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Ettari R. Cysteine Proteases as Validated Targets for the Treatment of Neglected and Poverty-Related Parasitic Diseases. Int J Mol Sci 2023; 24:10097. [PMID: 37373243 DOI: 10.3390/ijms241210097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Neglected tropical diseases (NTDs) include 20 diverse infections mainly prevalent in tropical areas that mostly affect disadvantaged communities and women and children [...].
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Affiliation(s)
- Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
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2
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Patra J, Rana D, Arora S, Pal M, Mahindroo N. Falcipains: Biochemistry, target validation and structure-activity relationship studies of inhibitors as antimalarials. Eur J Med Chem 2023; 252:115299. [PMID: 36996716 DOI: 10.1016/j.ejmech.2023.115299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Malaria is a tropical disease with significant morbidity and mortality burden caused by Plasmodium species in Africa, the Middle East, Asia, and South America. Pathogenic Plasmodium species have lately become increasingly resistant to approved chemotherapeutics and combination therapies. Therefore, there is an emergent need for identifying new druggable targets and novel chemical classes against the parasite. Falcipains, cysteine proteases required for heme metabolism in the erythrocytic stage, have emerged as promising drug targets against Plasmodium species that infect humans. This perspective discusses the biology, biochemistry, structural features, and genetics of falcipains. The efforts to identify selective or dual inhibitors and their structure-activity relationships are reviewed to give a perspective on the design of novel compounds targeting falcipains for antimalarial activity evaluating reasons for hits and misses for this important target.
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Affiliation(s)
- Jeevan Patra
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Devika Rana
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India
| | - Smriti Arora
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Mintu Pal
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, 151001, India
| | - Neeraj Mahindroo
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India; School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, 124 Paud Road, Kothrud, Pune, Maharashtra, 411038, India.
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3
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Uddin A, Gupta S, Mohammad T, Shahi D, Hussain A, Alajmi MF, El-Seedi HR, Hassan I, Singh S, Abid M. Target-Based Virtual Screening of Natural Compounds Identifies a Potent Antimalarial With Selective Falcipain-2 Inhibitory Activity. Front Pharmacol 2022; 13:850176. [PMID: 35462917 PMCID: PMC9020225 DOI: 10.3389/fphar.2022.850176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
We employed a comprehensive approach of target-based virtual high-throughput screening to find potential hits from the ZINC database of natural compounds against cysteine proteases falcipain-2 and falcipain-3 (FP2 and FP3). Molecular docking studies showed the initial hits showing high binding affinity and specificity toward FP2 were selected. Furthermore, the enzyme inhibition and surface plasmon resonance assays were performed which resulted in a compound ZINC12900664 (ST72) with potent inhibitory effects on purified FP2. ST72 exhibited strong growth inhibition of chloroquine-sensitive (3D7; EC50 = 2.8 µM) and chloroquine-resistant (RKL-9; EC50 = 6.7 µM) strains of Plasmodium falciparum. Stage-specific inhibition assays revealed a delayed and growth defect during parasite growth and development in parasites treated with ST72. Furthermore, ST72 significantly reduced parasite load and increased host survival in a murine model infected with Plasmodium berghei ANKA. No Evans blue staining in ST72 treatment indicated that ST72 mediated protection of blood–brain barrier integrity in mice infected with P. berghei. ST72 did not show any significant hemolysis or cytotoxicity against human HepG2 cells suggesting a good safety profile. Importantly, ST72 with CQ resulted in improved growth inhibitory activity than individual drugs in both in vitro and in vivo studies.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonal Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Diksha Shahi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hesham R. El-Seedi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
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Chakraborty S, Alam B, Biswas S. New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain. Biochem Biophys Res Commun 2022; 590:145-151. [PMID: 34974303 DOI: 10.1016/j.bbrc.2021.12.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022]
Abstract
Malaria identifies as a tropical hallmark, conforming to the burgeoning notion of escalating drug resistance among virulent strains, with the burdensome Plasmodium falciparum under its wing. The cysteine protease Falcipain-2 (FP2) is released in the parasite's food vacuole in the trophozoite stage and contributes to disease progression through its hemoglobinase activity. In the present study, we have determined the crystal structure of FP2 from a drug resistant P. falciparum 3D7 strain. FP2-3D7 sequence has detected four amino acid variants, R12K, E14 N, P100T and G102D, in the mature domain of the protease, when compared with other reported structures. FP2-3D7 protease has been crystallized in the presence of two inhibitors E-64 and Iodoacetamide, which diffracted up to 3.5 Å and 3.4 Å respectively. Structural analyses of the mature domain helped unveil two solvent-exposed pockets with bound ligands where one is structurally homologous to the allosteric binding site of human Cathepsin-K and thus, could be exploited for designing allosteric modifiers of FP2. The structure has also revealed (poly)ethylene glycol molecules along the catalytic cleft, providing interesting insights for exploring FP2 as a chemotherapeutic target and for PEGylation in drug delivery. The side-chains of P2 and P3 residues of E-64 also adopt different rotamer conformations, compared with previously reported structure, emphasizing strain-specific multiple binding-modes of active-site targeted inhibitors. Docking studies, along with normal mode analyses, highlight the mode of hemoglobin binding and the active/inactive switch in hemoglobinase activity, conjecturing the formation of a stable dimeric state with a symmetry related copy in crystal packing.
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Affiliation(s)
- Subhoja Chakraborty
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, 700064, India
| | - Benazir Alam
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, 700064, India
| | - Sampa Biswas
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, 700064, India.
