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Mahanta PJ, Lhouvum K. Plasmodium falciparum proteases as new drug targets with special focus on metalloproteases. Mol Biochem Parasitol 2024; 258:111617. [PMID: 38554736 DOI: 10.1016/j.molbiopara.2024.111617] [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: 10/17/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Malaria poses a significant global health threat particularly due to the prevalence of Plasmodium falciparum infection. With the emergence of parasite resistance to existing drugs including the recently discovered artemisinin, ongoing research seeks novel therapeutic avenues within the malaria parasite. Proteases are promising drug targets due to their essential roles in parasite biology, including hemoglobin digestion, merozoite invasion, and egress. While exploring the genomic landscape of Plasmodium falciparum, it has been revealed that there are 92 predicted proteases, with only approximately 14 of them having been characterized. These proteases are further distributed among 26 families grouped into five clans: aspartic proteases, cysteine proteases, metalloproteases, serine proteases, and threonine proteases. Focus on metalloprotease class shows further role in organelle processing for mitochondria and apicoplasts suggesting the potential of metalloproteases as viable drug targets. Holistic understanding of the parasite intricate life cycle and identification of potential drug targets are essential for developing effective therapeutic strategies against malaria and mitigating its devastating global impact.
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Affiliation(s)
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
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2
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Cheuka PM, Dziwornu G, Okombo J, Chibale K. Plasmepsin Inhibitors in Antimalarial Drug Discovery: Medicinal Chemistry and Target Validation (2000 to Present). J Med Chem 2020; 63:4445-4467. [PMID: 31913032 DOI: 10.1021/acs.jmedchem.9b01622] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmepsins represent novel antimalarial drug targets. However, plasmepsin-based antimalarial drug discovery efforts in the past 2 decades have generally suffered some drawbacks including lack of translatability of target inhibition to potent parasite inhibition in vitro and in vivo as well as poor selectivity over the related human aspartic proteases. Most studies reported in this period have over-relied on the use of hemoglobinase plasmepsins I-IV (particularly I and II) as targets for the new inhibitors even though these are known to be nonessential at the asexual stage of parasite development. Therefore, future antimalarial drug discovery efforts seeking to identify plasmepsin inhibitors should focus on incorporating non-hemoglobinase plasmepsins such as V, IX, and X in their screening in order to maximize chances of success. Additionally, there is need to go beyond just target enzymatic activity profiling to establishing cellular activity, physicochemical as well as drug metabolism and pharmacokinetics properties and finally in vivo proof-of-concept while ensuring selectivity over related human host proteases.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, University of Zambia, Great East Road Campus, P.O. Box 32379, Lusaka, Zambia
| | - Godwin Dziwornu
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University, 701 West 168th Street, New York, New York 10032, United States
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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3
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Mishra V, Rathore I, Arekar A, Sthanam LK, Xiao H, Kiso Y, Sen S, Patankar S, Gustchina A, Hidaka K, Wlodawer A, Yada RY, Bhaumik P. Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. FEBS J 2018; 285:3077-3096. [PMID: 29943906 DOI: 10.1111/febs.14598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/10/2018] [Accepted: 06/22/2018] [Indexed: 11/28/2022]
Abstract
Malaria is a deadly disease killing worldwide hundreds of thousands people each year and the responsible parasite has acquired resistance to the available drug combinations. The four vacuolar plasmepsins (PMs) in Plasmodium falciparum involved in hemoglobin (Hb) catabolism represent promising targets to combat drug resistance. High antimalarial activities can be achieved by developing a single drug that would simultaneously target all the vacuolar PMs. We have demonstrated for the first time the use of soluble recombinant plasmepsin II (PMII) for structure-guided drug discovery with KNI inhibitors. Compounds used in this study (KNI-10742, 10743, 10395, 10333, and 10343) exhibit nanomolar inhibition against PMII and are also effective in blocking the activities of PMI and PMIV with the low nanomolar Ki values. The high-resolution crystal structures of PMII-KNI inhibitor complexes reveal interesting features modulating their differential potency. Important individual characteristics of the inhibitors and their importance for potency have been established. The alkylamino analog, KNI-10743, shows intrinsic flexibility at the P2 position that potentiates its interactions with Asp132, Leu133, and Ser134. The phenylacetyl tripeptides, KNI-10333 and KNI-10343, accommodate different ρ-substituents at the P3 phenylacetyl ring that determine the orientation of the ring, thus creating novel hydrogen-bonding contacts. KNI-10743 and KNI-10333 possess significant antimalarial activity, block Hb degradation inside the food vacuole, and show no cytotoxicity on human cells; thus, they can be considered as promising candidates for further optimization. Based on our structural data, novel KNI derivatives with improved antimalarial activity could be designed for potential clinical use. DATABASE: Structural data are available in the PDB under the accession numbers 5YIE, 5YIB, 5YID, 5YIC, and 5YIA.
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Affiliation(s)
- Vandana Mishra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anagha Arekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Lakshmi Kavitha Sthanam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Yoshiaki Kiso
- Laboratory of Peptide Sciences, Nagahama Institute of Bio-Science and Technology, Japan
| | - Shamik Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Koushi Hidaka
- Division of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Japan
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Rickey Y Yada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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4
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Abiri A. Plerixafor and related macrocyclic amines are potential drug candidates in treatment of malaria by "filling the flap" region of plasmepsin enzymes. Med Hypotheses 2018; 118:68-73. [PMID: 30037618 DOI: 10.1016/j.mehy.2018.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/24/2018] [Accepted: 06/19/2018] [Indexed: 11/30/2022]
Abstract
Death by Plasmodium falsiparum, the leading cause of malaria, is going to remain a major obstacle among the infectious diseases. Plasmepsin aspartic proteases are key proteins in the pathogenesis of plasmodium species which break down the hemoglobin and exploit it as a source of amino acids. These enzymes are one of the favorite targeting agents for medicinal chemists to design new drugs. Plasmepsin proteins show a "flap" region in their N-terminal domain, predisposing them to a good "filler" drug with an exceptional affinity to this enzyme. Plerixafor (Mozobil®, AMD3100), a CXCR4 antagonist with a bicyclam ring, historically discovered as an impurity in a mixture which had anti-HIV properties, is now a FDA approved drug for mobilizing haematopoietic stem cells in cancer patients. In this hypothesis, we focused on the similarity of the structure of plerixafor and its analogues with heme functional group of hemoglobin, the main substrate of plasmepsin, and also with some other recent azamacrocyclic compounds demonstrating antimalarial activity, to test whether these compounds are capable of exhibiting antimalarial activity by inhibiting plasmepsin or not. A preliminary in silico docking study was used to evaluate this hypothesis and docking results indicated that macrocyclic cyclams and cyclens can reliably act as potent lead drug or central pharmacophore in developing new plasmepsin inhibitors as compared with previously designed plasmepsin II inhibitors.
