson DM, Hughes SP, Thompson AL, Heightman TD. Terminal aziridines by alpha-deprotonation/electrophile trapping of N-protected aziridine. Org Lett 2008; 10:3453-6. [PMID: 18613698 DOI: 10.1021/ol801224g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-tert-Butylsulfonyl and N-tert-butylsulfinyl aziridine undergo alpha-lithiation/electrophile trapping providing a new entry to terminal aziridines. With N-tert-butylsulfinyl aziridine complete asymmetric induction is observed alpha to nitrogen.
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Affiliation(s)
- David M Hodgson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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Mladenovic M, Junold K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors. J Phys Chem B 2008; 112:5458-69. [PMID: 18393547 DOI: 10.1021/jp711287c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epoxides and aziridines are important building blocks for inhibitors of cysteine proteases which are promising drug targets for many diseases. In spite of the large amount of experimental data concerning inhibition potency, structure-activity relationships, and structural arrangements of enzyme-inhibitor complexes, little is known about the basic principles which connect the substitution pattern with the resulting activities. To shed some light on this issue which is essential for the rational design of improved compounds, we have studied the inhibition processes theoretically for various inhibitors using quantum mechanical/molecular mechanical hybrid approaches and classical molecular dynamics simulations. The careful analysis of the computational results allows insight into the interactions which govern the regio- and stereospecificity of the interactions. Known structure-activity relationships are rationalized in terms of the same interactions that determine the measured pH dependencies. Inconsistencies in existing X-ray structures are resolved through comparison with the computed structures, which leads to a reassessment of the factors that control the inhibition potency. Similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated. Finally the small reaction barriers computed for the irreversible step in E64 analogues call into question the commonly accepted two-step model of inhibition since the second, irreversible step is predicted to be so fast that suitably oriented enzyme-inhibitor complexes will react rather than dissociate and equilibrate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, and Institut für Pharmazie und Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Ettari R, Nizi E, Di Francesco ME, Dude MA, Pradel G, Vičík R, Schirmeister T, Micale N, Grasso S, Zappalà M. Development of Peptidomimetics with a Vinyl Sulfone Warhead as Irreversible Falcipain-2 Inhibitors. J Med Chem 2008; 51:988-96. [DOI: 10.1021/jm701141u] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rupp I, Bosse R, Schirmeister T, Pradel G. Effect of protease inhibitors on exflagellation in Plasmodium falciparum. Mol Biochem Parasitol 2008; 158:208-12. [PMID: 18243365 DOI: 10.1016/j.molbiopara.2007.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 12/13/2007] [Accepted: 12/14/2007] [Indexed: 11/19/2022]
Abstract
Enzymes involved in sexual differentiation and fertilization of the human malaria parasite Plasmodium falciparum represent potential targets for transmission blocking strategies. Parasite proteases are putatively involved in several steps during fertilization, but the types of proteases, their targets and modes of action remain hitherto unknown. We investigated the involvement of proteases in gametogenesis via exflagellation and immunofluorescence assays, using a variety of commercially available as well as newly designed protease inhibitors. The assays revealed a blockade of microgamete formation by the cysteine/serine protease inhibitors TLCK and TPCK. The serine protease inhibitor PMSF, the falcipain-targeting inhibitor RV112D, and the aspartic protease inhibitor EPNP also significantly decreased formation of microgametes. The metalloprotease inhibitor 1,10-phenanthroline, on the other hand, inhibited exflagellation by interfering with microgamete motility. Furthermore, EPNP reduced the activation of male and female gametocytes. Our data point to a major involvement of serine proteases and a non-thermolysin-like zinc metalloprotease in microgametocyte exflagellation.
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Affiliation(s)
- Ingrid Rupp
- Research Center for Infectious Diseases, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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Bringmann G, Gampe CM, Reichert Y, Bruhn T, Faber JH, Mikyna M, Reichert M, Leippe M, Brun R, Gelhaus C. Synthesis and Pharmacological Evaluation of Fluorescent and Photoactivatable Analogues of Antiplasmodial Naphthylisoquinolines. J Med Chem 2007; 50:6104-15. [DOI: 10.1021/jm061464w] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Christian M. Gampe
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Yanina Reichert
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Torsten Bruhn
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Johan H. Faber
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Martin Mikyna
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Matthias Reichert
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Matthias Leippe
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Reto Brun
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
| | - Christoph Gelhaus
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany, Zoological Institute, University of Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany, and Swiss Tropical Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
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