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5
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Hernández González JE, Alberca LN, Masforrol González Y, Reyes Acosta O, Talevi A, Salas-Sarduy E. Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site. J Chem Inf Model 2021; 62:159-175. [PMID: 34962803 DOI: 10.1021/acs.jcim.1c01189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric inhibitors regulate enzyme activity from remote and usually specific pockets. As they promise an avenue for less toxic and safer drugs, the identification and characterization of allosteric inhibitors has gained great academic and biomedical interest in recent years. Research on falcipain-2 (FP-2), the major papain-like cysteine hemoglobinase of Plasmodium falciparum, might benefit from this strategy to overcome the low selectivity against human cathepsins shown by active site-directed inhibitors. Encouraged by our previous finding that methacycline inhibits FP-2 noncompetitively, here we assessed other five tetracycline derivatives against this target and characterized their inhibition mechanism. As previously shown for methacycline, tetracycline derivatives inhibited FP-2 in a noncompetitive fashion, with Ki values ranging from 121 to 190 μM. A possible binding to the S' side of the FP-2 active site, similar to that described by X-ray crystallography (PDB: 6SSZ) for the noncompetitive inhibitor E-chalcone 48 (EC48), was experimentally discarded by kinetic analysis using a large peptidyl substrate spanning the whole active site. By combining lengthy molecular dynamics (MD) simulations that allowed methacycline to diffuse from solution to different FP-2 surface regions and free energy calculations, we predicted the most likely binding mode of the ligand. Of note, the proposed binding pose explains the low differences in Ki values observed for the tested tetracycline derivatives and the calculated binding free energies match the experimental values. Overall, this study has implications for the design of novel allosteric inhibitors against FP-2 and sets the basis for further optimization of the tetracycline scaffold to produce more potent and selective inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto, São Paulo CEP 15054-000, Brazil
| | - Lucas N Alberca
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | | | - Osvaldo Reyes Acosta
- Chemistry and Physics Department, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Alan Talevi
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde"─Universidad Nacional de San Martín─CONICET, San Martín B1650HMP, Buenos Aires, Argentina
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Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models. Sci Pharm 2021. [DOI: 10.3390/scipharm89040044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this work, antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) are proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities ( IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure–activity relationships (QSAR) model based on a linear correlation between computed GFE (ΔΔGcom) and the experimentally measured IC50exp. Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogues where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictive inhibitory activities falling within the low nanomolar concentration range.
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Ettari R, Previti S, Di Chio C, Zappalà M. Falcipain-2 and Falcipain-3 Inhibitors as Promising Antimalarial Agents. Curr Med Chem 2021; 28:3010-3031. [PMID: 32744954 DOI: 10.2174/0929867327666200730215316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/01/2020] [Accepted: 07/11/2020] [Indexed: 11/22/2022]
Abstract
Malaria remains a serious problem in global public health, particularly widespread in South America and in tropical regions of Africa and Asia. Chemotherapy is actually the only way to treat this poverty-related disease, since an effective vaccine is not currently available. However, the onset of resistance to the most common antimalarial drugs sometimes makes the current therapeutic regimen problematic. Therefore, the identification of new targets for a new drug discovery process is an urgent priority. In this context, falcipain-2 and falcipain- 3 of P. falciparum represent the key enzymes in the life-cycle of the parasite. Both falcipain- 2 and falcipain-3 are involved in hemoglobin hydrolysis, an essential pathway to provide free amino acids for the parasite metabolic needs. In addition, falcipain-2 is involved in cleaving ankirin and band 4.1 protein, which are cytoskeletal elements essential for the stability of the red cell membrane. This review article is focused on the most recent and effective inhibitors of falcipain-2 and falcipain-3, with particular attention to peptide, peptidomimetic or nonpeptide inhibitors, which targeted one or both the malarial cysteine proteases, endowed with a consistent activity against P. falciparum.
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Affiliation(s)
- Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Santo Previti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
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Kinetic characterization of a novel cysteine peptidase from the protozoan Babesia bovis, a potential target for drug design. Biochimie 2020; 179:127-134. [PMID: 32946988 DOI: 10.1016/j.biochi.2020.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/12/2020] [Indexed: 11/22/2022]
Abstract
C1A cysteine peptidases have been shown to play an important role during apicomplexan invasion and egress of host red blood cells (RBCs) and therefore have been exploited as targets for drug development, in which peptidase specificity is deterministic. Babesia bovis genome is currently available and from the 17 putative cysteine peptidases annotated four belong to the C1A subfamily. In this study, we describe the biochemical characterization of a C1A cysteine peptidase, named here BbCp (B. bovis cysteine peptidase) and evaluate its possible participation in the parasite asexual cycle in host RBCs. The recombinant protein was obtained in bacterial inclusion bodies and after a refolding process, presented typical kinetic features of the cysteine peptidase family, enhanced activity in the presence of a reducing agent, optimum pH between 6.5 and 7.0 and was inhibited by cystatins from R. microplus. Moreover, rBbCp substrate specificity evaluation using a peptide phage display library showed a preference for Val > Leu > Phe. Finally, antibodies anti-rBbCp were able to interfere with B. bovis growth in vitro, which highlights the BbCp as a potential target for drug design.
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9
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Machin JM, Kantsadi AL, Vakonakis I. The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site. Malar J 2019; 18:388. [PMID: 31791339 PMCID: PMC6889325 DOI: 10.1186/s12936-019-3043-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/27/2019] [Indexed: 12/03/2022] Open
Abstract
Background Malaria kills over 400,000 people each year and nearly half the world’s population live in at-risk areas. Progress against malaria has recently stalled, highlighting the need for developing novel therapeutics. The parasite haemoglobin degradation pathway, active in the blood stage of the disease where malaria symptoms and lethality manifest, is a well-established drug target. A key enzyme in this pathway is the papain-type protease falcipain-2. Methods The crystallographic structure of falcipain-2 at 3.45 Å resolution was resolved in complex with an (E)-chalcone small-molecule inhibitor. The falcipain-2–(E)-chalcone complex was analysed with reference to previous falcipain complexes and their similarity to human cathepsin proteases. Results The (E)-chalcone inhibitor binds falcipain-2 to the rear of the substrate-binding cleft. This is the first structure of a falcipain protease where the rear of the substrate cleft is bound by a small molecule. In this manner, the (E)-chalcone inhibitor mimics interactions observed in protein-based falcipain inhibitors, which can achieve high interaction specificity. Conclusions This work informs the search for novel anti-malaria therapeutics that target falcipain-2 by showing the binding site and interactions of the medically privileged (E)-chalcone molecule. Furthermore, this study highlights the possibility of chemically combining the (E)-chalcone molecule with an existing active-site inhibitor of falcipain, which may yield a potent and selective compound for blocking haemoglobin degradation by the malaria parasite.