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Affiliation(s)
- Ardavan Abiri
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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5
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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: 3.7] [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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6
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Hamada Y, Kiso Y. New directions for protease inhibitors directed drug discovery. Biopolymers 2016; 106:563-79. [PMID: 26584340 PMCID: PMC7161749 DOI: 10.1002/bip.22780] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/25/2015] [Accepted: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms-from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, β-secretase, virus proteases, and dipeptidyl peptidase-4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T-lymphotropic virus type I protease, plasmepsins, and β-secretase, as drug candidates for hypertension, adult T-cell leukaemia, human T-lymphotropic virus type I-associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563-579, 2016.
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Affiliation(s)
- Yoshio Hamada
- Medicinal Chemistry LaboratoryKobe Pharmaceutical University, MotoyamakitaHigashinada‐kuKobe658‐8558Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Nagahama Institute of Bio‐Science and TechnologyTamura‐choNagahama526‐0829Japan
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7
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Aneja B, Kumar B, Jairajpuri MA, Abid M. A structure guided drug-discovery approach towards identification of Plasmodium inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra19673f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
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Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
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8
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Liu P, Robbins AH, Marzahn MR, McClung SH, Yowell CA, Stevens SM, Dame JB, Dunn BM. Enzymatic Characterization of Recombinant Food Vacuole Plasmepsin 4 from the Rodent Malaria Parasite Plasmodium berghei. PLoS One 2015; 10:e0141758. [PMID: 26510189 PMCID: PMC4624963 DOI: 10.1371/journal.pone.0141758] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/12/2015] [Indexed: 01/17/2023] Open
Abstract
The rodent malaria parasite Plasmodium berghei is a practical model organism for experimental studies of human malaria. Plasmepsins are a class of aspartic proteinase isoforms that exert multiple pathological effects in malaria parasites. Plasmepsins residing in the food vacuole (FV) of the parasite hydrolyze hemoglobin in red blood cells. In this study, we cloned PbPM4, the FV plasmepsin gene of P. berghei that encoded an N-terminally truncated pro-segment and the mature enzyme from genomic DNA. We over-expressed this PbPM4 zymogen as inclusion bodies (IB) in Escherichia coli, and purified the protein following in vitro IB refolding. Auto-maturation of the PbPM4 zymogen to mature enzyme was carried out at pH 4.5, 5.0, and 5.5. Interestingly, we found that the PbPM4 zymogen exhibited catalytic activity regardless of the presence of the pro-segment. We determined the optimal catalytic conditions for PbPM4 and studied enzyme kinetics on substrates and inhibitors of aspartic proteinases. Using combinatorial chemistry-based peptide libraries, we studied the active site preferences of PbPM4 at subsites S1, S2, S3, S1’, S2’ and S3’. Based on these results, we designed and synthesized a selective peptidomimetic compound and tested its inhibition of PbPM4, seven FV plasmepsins from human malaria parasites, and human cathepsin D (hcatD). We showed that this compound exhibited a >10-fold selectivity to PbPM4 and human malaria parasite plasmepsin 4 orthologs versus hcatD. Data from this study furthesr our understanding of enzymatic characteristics of the plasmepsin family and provides leads for anti-malarial drug design.
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Affiliation(s)
- Peng Liu
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (PL); (BMD)
| | - Arthur H. Robbins
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Melissa R. Marzahn
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Scott H. McClung
- Protein Core, Interdisciplinary Center for Biotechnology Research, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Charles A. Yowell
- Department of Infectious Diseases and Pathology, University of Florida, College of Veterinary Medicine, Gainesville, Florida, United States of America
| | - Stanley M. Stevens
- Protein Core, Interdisciplinary Center for Biotechnology Research, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - John B. Dame
- Department of Infectious Diseases and Pathology, University of Florida, College of Veterinary Medicine, Gainesville, Florida, United States of America
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- * E-mail: (PL); (BMD)
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9
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New paradigm of an old target: an update on structural biology and current progress in drug design towards plasmepsin II. Eur J Med Chem 2015; 95:324-48. [PMID: 25827401 DOI: 10.1016/j.ejmech.2015.03.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/09/2015] [Accepted: 03/20/2015] [Indexed: 11/20/2022]
Abstract
Malaria is one of the major parasitic disease whose rapid spreading and mortality rate affects all parts of the world especially several parts of Asia as well as Africa. The emergence of multi-drug resistant strains hamper the progress of current antimalarial therapy and displayed an urgent need for new antimalarials by targeting novel drug targets. Until now, several promising targets were explored in order to develop a promising Achilles hill to counter malaria. Plasmepsin, an aspartic protease, which is involved in the hemoglobin breakdown into smaller peptides emerged as a crucial target to develop new chemical entities to counter malaria. Due to early crystallographic evidence, plasmepsin II (Plm II) emerged as well explored target to develop novel antimalarials as well as a starting point to develop inhibitors targeting some other subtypes of plasmepsins i.e. Plm I, II, IV and V. With the advancements in drug discovery, several computational and synthetic approaches were employed in order to develop novel inhibitors targeting Plm II. Strategies such as fragment based drug design, molecular dynamics simulation, double drug approach etc. were employed in order to develop new chemical entities targeting Plm II. But majority of Plm II inhibitors suffered from poor selectivity over cathepsin D as well as other subtypes of plasmepsins. This review highlights an updated account of drug discovery efforts targeting plasmepsin II from a medicinal chemistry perspective.
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10
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Miura T, Hidaka K, Azai Y, Kashimoto K, Kawasaki Y, Chen SE, de Freitas RF, Freire E, Kiso Y. Optimization of plasmepsin inhibitor by focusing on similar structural feature with chloroquine to avoid drug-resistant mechanism of Plasmodium falciparum. Bioorg Med Chem Lett 2014; 24:1698-701. [DOI: 10.1016/j.bmcl.2014.02.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/12/2014] [Accepted: 02/19/2014] [Indexed: 11/17/2022]
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11
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Song Y, Jin H, Liu X, Zhu L, Huang J, Li H. Discovery of non-peptide inhibitors of Plasmepsin II by structure-based virtual screening. Bioorg Med Chem Lett 2013; 23:2078-82. [DOI: 10.1016/j.bmcl.2013.01.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/26/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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Alam A, Goyal M, Iqbal MS, Pal C, Dey S, Bindu S, Maity P, Bandyopadhyay U. Novel antimalarial drug targets: hope for new antimalarial drugs. Expert Rev Clin Pharmacol 2012; 2:469-89. [PMID: 22112223 DOI: 10.1586/ecp.09.28] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Malaria is a major global threat, that results in more than 2 million deaths each year. The treatment of malaria is becoming extremely difficult due to the emergence of drug-resistant parasites, the absence of an effective vaccine, and the spread of insecticide-resistant vectors. Thus, malarial therapy needs new chemotherapeutic approaches leading to the search for new drug targets. Here, we discuss different approaches to identifying novel antimalarial drug targets. We have also given due attention to the existing validated targets with a view to develop novel, rationally designed lead molecules. Some of the important parasite proteins are claimed to be the targets; however, further in vitro or in vivo structure-function studies of such proteins are crucial to validate these proteins as suitable targets. The interactome analysis among apicoplast, mitochondrion and genomic DNA will also be useful in identifying vital pathways or proteins regulating critical pathways for parasite growth and survival, and could be attractive targets. Molecules responsible for parasite invasion to host erythrocytes and ion channels of infected erythrocytes, essential for intra-erythrocyte survival and stage progression of parasites are also becoming attractive targets. This review will discuss and highlight the current understanding regarding the potential antimalarial drug targets, which could be utilized to develop novel antimalarials.
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Affiliation(s)
- Athar Alam
- Division of Infectious Diseases and Immunology, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India.
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Dali B, Keita M, Megnassan E, Frecer V, Miertus S. Insight into Selectivity of Peptidomimetic Inhibitors with Modified Statine Core for Plasmepsin II of Plasmodium falciparum over Human Cathepsin D. Chem Biol Drug Des 2012; 79:411-30. [DOI: 10.1111/j.1747-0285.2011.01276.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Bhaumik P, Gustchina A, Wlodawer A. Structural studies of vacuolar plasmepsins. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:207-23. [PMID: 21540129 PMCID: PMC3154504 DOI: 10.1016/j.bbapap.2011.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Plasmepsins (PMs) are pepsin-like aspartic proteases present in different species of parasite Plasmodium. Four Plasmodium spp. (P. vivax, P. ovale, P. malariae, and the most lethal P. falciparum) are mainly responsible for causing human malaria that affects millions worldwide. Due to the complexity and rate of parasite mutation coupled with regional variations, and the emergence of P. falciparum strains which are resistant to antimalarial agents such as chloroquine and sulfadoxine/pyrimethamine, there is constant pressure to find new and lasting chemotherapeutic drug therapies. Since many proteases represent therapeutic targets and PMs have been shown to play an important role in the survival of parasite, these enzymes have recently been identified as promising targets for the development of novel antimalarial drugs. The genome of P. falciparum encodes 10 PMs (PMI, PMII, PMIV-X and histo-aspartic protease (HAP)), 4 of which (PMI, PMII, PMIV and HAP) reside within the food vacuole, are directly involved in degradation of human hemoglobin, and share 50-79% amino acid sequence identity. This review focuses on structural studies of only these four enzymes, including their orthologs in other Plasmodium spp.. Almost all original crystallographic studies were performed with PMII, but more recent work on PMIV, PMI, and HAP resulted in a more complete picture of the structure-function relationship of vacuolar PMs. Many structures of inhibitor complexes of vacuolar plasmepsins, as well as their zymogens, have been reported in the last 15 years. Information gained by such studies will be helpful for the development of better inhibitors that could become a new class of potent antimalarial drugs. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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15
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Miura T, Hidaka K, Uemura T, Kashimoto K, Hori Y, Kawasaki Y, Ruben AJ, Freire E, Kimura T, Kiso Y. Improvement of both plasmepsin inhibitory activity and antimalarial activity by 2-aminoethylamino substitution. Bioorg Med Chem Lett 2010; 20:4836-9. [DOI: 10.1016/j.bmcl.2010.06.099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/17/2010] [Accepted: 06/19/2010] [Indexed: 10/19/2022]
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16
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Luksch T, Blum A, Klee N, Diederich W, Sotriffer C, Klebe G. Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein. ChemMedChem 2010; 5:443-54. [DOI: 10.1002/cmdc.200900452] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Li F, Patra KP, Yowell CA, Dame JB, Chin K, Vinetz JM. Apical surface expression of aspartic protease Plasmepsin 4, a potential transmission-blocking target of the plasmodium ookinete. J Biol Chem 2010; 285:8076-83. [PMID: 20056606 DOI: 10.1074/jbc.m109.063388] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To invade its definitive host, the mosquito, the malaria parasite must cross the midgut peritrophic matrix that is composed of chitin cross-linked by chitin-binding proteins and then develop into an oocyst on the midgut basal lamina. Previous evidence indicates that Plasmodium ookinete-secreted chitinase is important in midgut invasion. The mechanistic role of other ookinete-secreted enzymes in midgut invasion has not been previously examined. De novo mass spectrometry sequencing of a protein obtained by benzamidine affinity column of Plasmodium gallinaceum ookinete axenic culture supernatant demonstrated the presence of an ookinete-secreted plasmepsin, an aspartic protease previously only known to be present in the digestive vacuole of asexual stage malaria parasites. This plasmepsin, the ortholog of Plasmodium falciparum plasmepsin 4, was designated PgPM4. PgPM4 and PgCHT2 (the P. gallinaceum ortholog of P. falciparum chitinase PfCHT1) are both localized on the ookinete apical surface, and both are present in micronemes. Aspartic protease inhibitors (peptidomimetic and natural product), calpain inhibitors, and anti-PgPM4 monoclonal antibodies significantly reduced parasite infectivity for mosquitoes. These results suggest that plasmepsin 4, previously known only to function in the digestive vacuole of asexual blood stage Plasmodium, plays a role in how the ookinete interacts with the mosquito midgut interactions as it becomes an oocyst. These data are the first to delineate a role for an aspartic protease in mediating Plasmodium invasion of the mosquito and demonstrate the potential for plasmepsin 4 as a malaria transmission-blocking vaccine target.