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Affiliation(s)
- Jonathan M Machin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anastassia L Kantsadi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ioannis Vakonakis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Cianni L, Feldmann CW, Gilberg E, Gütschow M, Juliano L, Leitão A, Bajorath J, Montanari CA. Can Cysteine Protease Cross-Class Inhibitors Achieve Selectivity? J Med Chem 2019; 62:10497-10525. [DOI: 10.1021/acs.jmedchem.9b00683] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lorenzo Cianni
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Christian Wolfgang Feldmann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Erik Gilberg
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Luiz Juliano
- A. C. Camargo Cancer Center and São Paulo Medical School of Federal University of São Paulo, Rua Professor Antônio Prudente, 211, 01509-010 São Paulo, SP, Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Carlos A. Montanari
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense, 400, 23566-590 São Carlos, SP, Brazil
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Sharma K, Shrivastava A, Mehra RN, Deora GS, Alam MM, Zaman MS, Akhter M. Synthesis of novel benzimidazole acrylonitriles for inhibition of Plasmodium falciparum growth by dual target inhibition. Arch Pharm (Weinheim) 2017; 351. [PMID: 29227011 DOI: 10.1002/ardp.201700251] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 11/08/2022]
Abstract
Antimalarial drug resistance has emerged as a threat for treating malaria, generating a need to design and develop newer, more efficient antimalarial agents. This research aimed to identify novel leads as antimalarials. Dual receptor mechanism could be a good strategy to combat developing drug resistance. A series of benzimidazole acrylonitriles containing 18 compounds were designed, synthesized and evaluated for cytotoxicity, heme binding, ferriprotoporphyrin IX biomineralisation inhibition, and falcipain-2 enzyme assay. Furthermore, in silico docking and MD simulation studies were also performed.The tests revealed quite encouraging results. Three compounds, viz. R-01 (0.69 μM), R-04 (1.60 μM), and R-08 (1.61 μM), were found to have high antimalarial activity. These compounds were found to be in bearable cytotoxicity limits and their biological assay suggested that they had inhibitory activity against falcipain-2 and hemozoin formation. The docking revealed the binding mode of benzimidazole acrylonitrile derivatives and MD simulation studies revealed that the protein-ligand complex was stable. The agents exhibit good hemozoin formation inhibition activity and, hence, may be utilized as leads to design a newer drug class to overcome the drug resistance of hemozoin formation inhibitors such as chloroquine.
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Affiliation(s)
- Kalicharan Sharma
- Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy and Bioinformatics Infrastructure Facility, Department of Pharmaceutical Chemistry, Jamia Hamdard, New Delhi, India
| | - Apeksha Shrivastava
- Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy and Bioinformatics Infrastructure Facility, Department of Pharmaceutical Chemistry, Jamia Hamdard, New Delhi, India
| | - Ram N Mehra
- School of Pharmaceutical Sciences, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal, Madhya Pradesh, India
| | - Girdhar S Deora
- School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Mohammad M Alam
- Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy and Bioinformatics Infrastructure Facility, Department of Pharmaceutical Chemistry, Jamia Hamdard, New Delhi, India
| | - Mohammad S Zaman
- Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy and Bioinformatics Infrastructure Facility, Department of Pharmaceutical Chemistry, Jamia Hamdard, New Delhi, India
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Faculty of Pharmacy and Bioinformatics Infrastructure Facility, Department of Pharmaceutical Chemistry, Jamia Hamdard, New Delhi, India
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Previti S, Ettari R, Cosconati S, Amendola G, Chouchene K, Wagner A, Hellmich UA, Ulrich K, Krauth-Siegel RL, Wich PR, Schmid I, Schirmeister T, Gut J, Rosenthal PJ, Grasso S, Zappalà M. Development of Novel Peptide-Based Michael Acceptors Targeting Rhodesain and Falcipain-2 for the Treatment of Neglected Tropical Diseases (NTDs). J Med Chem 2017; 60:6911-6923. [PMID: 28763614 DOI: 10.1021/acs.jmedchem.7b00405] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper describes the development of a class of peptide-based inhibitors as novel antitrypanosomal and antimalarial agents. The inhibitors are based on a characteristic peptide sequence for the inhibition of the cysteine proteases rhodesain of Trypanosoma brucei rhodesiense and falcipain-2 of Plasmodium falciparum. We exploited the reactivity of novel unsaturated electrophilic functions such as vinyl-sulfones, -ketones, -esters, and -nitriles. The Michael acceptors inhibited both rhodesain and falcipain-2, at nanomolar and micromolar levels, respectively. In particular, the vinyl ketone 3b has emerged as a potent rhodesain inhibitor (k2nd = 67 × 106 M-1 min-1), endowed with a picomolar binding affinity (Ki = 38 pM), coupled with a single-digit micromolar activity against Trypanosoma brucei brucei (EC50 = 2.97 μM), thus being considered as a novel lead compound for the discovery of novel effective antitrypanosomal agents.