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Affiliation(s)
- Fengwu Li
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California 92093, USA
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18
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Mohapatra SC, Tiwari HK, Singla M, Rathi B, Sharma A, Mahiya K, Kumar M, Sinha S, Chauhan SS. Antimalarial evaluation of copper(II) nanohybrid solids: inhibition of plasmepsin II, a hemoglobin-degrading malarial aspartic protease from Plasmodium falciparum. J Biol Inorg Chem 2009; 15:373-85. [PMID: 19946719 DOI: 10.1007/s00775-009-0610-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
Abstract
A new class of copper(II) nanohybrid solids, LCu(CH(3)COO)(2) and LCuCl(2), have been synthesized and characterized by transmission electron microscopy, dynamic light scattering, and IR spectroscopy, and have been found to be capped by a bis(benzimidazole) diamide ligand (L). The particle sizes of these nanohybrid solids were found to be in the ranges 5-10 and 60-70 nm, respectively. These nanohybrid solids were evaluated for their in vitro antimalarial activity against a chloroquine-sensitive isolate of Plasmodium falciparum (MRC 2). The interactions between these nanohybrid solids and plasmepsin II (an aspartic protease and a plausible novel target for antimalarial drug development), which is believed to be essential for hemoglobin degradation by the parasite, have been assayed by UV-vis spectroscopy and inhibition kinetics using Lineweaver-Burk plots. Our results suggest that these two compounds have antimalarial activities, and the IC(50) values (0.025-0.032 microg/ml) are similar to the IC(50) value of the standard drug chloroquine used in the bioassay. Lineweaver-Burk plots for inhibition of plasmepsin II by LCu(CH(3)COO)(2) and LCuCl(2) show that the inhibition is competitive with respect to the substrate. The inhibition constants of LCu(CH(3)COO)(2) and LCuCl(2) were found to be 10 and 13 microM, respectively. The IC(50) values for inhibition of plasmepsin II by LCu(CH(3)COO)(2) and LCuCl(2) were found to be 14 and 17 microM, respectively. Copper(II) metal capped by a benzimidazole group, which resembles the histidine group of copper proteins (galactose oxidase, beta-hydroxylase), could provide a suitable anchoring site on the nanosurface and thus could be useful for inhibition of target enzymes via binding to the S1/S3 pocket of the enzyme hydrophobically. Both copper(II) nanohybrid solids were found to be nontoxic against human hepatocellular carcinoma cells and were highly selective for plasmepsin II versus human cathepsin D. The pivotal mechanism of antimalarial activity of these compounds via plasmepsin II inhibition in the P. falciparum malaria parasite is demonstrated.
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Stroba A, Schaeffer F, Hindie V, Lopez-Garcia L, Adrian I, Fröhner W, Hartmann RW, Biondi RM, Engel M. 3,5-Diphenylpent-2-enoic Acids as Allosteric Activators of the Protein Kinase PDK1: Structure−Activity Relationships and Thermodynamic Characterization of Binding as Paradigms for PIF-Binding Pocket-Targeting Compounds†PDB code of 2Z with PDK1: 3HRF. J Med Chem 2009; 52:4683-93. [DOI: 10.1021/jm9001499] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adriana Stroba
- Pharmaceutical and Medicinal Chemistry, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
| | - Francis Schaeffer
- Unité de Biochimie Structurale (CNRS-URA 2185), Institut Pasteur, F-75724 Paris, France
| | - Valerie Hindie
- Department of Internal Medicine I, University of Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Laura Lopez-Garcia
- Department of Internal Medicine I, University of Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Iris Adrian
- Department of Internal Medicine I, University of Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Wolfgang Fröhner
- Pharmaceutical and Medicinal Chemistry, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
| | - Rolf W. Hartmann
- Pharmaceutical and Medicinal Chemistry, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
| | - Ricardo M. Biondi
- Department of Internal Medicine I, University of Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
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20
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Oda M, Saito M, Tsumuraya T, Fujii I. Contribution of the trifluoroacetyl group in the thermodynamics of antigen-antibody binding. J Mol Recognit 2009; 23:263-70. [DOI: 10.1002/jmr.958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Zürcher M, Hof F, Barandun L, Schütz A, Schweizer WB, Meyer S, Bur D, Diederich F. Synthesis ofexo-3-Amino-7-azabicyclo[2.2.1]heptanes as a Class of Malarial Aspartic Protease Inhibitors: Exploration of Two Binding Pockets. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801184] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Nguyen JT, Hamada Y, Kimura T, Kiso Y. Design of potent aspartic protease inhibitors to treat various diseases. Arch Pharm (Weinheim) 2008; 341:523-35. [PMID: 18763714 DOI: 10.1002/ardp.200700267] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this retrospective, personal review covering our research from the late 1980s until 2007, we outline nearly two-decade worth of our own work on several aspartic protease inhibitors including those affecting renin, HIV-1 protease, plasmepsins, beta-secretase, and HTLV-I protease and we report on aspartic protease inhibitors as potential drugs to treat hypertension, AIDS, malaria, Alzheimer's disease and adult T-cell leukemia, HTLV-I associated myelopathy / tropical spastic paraparesis, and various, respectively, associated diseases. Herein, we describe our methods for rational substrate-based drug design of peptidomimetics that potently inhibit the activity of renin, HIV-1 protease, plasmepsins, beta-secretase, and HTLV-I protease accordingly, using an appropriately selected inhibitory residue that contained a hydroxymethylcarbonyl isostere. Although this non-hydrolyzable isostere mimics the transition state that is formed during protein cleavage of a substrate, the isostere-containing inhibitor is not cleaved. We highlight our optimization studies in which we used various techniques and tools such as truncation studies, natural and non-natural amino acid substitution studies, various moieties to promote chemical and pharmacological stability, X-ray crystallography, computer-assisted docking and dynamic simulations, quantitative structure-activity relationship studies, and various other methods that this review can barely mention.
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Affiliation(s)
- Jeffrey-Tri Nguyen
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science and 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto, Japan
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23
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Hidaka K, Kimura T, Ruben AJ, Uemura T, Kamiya M, Kiso A, Okamoto T, Tsuchiya Y, Hayashi Y, Freire E, Kiso Y. Antimalarial activity enhancement in hydroxymethylcarbonyl (HMC) isostere-based dipeptidomimetics targeting malarial aspartic protease plasmepsin. Bioorg Med Chem 2008; 16:10049-60. [PMID: 18952439 DOI: 10.1016/j.bmc.2008.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/03/2008] [Accepted: 10/04/2008] [Indexed: 11/19/2022]
Abstract
Plasmepsin (Plm) is a potential target for new antimalarial drugs, but most reported Plm inhibitors have relatively low antimalarial activities. We synthesized a series of dipeptide-type HIV protease inhibitors, which contain an allophenylnorstatine-dimethylthioproline scaffold to exhibit potent inhibitory activities against Plm II. Their activities against Plasmodium falciparum in the infected erythrocyte assay were largely different from those against the target enzyme. To improve the antimalarial activity of peptidomimetic Plm inhibitors, we attached substituents on a structure of the highly potent Plm inhibitor KNI-10006. Among the derivatives, we identified alkylamino compounds such as 44 (KNI-10283) and 47 (KNI-10538) with more than 15-fold enhanced antimalarial activity, to the sub-micromolar level, maintaining their potent Plm II inhibitory activity and low cytotoxicity. These results suggest that auxiliary substituents on a specific basic group contribute to deliver the inhibitors to the target Plm.
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Affiliation(s)
- Koushi Hidaka
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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24
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Synthesis and activity of tetrapeptidic HTLV-I protease inhibitors possessing different P3-cap moieties. Bioorg Med Chem 2008; 16:5795-802. [PMID: 18400502 DOI: 10.1016/j.bmc.2008.03.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 03/21/2008] [Accepted: 03/22/2008] [Indexed: 11/24/2022]
Abstract
The causative agent behind adult T-cell leukemia and tropical spastic paraparesis/HTLV-I-associated myelopathy is the human T-cell leukemia virus type 1 (HTLV-I). Tetrapeptidic HTLV-I protease inhibitors were designed on a previously reported potent inhibitor KNI-10516, with modifications at the P(3)-cap moieties. All the inhibitors showed high HIV-1 protease inhibitory activity (over 98% inhibition at 50nM) and most exhibited highly potent inhibition against HTLV-I protease (IC(50) values were less than 100nM).
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25
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Ersmark K, Samuelsson B, Hallberg A. Plasmepsins as potential targets for new antimalarial therapy. Med Res Rev 2007; 26:626-66. [PMID: 16838300 DOI: 10.1002/med.20082] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Malaria is one of the major diseases in the world. Due to the rapid spread of parasite resistance to available antimalarial drugs there is an urgent need for new antimalarials with novel mechanisms of action. Several promising targets for drug intervention have been revealed in recent years. This review addresses the parasitic aspartic proteases termed plasmepsins (Plms) that are involved in the hemoglobin catabolism that occurs during the erythrocytic stage of the malarial parasite life cycle. Four Plasmodium species are responsible for human malaria; P. vivax, P. ovale, P. malariae, and P. falciparum. This review focuses on inhibitors of the haemoglobin-degrading plasmepsins of the most lethal species, P. falciparum; Plm I, Plm II, Plm IV, and histo-aspartic protease (HAP). Previously, Plm II has attracted the most attention. With the identification and characterization of new plasmepsins and the results from recent plasmepsin knockout studies, it now seems clear that in order to achieve high-antiparasitic activities in P. falciparum-infected erythrocytes it is necessary to inhibit several of the haemoglobin-degrading plasmepsins. Herein we summarize the structure-activity relationships of the Plm I, II, IV, and HAP inhibitors. These inhibitors represent all classes which, to the best of our knowledge, have been disclosed in journal articles to date. The 3D structures of inhibitor/plasmepsin II complexes available in the protein data bank are briefly discussed and compared.
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Affiliation(s)
- Karolina Ersmark
- Department of Medicinal Chemistry, Uppsala University, BMC, SE-751 23 Uppsala, Sweden
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26
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Synthesis of chiral β2,2,3-3-amino-2-hydroxyalkanoates and 3-alkyl-3-hydroxy-β-lactams by double asymmetric induction. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.05.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Sohma Y, Kiso Y. "Click peptides"--chemical biology-oriented synthesis of Alzheimer's disease-related amyloid beta peptide (abeta) analogues based on the "O-acyl isopeptide method". Chembiochem 2007; 7:1549-57. [PMID: 16915597 DOI: 10.1002/cbic.200600112] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A clear understanding of the pathological mechanism of amyloid beta peptide (Abeta) 1-42, a currently unexplained process, would be of great significance for the discovery of novel drug targets for Alzheimer's disease (AD) therapy. To date, though, the elucidation of these Abeta1-42 dynamic events has been a difficult issue because of uncontrolled polymerization, which also poses a significant obstacle in establishing experimental systems with which to clarify the pathological function of Abeta1-42. We have recently developed chemical biology-oriented pH- or phototriggered "click peptide" isoform precursors of Abeta1-42, based on the "O-acyl isopeptide method", in which a native amide bond at a hydroxyamino acid residue, such as Ser, is isomerized to an ester bond, the target peptide subsequently being generated by an O-N intramolecular acyl migration reaction. These click peptide precursors did not exhibit any self-assembling character under physiological conditions, thanks to the presence of the one single ester bond, and were able to undergo migration to give the target Abeta1-42 in a quick and easy, one-way (so-called "click")conversion reaction. The use of click peptides could be a useful strategy to investigate the biological functions of Abeta1-42 in AD through inducible activation of Abeta1-42 self-assembly.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry Center for Frontier Research in Medicinal Science 21st Century COE Program, Kyoto Pharmaceutical University Yamashina-ku, Kyoto 607-8412, Japan
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28
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Hidaka K, Kimura T, Tsuchiya Y, Kamiya M, Ruben AJ, Freire E, Hayashi Y, Kiso Y. Additional interaction of allophenylnorstatine-containing tripeptidomimetics with malarial aspartic protease plasmepsin II. Bioorg Med Chem Lett 2007; 17:3048-52. [PMID: 17400453 DOI: 10.1016/j.bmcl.2007.03.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 03/14/2007] [Accepted: 03/16/2007] [Indexed: 10/23/2022]
Abstract
Based on a highly potent allophenylnorstatine-containing inhibitor, KNI-10006, against the plasmepsins of Plasmodium falciparum, we synthesized a series of tripeptide-type compounds with various N-terminal moieties and evaluated their inhibitory activities against plasmepsin II. Certain phenylacetyl derivatives exhibited extremely high affinity with K(i) values of less than 0.1n M suggesting successful hydrophobic interactions.