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Affiliation(s)
- Santo Previti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina , Viale Annunziata, 98168 Messina, Italy
| | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina , Viale Annunziata, 98168 Messina, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli , Via Vivaldi 43, 81100 Caserta, Italy
| | - Giorgio Amendola
- DiSTABiF, University of Campania Luigi Vanvitelli , Via Vivaldi 43, 81100 Caserta, Italy
| | - Khawla Chouchene
- Laboratoire de Chimie des Substances Naturelles UR/11-ES-74, Faculté des Sciences de Sfax, Université de Sfax , Route de l'aeroport, 3000 Sfax, Tunisia
| | - Annika Wagner
- Institute of Pharmacy and Biochemistry, University of Mainz , Johann-Joachim-Becherweg 30, DE 55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt , Max-von-Laue-Strasse 9, DE 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Institute of Pharmacy and Biochemistry, University of Mainz , Johann-Joachim-Becherweg 30, DE 55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt , Max-von-Laue-Strasse 9, DE 60438 Frankfurt am Main, Germany
| | - Kathrin Ulrich
- Biochemistry Center, Heidelberg University , Im Neuenheimer Feld 328, DE 69120 Heidelberg, Germany
| | - R Luise Krauth-Siegel
- Biochemistry Center, Heidelberg University , Im Neuenheimer Feld 328, DE 69120 Heidelberg, Germany
| | - Peter R Wich
- Institute of Pharmacy and Biochemistry, University of Mainz , Staudingerweg 5, DE 55128 Mainz, Germany
| | - Ira Schmid
- Institute of Pharmacy and Biochemistry, University of Mainz , Staudingerweg 5, DE 55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Biochemistry, University of Mainz , Staudingerweg 5, DE 55128 Mainz, Germany
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California , 1001 Potrero Avenue, San Francisco, California 94110, United States
| | - Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California , 1001 Potrero Avenue, San Francisco, California 94110, United States
| | - Silvana Grasso
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina , Viale Annunziata, 98168 Messina, Italy
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina , Viale Annunziata, 98168 Messina, Italy
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Independent amino acid residues in the S2 pocket of falcipain-3 determine its specificity for P2 residues in substrates. Mol Biochem Parasitol 2015; 202:11-22. [DOI: 10.1016/j.molbiopara.2015.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 12/23/2022]
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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Omotuyi IO, Hamada T. Dynamical footprint of falcipain-2 catalytic triad in hemoglobin-β-bound state. J Biomol Struct Dyn 2014; 33:1027-36. [PMID: 24943200 DOI: 10.1080/07391102.2014.924878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malaria epidemic. Here, a theoretical FP-2/hemoglobin complex has been proposed and the dynamical footprint and energetics of binding have been investigated using molecular and quantum mechanics approaches. The mapped interaction interface comprises residues 34-51 of hemoglobin and cysteine-42/histidine-174/glutamine-36/asparagine-173/204 and subsites S1, S1', and S3 of FP-2. In hemoglobin-bound FP-2, asparagine-173 preferentially partners histidine-174, while glutamine-36 is preferred in ligand-free state. Cysteine-42 exhibits dihedral switch from 110° to 30° in free and bound states, respectively, with exclusion of water from the binding core upon hemoglobin binding. Hemoglobin similarly exhibits high occupancy within .2 nm distance with charged amido acid-rich subsites S1 and S3 of FP-2 functioning in tandem to reduce conformational flexibility of hemoglobin and facilitate the formation of a stabilizing anti-parallel β-sheet between Leucine-172-valine-176 of FP-2 and phenylalanine-45-asparate-47 of hemoglobin and to overcome the + 1.13e + 5 eV activation energy required to optimize the FP-2/hemoglobin-β conformation that precedes hydrolysis.
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Affiliation(s)
- I O Omotuyi
- a Department of Molecular Pharmacology and Neuroscience , Nagasaki University , Nagasaki , Japan
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Blocking Plasmodium falciparum development via dual inhibition of hemoglobin degradation and the ubiquitin proteasome system by MG132. PLoS One 2013; 8:e73530. [PMID: 24023882 PMCID: PMC3759421 DOI: 10.1371/journal.pone.0073530] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 07/22/2013] [Indexed: 12/31/2022] Open
Abstract
Among key potential drug target proteolytic systems in the malaria parasite Plasmodium falciparum are falcipains, a family of hemoglobin-degrading cysteine proteases, and the ubiquitin proteasomal system (UPS), which has fundamental importance in cellular protein turnover. Inhibition of falcipains blocks parasite development, primarily due to inhibition of hemoglobin degradation that serves as a source of amino acids for parasite growth. Falcipains prefer P2 leucine in substrates and peptides, and their peptidyl inhibitors with leucine at the P2 position show potent antimalarial activity. The peptidyl inhibitor MG132 (Z-Leu-Leu-Leu-CHO) is a widely used proteasome inhibitor, which also has P2 leucine, and has also been shown to inhibit parasite development. However, the antimalarial targets of MG132 are unclear. We investigated whether MG132 blocks malaria parasite development by inhibiting hemoglobin degradation and/or by targeting the UPS. P. falciparum was cultured with inhibitors of the UPS (MG132, epoxomicin, and lactacystin) or falcipains (E64), and parasites were assessed for morphologies, extent of hemoglobin degradation, and accumulation of ubiquitinated proteins. MG132, like E64 and unlike epoxomicin or lactacystin, blocked parasite development, with enlargement of the food vacuole and accumulation of undegraded hemoglobin, indicating inhibition of hemoglobin degradation by MG132, most likely due to inhibition of hemoglobin-degrading falcipain cysteine proteases. Parasites cultured with epoxomicin or MG132 accumulated ubiquitinated proteins to a significantly greater extent than untreated or E64-treated parasites, indicating that MG132 inhibits the parasite UPS as well. Consistent with these findings, MG132 inhibited both cysteine protease and UPS activities present in soluble parasite extracts, and it strongly inhibited recombinant falcipains. MG132 was highly selective for inhibition of P. falciparum (IC50 0.0476 µM) compared to human peripheral blood mononuclear cells (IC50 10.8 µM). Thus, MG132 inhibits two distinct proteolytic systems in P. falciparum, and it may serve as a lead molecule for development of dual-target inhibitors of malaria parasites.