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Affiliation(s)
- Koushi Hidaka
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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29
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Sohma Y, Yoshiya T, Taniguchi A, Kimura T, Hayashi Y, Kiso Y. Development of O-acyl isopeptide method. Biopolymers 2007; 88:253-62. [PMID: 17236207 DOI: 10.1002/bip.20683] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
During over a decade of study on aspartic protease inhibitors and water-soluble prodrugs, in 2003, we discovered that the presence of an O-acyl instead of N-acyl residue within the peptide backbone significantly changed the secondary structure of the native peptide. In addition, the target peptide was subsequently generated by an O-N intramolecular acyl migration reaction. These findings led to the development of a novel method, called "O-acyl isopeptide method," for the synthesis of peptides containing difficult sequence. Further application of the method to Alzheimer's Abeta1-42 revealed that the O-acyl isopeptide of Abeta1-42 could be effectively synthesized and stored without spontaneous self-assembly. Intact monomer Abeta1-42 could then be obtained from the isopeptide under physiological experimental conditions. We named the O-acyl isopeptide as "Click Peptide," because of its "quick and easy one-way conversion" to the parent Abeta1- 42. Application of the click peptide has provided a new basis for the investigation of the biological functions of Abeta1-42 by inducible activation of its self-assembly. The O-acyl isopeptide method has further evolved as a general method for peptides synthesis with our recent developments of "O-acyl isodipeptide units" and "racemization-free segment condensation methodology." Isodipeptide units have enabled routine use of the O-acyl isopeptide method by avoiding the often difficult esterification reaction on resin. "Racemizationfree segment condensation methodology" has been achieved by employing N-segments possessing a C-terminal urethaneprotected O-acyl Ser/Thr residues. The synthesis of long peptides/proteins by racemization-free segment condensation has thus become possible at Ser/Thr residues instead of Cterminal Gly/Pro residues. As the O-acyl isopeptide method becomes more widely utilized, we have composed this review to facilitate its application for the production of peptides and proteins.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Kyoto, Japan
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30
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Ziora Z, Kasai S, Hidaka K, Nagamine A, Kimura T, Hayashi Y, Kiso Y. Design and synthesis of BACE1 inhibitors containing a novel norstatine derivative (2R,3R)-3-amino-2-hydroxy-4-(phenylthio)butyric acid. Bioorg Med Chem Lett 2007; 17:1629-33. [PMID: 17251016 DOI: 10.1016/j.bmcl.2006.12.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 12/21/2006] [Accepted: 12/23/2006] [Indexed: 01/09/2023]
Abstract
A novel norstatine derivative, phenylthionorstatine [(2R,3R)-3-amino-2-hydroxy-4-(phenylthio)butyric acid; Ptns], containing a hydroxymethylcarbonyl (HMC) isostere was designed, synthesized, and stereochemically determined. Then, Ptns was introduced into the structure of BACE1 inhibitors at the P(1) position. Finally, Ptns was found as a suitable P(1) moiety for potent BACE1 inhibitor design.
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Affiliation(s)
- Zyta Ziora
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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31
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Dell'Agli M, Parapini S, Galli G, Vaiana N, Taramelli D, Sparatore A, Liu P, Dunn BM, Bosisio E, Romeo S. High antiplasmodial activity of novel plasmepsins I and II inhibitors. J Med Chem 2007; 49:7440-9. [PMID: 17149873 DOI: 10.1021/jm061033d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aim of this study was to develop new antiplasmodial compounds acting through distinct mechanisms during both the liver and the blood stages of the parasite life cycle. Compounds were designed on the basis of the "double-drug" approach: primaquine, which has been linked to statine-based inhibitors of plasmepsins (PLMs), the plasmodial aspartic proteases involved in degradation of hemeoglobin. The compounds were tested in vitro for anti-PLM I/PLM II activities and against chloroquine-sensitive (D10) and chloroquine-resistant (W2) strains of P. falciparum. An antiplasmodial activity (IC(50)) as low as 0.1 microM was obtained, an excellent improvement in comparison with inhibitors previously reported (IC(50) = 2-20 microM). The killing activity was equally directed against both P. falciparum strains and was correlated to lipophilicity (calculated as ALogP), for all compounds but one (9). All compounds inhibited PLM I and PLM II in the nanomolar range (K(i) = 1-700 nM). The most promising compounds (2, 6, 10) were not cytotoxic against human fibroblasts at 100 microM and were highly selective for PLMs vs human cathepsin D.
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Affiliation(s)
- Mario Dell'Agli
- Department of Pharmacological Sciences, School of Pharmacy, University of Milan, Milan 20100, Italy
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32
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Strömbergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JES, Komorowski J, Hvidsten TR. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins 2006; 65:568-79. [PMID: 16948162 DOI: 10.1002/prot.21163] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Modeling and understanding protein-ligand interactions is one of the most important goals in computational drug discovery. To this end, proteochemometrics uses structural and chemical descriptors from several proteins and several ligands to induce interaction-models. Here, we present a new and generalized approach in which proteins varying greatly in terms of sequence and structure are represented by a library of local substructures. Using linear regression and rule-based learning, we combine such local substructures with chemical descriptors from the ligands to model binding affinity for a training set of hydrolase and lyase enzymes. We evaluate the predictive performance of these models using cross validation and sets of unseen ligand with unknown three-dimensional structure. The models are shown to generalize by outperforming models using descriptors from only proteins or only ligands, or models using global structure similarities rather than local similarities. Thus, we demonstrate that this approach is capable of describing dependencies between local structural properties and ligands in otherwise dissimilar protein structures. These dependencies are often, but not always, associated with local substructures that are in contact with the ligands. Finally, we show that strongly bound enzyme-ligand complexes require the presence of particular local substructures, while weakly bound complexes may be described by the absence of certain properties. The results demonstrate that the alignment-independent approach using local substructures is capable of describing protein-ligand interaction for largely different proteins and hence opens up for proteochemometrics-analysis of the interaction-space of entire proteomes. Current approaches are limited to families of closely related proteins. families of closely related proteins.
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Affiliation(s)
- Helena Strömbergsson
- The Linnaeus Centre for Bioinformatics, Uppsala University, SE-751 24, Uppsala, Sweden
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33
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Seo WD, Curtis-Long MJ, Ryu YB, Lee JH, Yang MS, Lee WS, Park KH. Highly Diastereoselective Epimerization: Stereodivergent Synthesis of α-Hydroxy-β-amino Isopentanoic Acid. J Org Chem 2006; 71:5008-11. [PMID: 16776536 DOI: 10.1021/jo060309m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The high diastereoselectivity of the base-catalyzed epimerization of oxazolidin-2-ones 7 and 8 is shown to depend on the nature of the N-substituent (R group); when R = Bn, the 4,5-trans-product (4S,5R)-9 is formed, whereas when R = H the 4,5-cis-product (4S,5S)-10 is formed, both with >99:1 dr. The successful hydrolysis of the oxazolidin-2-one group in both cis- and trans-derivatives show this to be a stereodivergent route to enantiopure alpha-hydroxy-beta-amino isopentanoic acids (2R,3S)-1 and (2S,3S)-2.
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Affiliation(s)
- Woo Duck Seo
- Division of Applied Life Science (BK 21 Program), Department of Agricultural Chemistry, Research Institute of Life Science, Gyeongsang National University, 660-701, Korea
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34
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Affiliation(s)
- Adam J Ruben
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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35
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Ersmark K, Nervall M, Hamelink E, Janka LK, Clemente JC, Dunn BM, Blackman MJ, Samuelsson B, Aqvist J, Hallberg A. Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations. J Med Chem 2005; 48:6090-106. [PMID: 16162010 DOI: 10.1021/jm050463l] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of inhibitors of the malarial aspartic proteases Plm I and II have been synthesized with L-mannitol as precursor. These inhibitors are characterized by either a diacylhydrazine or a five-membered oxadiazole ring replacing backbone amide functionalities. Molecular dynamics simulations were applied in the design process. The computationally predicted Plm II Ki values were generally in excellent agreement with the biological results. The diacylhydrazine was found to be superior over the oxadiazole as an amide bond replacement in the Plm I and II inhibitors studied. An extensive flexibility of the S2' pocket was captured by the simulations predicting the binding mode of the unsymmetrical inhibitors. Plm I and II inhibitors with single digit nanomolar Ki values devoid of inhibitory activity toward human Cat D were identified. One compound, lacking amide bonds, was found to be Plm IV selective and very potent, with a Ki value of 35 nM.
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Affiliation(s)
- Karolina Ersmark
- Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, 751 23 Uppsala, Sweden
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36
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Johansson PO, Lindberg J, Blackman MJ, Kvarnström I, Vrang L, Hamelink E, Hallberg A, Rosenquist A, Samuelsson B. Design and synthesis of potent inhibitors of plasmepsin I and II: X-ray crystal structure of inhibitor in complex with plasmepsin II. J Med Chem 2005; 48:4400-9. [PMID: 15974592 DOI: 10.1021/jm040884n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New and potent inhibitors of the malarial aspartic proteases plasmepsin (Plm) I and II, from the deadliest malaria parasite Plasmodium falciparum, have been synthesized utilizing Suzuki coupling reactions on previously synthesized bromobenzyloxy-substituted statine-like inhibitors. The enzyme inhibition activity has been improved up to eight times by identifying P1 substituents that effectively bind to the continuous S1-S3 crevice of Plasmepsin I and II. By replacement of the bromo atom in the P1 p-bromobenzyloxy-substituted inhibitors with different aryl substituents, several inhibitors exhibiting K(i) values in the low nanomolar range for both Plm I and II have been identified. Some of these inhibitors are also effective in attenuating parasite growth in red blood cells, with the best inhibitors, compounds 2 and 4, displaying 70% and 83% inhibition, respectively, at a concentration of 5 microM. The design was partially guided by the X-ray crystal structure disclosed herein of the previously synthesized inhibitor 1 in complex with plasmepsin II.
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Affiliation(s)
- Per-Ola Johansson
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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37
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Sharma A, Eapen A, Subbarao SK. Purification and Characterization of a Hemoglobin Degrading Aspartic Protease from the Malarial Parasite Plasmodium vivax. ACTA ACUST UNITED AC 2005; 138:71-8. [PMID: 16046450 DOI: 10.1093/jb/mvi105] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Aspartic proteases of human malarial parasites are thought to play key roles in essential pathways of merozoite release, invasion and host cell hemoglobin degradation during the intraerythrocytic stages of their life cycle. Therefore, we have purified and characterized Plasmodium vivax aspartic protease, to determine if this enzyme can be used as potential drug target/immunogen, and its inhibitors as potential antimalarial drug. The P. vivax aspartic protease has been purified by a combination of ion exchange and size exclusion chromatographies and HPLC. Its properties were examined in order to define a role in the hemoglobin degradation process. The purified enzyme migrated as a single band on native PAGE and SDS/PAGE with a molecular mass of 40 kDa. Gelatin zymogram analyses revealed a clear zone of proteolytic activity corresponding to the band obtained on native PAGE and SDS/PAGE. The enzyme has an optimal pH of 4.0 and exhibits its highest activity at 37 degrees C. The enzyme is inhibited by pepstatin, but not by other inhibitors including o-phenanthroline, EDTA, PMSF or E-64, supporting its designation as an aspartic protease; its IC50 value was found to be 3.0 microM. A Lineweaver Burk double reciprocal plot with pepstatin shows that the inhibition is competitive with respect to the substrate. Ca2+ and Mg2+ ions enhance the protease activity, whereas Cu2+ and Hg2+ ions were found to be inhibitory. The pivotal role of aspartic protease in initiating hemoglobin degradation in P. vivax malaria parasite is also demonstrated.
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Affiliation(s)
- Arun Sharma
- Malaria Research Centre, 22 Sham Nath Marg, Delhi-110 054, India.
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Abdel-Rahman HM, Kimura T, Hidaka K, Kiso A, Nezami A, Freire E, Hayashi Y, Kiso Y. Design of inhibitors against HIV, HTLV-I, and Plasmodium falciparum aspartic proteases. Biol Chem 2005; 385:1035-9. [PMID: 15576323 DOI: 10.1515/bc.2004.134] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aspartic proteases have emerged as targets for substrate-based inhibitor design due to their vital roles in the life cycles of the organisms that cause AIDS, malaria, leukemia, and other infectious diseases. Based on the concept of mimicking the substrate transition-state, we designed and synthesized a novel class of aspartic protease inhibitors containing the hydroxymethylcarbonyl (HMC) isostere. An unnatural amino acid, allophenylnorstatine [Apns; (2 S ,3 S )-3-amino-2-hydroxy-4-phenylbutyric acid], was incorporated at the P1 site in a series of peptidomimetic compounds that mimic the natural substrates of the HIV, HTLV-I, and malarial aspartic proteases. From extensive structure-activity relationship studies, we were able to identify a series of highly potent peptidomimetic inhibitors of HIV protease. One highly potent inhibitor of the malarial aspartic protease (plasmepsin II) was identified. Finally, a promising lead compound against the HTLV-I protease was identified.