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Oliveira R, Newton AS, Guedes RC, Miranda D, Amewu RK, Srivastava A, Gut J, Rosenthal PJ, O'Neill PM, Ward SA, Lopes F, Moreira R. An Endoperoxide‐Based Hybrid Approach to Deliver Falcipain Inhibitors Inside Malaria Parasites. ChemMedChem 2013; 8:1528-36. [DOI: 10.1002/cmdc.201300202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/14/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Rudi Oliveira
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
| | - Ana S. Newton
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
| | - Rita C. Guedes
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
| | - Daniela Miranda
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool, L69 3BX (UK)
| | - Abhishek Srivastava
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA (UK)
| | - Jiri Gut
- Department of Medicine, University of California, San Francisco, CA 94143 (USA)
| | - Philip J. Rosenthal
- Department of Medicine, University of California, San Francisco, CA 94143 (USA)
| | - Paul M. O'Neill
- Department of Chemistry, University of Liverpool, Liverpool, L69 3BX (UK)
| | - Stephen A. Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA (UK)
| | - Francisca Lopes
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
| | - Rui Moreira
- iMed.UL and Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, Lisbon, 1649‐003 (Portugal)
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Ehmke V, Winkler E, Banner DW, Haap W, Schweizer WB, Rottmann M, Kaiser M, Freymond C, Schirmeister T, Diederich F. Optimization of triazine nitriles as rhodesain inhibitors: structure-activity relationships, bioisosteric imidazopyridine nitriles, and X-ray crystal structure analysis with human cathepsin L. ChemMedChem 2013; 8:967-75. [PMID: 23658062 DOI: 10.1002/cmdc.201300112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Indexed: 11/10/2022]
Abstract
The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 substituent led to high-affinity ligands with inhibition constants down to 2 nM for compounds bearing cyclohexyl substituents. Systematic investigations on the S3 pocket revealed its potential to achieve high activities with aromatic vectors that undergo stacking interactions with the planar peptide backbone forming part of the pocket. X-ray crystal structure analysis with the structurally related enzyme human cathepsin L confirmed the binding mode of the triazine ligand series as proposed by molecular modeling. Sub-micromolar inhibition of the proliferation of cultured parasites was achieved for ligands decorated with the best substituents identified through the optimization cycles. In cell-based assays, the introduction of a basic side chain on the inhibitors resulted in a 35-fold increase in antitrypanosomal activity. Finally, bioisosteric imidazopyridine nitriles were studied in order to prevent off-target effects with unselective nucleophiles by decreasing the inherent electrophilicity of the triazine nitrile headgroup. Using this ligand, the stabilization by intramolecular hydrogen bonding of the thioimidate intermediate, formed upon attack of the catalytic cysteine residue, compensates for the lower reactivity of the headgroup. The imidazopyridine nitrile ligand showed excellent stability toward the thiol nucleophile glutathione in a quantitative in vitro assay and fourfold lower cytotoxicity than the parent triazine nitrile.
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Affiliation(s)
- Veronika Ehmke
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
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Expression, characterization, and cellular localization of knowpains, papain-like cysteine proteases of the Plasmodium knowlesi malaria parasite. PLoS One 2012; 7:e51619. [PMID: 23251596 PMCID: PMC3520923 DOI: 10.1371/journal.pone.0051619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/02/2012] [Indexed: 01/09/2023] Open
Abstract
Papain-like cysteine proteases of malaria parasites degrade haemoglobin in an acidic food vacuole to provide amino acids for intraerythrocytic parasites. These proteases are potential drug targets because their inhibitors block parasite development, and efforts are underway to develop chemotherapeutic inhibitors of these proteases as the treatments for malaria. Plasmodium knowlesi has recently been shown to be an important human pathogen in parts of Asia. We report expression and characterization of three P. knowlesi papain-like proteases, termed knowpains (KP2-4). Recombinant knowpains were produced using a bacterial expression system, and tested for various biochemical properties. Antibodies against recombinant knowpains were generated and used to determine their cellular localization in parasites. Inhibitory effects of the cysteine protease inhibitor E64 were assessed on P. knowlesi culture to validate drug target potential of knowpains. All three knowpains were present in the food vacuole, active in acidic pH, and capable of degrading haemoglobin at the food vacuolar pH (≈5.5), suggesting roles in haemoglobin degradation. The proteases showed absolute (KP2 and KP3) to moderate (KP4) preference for peptide substrates containing leucine at the P2 position; KP4 preferred arginine at the P2 position. While the three knowpains appear to have redundant roles in haemoglobin degradation, KP4 may also have a role in degradation of erythrocyte cytoskeleton during merozoite egress, as it displayed broad substrate specificity and was primarily localized at the parasite periphery. Importantly, E64 blocked erythrocytic development of P. knowlesi, with enlargement of food vacuoles, indicating inhibition of haemoglobin hydrolysis and supporting the potential for inhibition of knowpains as a strategy for the treatment of malaria. Functional expression and characterization of knowpains should enable simultaneous screening of available cysteine protease inhibitor libraries against knowpains for developing broadly effective compounds active against multiple human malaria parasites.
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Shah F, Gut J, Legac J, Shivakumar D, Sherman W, Rosenthal PJ, Avery MA. Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis. J Chem Inf Model 2012; 52:696-710. [PMID: 22332946 DOI: 10.1021/ci2005516] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure-activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand-protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand-protein interactions.
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Affiliation(s)
- Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, USA
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22
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Structure-function of falcipains: malarial cysteine proteases. J Trop Med 2012; 2012:345195. [PMID: 22529862 PMCID: PMC3317066 DOI: 10.1155/2012/345195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/12/2011] [Accepted: 10/27/2011] [Indexed: 02/05/2023] Open
Abstract
Evidence indicates that cysteine proteases play essential role in malaria parasites; therefore an obvious area of investigation is the inhibition of these enzymes to treat malaria. Studies with cysteine protease inhibitors and manipulating cysteine proteases genes have suggested a role for cysteine proteases in hemoglobin hydrolysis. The best characterized Plasmodium cysteine proteases are falcipains, which are papain family enzymes. Falcipain-2 and falcipain-3 are major hemoglobinases of P. falciparum. Structural and functional analysis of falcipains showed that they have unique domains including a refolding domain and a hemoglobin binding domain. Overall, the complexes of falcipain-2 and falcipain-3 with small and macromolecular inhibitors provide structural insight to facilitate the design or modification of effective drug treatment against malaria. Drug development targeting falcipains should be aided by a strong foundation of biochemical and structural studies.
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Centenary celebrations article: Cysteine proteases of human malaria parasites. J Parasit Dis 2011; 35:94-103. [PMID: 23024488 DOI: 10.1007/s12639-011-0084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/09/2011] [Indexed: 01/07/2023] Open
Abstract
There is an urgent need for new drugs against malaria, which takes millions of lives annually. Cysteine proteases are potential new drug targets, especially when current drugs are showing resistance. Falcipains and vivapains are well characterized cysteine proteases of P. falciparum and P. vivax, respectively. Studies with cysteine protease inhibitors and manipulating cysteine proteases specific genes have suggested their roles in hemoglobin hydrolysis. In P. falciparum, falcipain-2 and falcipain-3 are major hemoglobinases that hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. It is confirmed that disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis, and disruption of falcipain-3 gene was not possible, suggesting that protease is essential for erythrocytic parasites. On the other hand, vivapain-2, vivapain-3 and vivapain-4 are important cysteine proteases of P. vivax, which shared a number of features with falcipain-2 and falcipain-3. A recent study indicates that vivapains and aspartic protease of P. vivax works collaboratively to enhance the parasites' ability to hydrolyze host erythrocyte hemoglobin. Studies also indicate that falcipains and vivapains also hydrolyse the erythrocyte cytoskeleton proteins and involved in rupture of red blood cell. Structural and biochemical analysis of falcipains and vivapains showed that they have unique domains for specific functions. Overall, the complexes of cysteine proteases with small and macromolecular inhibitors provide structural insight to facilitate the drug design. Therefore, giving due importance to the cysteine proteases, this review will briefly focus the recent advancement in the field of cysteine proteases of human malaria parasites.
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Potshangbam AM, Tanneeru K, Reddy BM, Guruprasad L. 3D-QSAR and molecular docking studies of 2-pyrimidinecarbonitrile derivatives as inhibitors against falcipain-3. Bioorg Med Chem Lett 2011; 21:7219-23. [DOI: 10.1016/j.bmcl.2011.09.107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/07/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
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Hammann F, Suenderhauf C, Huwyler J. A binary ant colony optimization classifier for molecular activities. J Chem Inf Model 2011; 51:2690-6. [PMID: 21854036 DOI: 10.1021/ci200186m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chemical fingerprints encode the presence or absence of molecular features and are available in many large databases. Using a variation of the Ant Colony Optimization (ACO) paradigm, we describe a binary classifier based on feature selection from fingerprints. We discuss the algorithm and possible cross-validation procedures. As a real-world example, we use our algorithm to analyze a Plasmodium falciparum inhibition assay and contrast its performance with other machine learning paradigms in use today (decision tree induction, random forests, support vector machines, artificial neural networks). Our algorithm matches established paradigms in predictive power, yet supplies the medicinal chemist and basic researcher with easily interpretable results. Furthermore, models generated with our paradigm are easy to implement and can complement virtual screenings by additionally exploiting the precalculated fingerprint information.
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Affiliation(s)
- Felix Hammann
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50 4056, Basel, Switzerland.
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Lu J, Arai C, Bakar Md A, Ihara M. Plasmodium berghei proteome changes in response to SSJ-183 treatment. Bioorg Med Chem 2011; 19:4144-7. [DOI: 10.1016/j.bmc.2011.04.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 04/26/2011] [Accepted: 04/28/2011] [Indexed: 11/28/2022]
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27
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Ang KKH, Ratnam J, Gut J, Legac J, Hansell E, Mackey ZB, Skrzypczynska KM, Debnath A, Engel JC, Rosenthal PJ, McKerrow JH, Arkin MR, Renslo AR. Mining a cathepsin inhibitor library for new antiparasitic drug leads. PLoS Negl Trop Dis 2011; 5:e1023. [PMID: 21572521 PMCID: PMC3086806 DOI: 10.1371/journal.pntd.0001023] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/14/2011] [Indexed: 01/21/2023] Open
Abstract
The targeting of parasite cysteine proteases with small molecules is emerging as a possible approach to treat tropical parasitic diseases such as sleeping sickness, Chagas' disease, and malaria. The homology of parasite cysteine proteases to the human cathepsins suggests that inhibitors originally developed for the latter may be a source of promising lead compounds for the former. We describe here the screening of a unique ∼ 2,100-member cathepsin inhibitor library against five parasite cysteine proteases thought to be relevant in tropical parasitic diseases. Compounds active against parasite enzymes were subsequently screened against cultured Plasmodium falciparum, Trypanosoma brucei brucei and/or Trypanosoma cruzi parasites and evaluated for cytotoxicity to mammalian cells. The end products of this effort include the identification of sub-micromolar cell-active leads as well as the elucidation of structure-activity trends that can guide further optimization efforts.
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Affiliation(s)
- Kenny K. H. Ang
- The Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Joseline Ratnam
- The Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer Legac
- Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Elizabeth Hansell
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
| | - Zachary B. Mackey
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
| | - Katarzyna M. Skrzypczynska
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
| | - Anjan Debnath
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
| | - Juan C. Engel
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - James H. McKerrow
- The Sandler Center for Drug Discovery, University of California San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Michelle R. Arkin
- The Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MRA); (ARR)
| | - Adam R. Renslo
- The Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (MRA); (ARR)
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Shah F, Mukherjee P, Gut J, Legac J, Rosenthal PJ, Tekwani BL, Avery MA. Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library. J Chem Inf Model 2011; 51:852-64. [PMID: 21428453 DOI: 10.1021/ci200029y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.
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Affiliation(s)
- Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi , University, Mississippi 38677, USA
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Rosenthal PJ. Falcipains and other cysteine proteases of malaria parasites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 712:30-48. [PMID: 21660657 DOI: 10.1007/978-1-4419-8414-2_3] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of cysteine proteases of malaria parasites have been described and many more are suggested by analysis of the Plasmodium falciparum genome sequence. The best characterized of these proteases are the falcipains, a family of four papain-family enzymes. Falcipain-2 and falcipain-3 act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. Disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis and parasites with increased sensitivity to protease inhibitors. Disruption of the falcipain-3 gene was not possible, strongly suggesting that this protease is essential for erythrocytic parasites. Disruption of the falcipain-1 gene did not alter development in erythrocytes, but led to decreased production of oocysts in mosquitoes. other papain-family proteases predicted by the genome sequence include dipeptidyl peptidases, a calpain homolog and serine-repeat antigens (SERAs). Dipeptidyl aminopeptidase 1 appears to be essential and localized to the food vacuole, suggesting a role in hemoglobin hydrolysis. Dipeptidyl aminopeptidase 3 appears to play a role in the rupture of erythrocytes by mature parasites. the P. falciparum calpain homolog gene could not be disrupted, suggesting that the protein is essential and a role in the parasite cell cycle has been suggested. Nine P. falciparum SERAs have cysteine protease motifs, but in some the active site cys is replaced by a Ser. Gene disruption studies suggested that SERA-5 and SERA-6 are essential. activation of SERA-5 by a serine protease seems to be required for merozoite egress from the erythrocyte. New drugs for malaria are greatly needed and cysteine proteases represent potential drug targets. cysteine protease inhibitors have demonstrated potent antimalarial effects and the optimization and testing of falcipain inhibitor antimalarials is underway.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA.
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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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31
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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: 3.1] [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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32
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Löser R, Gut J, Rosenthal PJ, Frizler M, Gütschow M, Andrews KT. Antimalarial activity of azadipeptide nitriles. Bioorg Med Chem Lett 2009; 20:252-5. [PMID: 19913414 DOI: 10.1016/j.bmcl.2009.10.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 10/27/2009] [Indexed: 10/20/2022]
Abstract
Azadipeptide nitriles-novel cysteine protease inhibitors-display structure-dependent antimalarial activity against both chloroquine-sensitive and chloroquine-resistant lines of cultured Plasmodium falciparum malaria parasites. Inhibition of parasite's hemoglobin-degrading cysteine proteases was also investigated, revealing the azadipeptide nitriles as potent inhibitors of falcipain-2 and -3. A correlation between the cysteine protease-inhibiting activity and the antimalarial potential of the compounds was observed. These first generation azadipeptide nitriles represent a promising new class of compounds for antimalarial drug development.
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Affiliation(s)
- Reik Löser
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.
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33
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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: 1.0] [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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34
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Ettari R, Micale N, Schirmeister T, Gelhaus C, Leippe M, Nizi E, Di Francesco ME, Grasso S, Zappalà M. Novel peptidomimetics containing a vinyl ester moiety as highly potent and selective falcipain-2 inhibitors. J Med Chem 2009; 52:2157-60. [PMID: 19296600 DOI: 10.1021/jm900047j] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the synthesis and biological evaluation of a new class of peptidomimetic falcipain-2 inhibitors based on a 1,4-benzodiazepine scaffold combined with various alpha,beta-unsaturated electrophilic functions such as vinyl-ketone, -amide, -ester, and -nitrile. The profile of reactivity of this class of derivatives has been evaluated and 4c, containing a vinyl ester warhead, proved to be a highly potent and selective falcipain-2 inhibitor.
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Affiliation(s)
- Roberta Ettari
- Dipartimento Farmaco-Chimico, University of Messina, Viale Annunziata, Messina, Italy.
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35
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Kerr ID, Lee JH, Pandey KC, Harrison A, Sajid M, Rosenthal PJ, Brinen LS. Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity. J Med Chem 2009; 52:852-7. [PMID: 19128015 PMCID: PMC2651692 DOI: 10.1021/jm8013663] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Falcipain-2 and falcipain-3 are critical hemoglobinases of Plasmodium falciparum, the most virulent human malaria parasite. We have determined the 2.9 Å crystal structure of falcipain-2 in complex with the epoxysuccinate E64 and the 2.5 Å crystal structure of falcipain-3 in complex with the aldehyde leupeptin. These complexes represent the first crystal structures of plasmodial cysteine proteases with small molecule inhibitors and the first reported crystal structure of falcipain-3. Our structural analyses indicate that the relative shape and flexibility of the S2 pocket are affected by a number of discrete amino acid substitutions. The cumulative effect of subtle differences, including those at “gatekeeper” positions, may explain the observed kinetic differences between these two closely related enzymes.
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Affiliation(s)
- Iain D Kerr
- Department of Cellular and Molecular Pharmacology and Department of Pathology, University of California, San Francisco, California 94158, USA
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36
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Lim MD, Craik CS. Using specificity to strategically target proteases. Bioorg Med Chem 2009; 17:1094-100. [PMID: 18434168 PMCID: PMC2663002 DOI: 10.1016/j.bmc.2008.03.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/24/2008] [Indexed: 01/05/2023]
Abstract
Proteases are a family of naturally occurring enzymes in the body whose dysregulation has been implicated in numerous diseases and cancers. Their ability to selectively and catalytically turnover substrate adds both signal amplification and functionality as parameters for the detection of disease. This review will focus on the development of activity-based methodologies to characterize proteases, and in particular, the use of positional scanning, synthetic combinatorial libraries (PS-SCL's), and substrate activity screening (SAS) assays. The use of these approaches to better understand a protease's natural substrate will be discussed as well as the technologies that emerged.
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Affiliation(s)
- Mark D Lim
- Department of Pharmaceutical Chemistry, University of California, School of Pharmacy, 513 Parnassus Avenue Room S-926, San Francisco, CA 94158, USA
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37
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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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38
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Schulz F, Gelhaus C, Degel B, Vicik R, Heppner S, Breuning A, Leippe M, Gut J, Rosenthal PJ, Schirmeister T. Screening of protease inhibitors as antiplasmodial agents. Part I: Aziridines and epoxides. ChemMedChem 2008; 2:1214-24. [PMID: 17562535 DOI: 10.1002/cmdc.200700070] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A broad protease-based and cell-based screening of protease inhibitors yielded the aziridine-2-carboxylic acid derivative 2 a and the N-acylated aziridine-2,3-dicarboxylic acid derivatives 32 a and 34 b as the most potent inhibitors of falcipain-2 and falcipain-3 (IC(50) falcipain-2: 0.079-5.4 microM, falcipain-3: 0.25-39.8 microM). As the compounds also display in vitro activity against the P. falciparum parasite in the submicromolar and low micromolar range, these compound classes are leads for new antiplasmodial falcipain inhibitors.
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Affiliation(s)
- Franziska Schulz
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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39
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Drew ME, Banerjee R, Uffman EW, Gilbertson S, Rosenthal PJ, Goldberg DE. Plasmodium food vacuole plasmepsins are activated by falcipains. J Biol Chem 2008; 283:12870-6. [PMID: 18308731 DOI: 10.1074/jbc.m708949200] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Intraerythrocytic malaria parasites use host hemoglobin as a major nutrient source. Aspartic proteases (plasmepsins) and cysteine proteases (falcipains) function in the early steps of the hemoglobin degradation pathway. There is extensive functional redundancy within and between these protease families. Plasmepsins are synthesized as integral membrane proenzymes that are activated by cleavage from the membrane. This cleavage is mediated by a maturase activity whose identity has been elusive. We have used a combination of cell biology, chemical biology, and enzymology approaches to analyze this processing event. These studies reveal that plasmepsin processing occurs primarily via the falcipains; however, if falcipain activity is blocked, autoprocessing can take place, serving as an alternate activation system. These results establish a further level of redundancy between the protease families involved in Plasmodium hemoglobin degradation.
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Affiliation(s)
- Mark E Drew
- Department of Medicine and Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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40
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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: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Dorin-Semblat D, Quashie N, Halbert J, Sicard A, Doerig C, Peat E, Ranford-Cartwright L, Doerig C. Functional characterization of both MAP kinases of the human malaria parasite Plasmodium falciparum by reverse genetics. Mol Microbiol 2007; 65:1170-80. [PMID: 17651389 DOI: 10.1111/j.1365-2958.2007.05859.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinome of the human malaria parasite Plasmodium falciparum includes two genes encoding mitogen-activated protein kinase (MAPK) homologues, pfmap-1 and pfmap-2, but no clear orthologue of the MAPK kinase (MAPKK) family, raising the question of the mode of activation and function of the plasmodial MAPKs. Functional studies in the rodent malaria model Plasmodium berghei recently showed the map-2 gene to be dispensable for asexual growth and gametocytogenesis, but essential for male gametogenesis in the mosquito vector. Here, we demonstrate by using a reverse genetics approach that the map-2 gene is essential for completion of the asexual cycle of P. falciparum, an unexpected result in view of the non-essentiality of the orthologous gene for P. berghei erythrocytic schizogony. This validates Pfmap-2 as a potential target for chemotherapeutic intervention. In contrast, the other P. falciparum MAPK, Pfmap-1, is required neither for in vitro schizogony and gametocytogenesis in erythrocytes, nor for gametogenesis and sporogony in the mosquito vector. However, Pfmap-2 protein levels are elevated in pfmap-1(-) parasites, suggesting that Pfmap-1 fulfils an important function in asexual parasites that necessitates compensatory adaptation in parasites lacking this enzyme.
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Affiliation(s)
- Dominique Dorin-Semblat
- INSERM U609, Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, Scotland, UK
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42
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Stack CM, Lowther J, Cunningham E, Donnelly S, Gardiner DL, Trenholme KR, Skinner-Adams TS, Teuscher F, Grembecka J, Mucha A, Kafarski P, Lua L, Bell A, Dalton JP. Characterization of the Plasmodium falciparum M17 Leucyl Aminopeptidase. J Biol Chem 2007; 282:2069-80. [PMID: 17107951 DOI: 10.1074/jbc.m609251200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amino acids generated from the catabolism of hemoglobin by intra-erythrocytic malaria parasites are not only essential for protein synthesis but also function in maintaining an osmotically stable environment, and creating a gradient by which amino acids that are rare or not present in hemoglobin are drawn into the parasite from host serum. We have proposed that a Plasmodium falciparum M17 leucyl aminopeptidase (PfLAP) generates and regulates the internal pool of free amino acids and therefore represents a target for novel antimalarial drugs. This enzyme has been expressed in insect cells as a functional 320-kDa homo-hexamer that is optimally active at neutral or alkaline pH, is dependent on metal ions for activity, and exhibits a substrate preference for N-terminally exposed hydrophobic amino acids, particularly leucine. PfLAP is produced by all stages in the intra-erythrocytic developmental cycle of malaria but was most highly expressed by trophozoites, a stage at which hemoglobin degradation and parasite protein synthesis are elevated. The enzyme was located by immunohistochemical methods and by transfecting malaria cells with a PfLAP-green fluorescent protein construct, to the cytosolic compartment of the cell at all developmental stages, including segregated merozoites. Amino acid dipeptide analogs, such as bestatin and its derivatives, are potent inhibitors of the protease and also block the growth of P. falciparum malaria parasites in culture. This study provides a biochemical basis for the antimalarial activity of aminopeptidase inhibitors. Availability of functionally active recombinant PfLAP, coupled with a simple enzymatic readout, will aid medicinal chemistry and/or high throughput approaches for the future design/discovery of new antimalarial drugs.
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Affiliation(s)
- Colin M Stack
- Institute for the Biotechnology of Infectious Diseases, University of Technology Sydney, Level 6, Building 4, Corner of Thomas and Harris Street, Ultimo, Sydney, New South Wales 2007, Australia
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43
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Eksi S, Czesny B, van Gemert GJ, Sauerwein RW, Eling W, Williamson KC. Inhibition of Plasmodium falciparum oocyst production by membrane-permeant cysteine protease inhibitor E64d. Antimicrob Agents Chemother 2006; 51:1064-70. [PMID: 17178799 PMCID: PMC1803139 DOI: 10.1128/aac.01012-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During asexual intraerythrocytic growth, Plasmodium falciparum utilizes hemoglobin obtained from the host red blood cell (RBC) as a nutrient source. Papain-like cysteine proteases, falcipains 2 and 3, have been reported to be involved in hemoglobin digestion and are targets of current antimalarial drug development efforts. However, their expression during gametocytogenesis, which is required for malaria parasite transmission, has not been studied. Many of the available antimalarials do not inhibit development of sexual stage parasites, and therefore, the persistence of gametocytes after drug treatment allows continued transmission of the disease. In the work reported here, incubation of stage V gametocytes with membrane-permeant cysteine protease inhibitor E64d significantly inhibited oocyst production (80 to 100%). The same conditions inhibited processing of gametocyte-surface antigen Pfs230 during gametogenesis but did not alter the morphology of the food vacuole in gametocytes, inhibit emergence, or block male exflagellation. E64d reduced the level of oocyst production more effectively than that reported previously for falcipain 1-knockout parasites, suggesting that falcipains 2 and 3 may also be involved in malaria parasite transmission. However, in this study only falcipain 3 and not falcipain 2 was found to be expressed in stage V gametocytes. Interestingly, during gametocytogenesis falcipain 3 was transported into the red blood cell and by stage V was localized in vesicles along the RBC surface, consistent with a role during gamete emergence. The ability of a membrane-permeant cysteine protease inhibitor to significantly reduce malaria parasite transmission suggests that future drug design should include evaluation of gametogenesis and sporogonic development.
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Affiliation(s)
- S Eksi
- Department of Biology, Loyola University Chicago, 6525 N. Sheridan Rd., Chicago, IL 60626, USA
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