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Affiliation(s)
- Hamdy M Abdel-Rahman
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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Maegawa H, Kimura T, Arii Y, Matsui Y, Kasai S, Hayashi Y, Kiso Y. Identification of peptidomimetic HTLV-I protease inhibitors containing hydroxymethylcarbonyl (HMC) isostere as the transition-state mimic. Bioorg Med Chem Lett 2005; 14:5925-9. [PMID: 15501070 DOI: 10.1016/j.bmcl.2004.09.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 09/03/2004] [Indexed: 11/26/2022]
Abstract
Towards the development of chemotherapy for the infection by human T-cell leukemia virus type I (HTLV-I), we have established evaluation systems for HTLV-I protease (PR) inhibitors using both recombinant and chemically synthesized HTLV-I PRs. Newly synthesized substrate-based inhibitors containing hydroxymethylcarbonyl (HMC) isostere showed potent anti-HTLV-I PR activity.
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Affiliation(s)
- Hikoichiro Maegawa
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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Li T, Yowell CA, Beyer BB, Hung SH, Westling J, Lam MT, Dunn BM, Dame JB. Recombinant expression and enzymatic subsite characterization of plasmepsin 4 from the four Plasmodium species infecting man. Mol Biochem Parasitol 2005; 135:101-9. [PMID: 15287591 DOI: 10.1016/j.molbiopara.2004.01.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plasmepsin 4 from Plasmodium falciparum and orthologs from Plasmodium malariae, Plasmodium ovale and Plasmodium vivax have been expressed in recombinant form, and properties of the active site of each enzyme characterized by kinetic analysis. A panel of chromogenic peptide substrates systematically substituted at the P3, P2, P2' and P3' positions was used to estimate enzyme/ligand interactions in the corresponding enzyme subsites based upon kinetic data. The kinetic parameters kcat, Km and kcat/Km were measured to identify optimal substrates for each enzyme and also sequences that were readily cleaved by the plasmepsins but poorly by host aspartic peptidases. Computer generated models were utilized to compare enzyme structures and interpret kinetic results. The orthologous plasmepsins share highly similar subsite specificities. In the S3 and S2 subsites, the plasmepsin 4 orthologs all preferred hydrophobic amino acid residues, Phe or Ile, but rejected charged residues such as Lys or Asp. In S2' and S3' subsites, these plasmepsins tolerated both hydrophobic and hydrophilic residues. Subsite specificities of the plasmepsin 4 family of orthologs are similar to those of human cathepsins D and E, except in S3' where the plasmepsins accept substrates containing Ser significantly better than either of these human aspartic proteases. Peptidomimetic methyleneamino reduced-peptide inhibitors, which have inhibition constants in the picomolar range, were prepared for each plasmepsin 4 ortholog based upon substrate preferences. A peptidomimetic inhibitor designed for plasmepsin 4 from P. falciparum having Ser in P3' had the lowest Ki of the series of inhibitors prepared, but did not significantly improve the selectivity of the inhibitor for plasmepsin 4 versus human cathepsin D.
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Affiliation(s)
- Tang Li
- Department of Pathobiology, University of Florida, P.O. Box 110880, Gainesville, FL 32611-0880, USA
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Sohma Y, Hayashi Y, Kimura M, Chiyomori Y, Taniguchi A, Sasaki M, Kimura T, Kiso Y. The ‘O-acyl isopeptide method’ for the synthesis of difficult sequence-containing peptides: application to the synthesis of Alzheimer's disease-related amyloid β peptide (Aβ) 1-42. J Pept Sci 2005; 11:441-51. [PMID: 15761877 DOI: 10.1002/psc.649] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An efficient 'O-acyl isopeptide method' for the synthesis of difficult sequence-containing peptides was applied successfully to the synthesis of amyloid beta peptide (Abeta) 1-42 via a water-soluble O-acyl isopeptide of Abeta1-42, i.e. '26-O-acyl isoAbeta1-42' (6). This paper describes the detailed synthesis of Abeta1-42 focusing on the importance of resin selection and the analysis of side reactions in the O-acyl isopeptide method. Protected '26-O-acyl isoAbeta1-42' peptide resin was synthesized using 2-chlorotrityl chloride resin with minimum side reactions in comparison with other resins and deprotected crude 26-O-acyl isoAbeta1-42 was easily purified by HPLC due to its relatively good purity and narrow elution with reasonable water solubility. This suggests that only one insertion of the isopeptide structure into the sequence of the 42-residue peptide can suppress the unfavourable nature of its difficult sequence. The migration of O-acyl isopeptide to intact Abeta1-42 under physiological conditions (pH 7.4) via O--N intramolecular acyl migration reaction was very rapid and no other by-product formation was observed while 6 was stable under storage conditions. These results concluded that our strategy not only overcomes the solubility problem in the synthesis of Abeta1-42 and can provide intact Abeta1-42 efficiently, but is also applicable in the synthesis of large difficult sequence-containing peptides at least up to 50 amino acids. This synthesis method would provide a biological evaluation system in Alzheimer's disease research, in which 26-O-acyl isoAbeta1-42 can be stored in a solubilized form before use and then rapidly produces intact Abeta1-42 in situ during biological experiments.
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Affiliation(s)
- Youhei Sohma
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, 21st Century COE Program, Kyoto Pharmaceutical University, Yamashina-Ku, Japan
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Battaglia A, Guerrini A, Bertucci C. Synthesis of Optically Active Constrained 2-Substituted Norstatines: A Straightforward Application of Seebach's “SRS” Synthetic Principle. J Org Chem 2004; 69:9055-62. [PMID: 15609938 DOI: 10.1021/jo0486793] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A straightforward two-step methodology of synthesis of optically active (2R)-substituted norstatines via addition of N-tert-butoxycarbonyl-substituted aldimines to (2S)-chiral enolates of 1,3-dioxolan-4-ones has been developed. In particular, the use of the natural (2S)-malic acid is examined for the synthesis of potential GABAergic spirocyclic gamma-lactams.
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Affiliation(s)
- Arturo Battaglia
- Istituto CNR per la Sintesi Organica e Fotoreattività I.S.O.F., Area della Ricerca di Bologna, via P. Gobetti 101, 40129 Bologna, Italy.
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Omara-Opyene AL, Moura PA, Sulsona CR, Bonilla JA, Yowell CA, Fujioka H, Fidock DA, Dame JB. Genetic disruption of the Plasmodium falciparum digestive vacuole plasmepsins demonstrates their functional redundancy. J Biol Chem 2004; 279:54088-96. [PMID: 15491999 DOI: 10.1074/jbc.m409605200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The digestive vacuole plasmepsins PfPM1, PfPM2, PfPM4, and PfHAP (a histoaspartic proteinase) are 4 aspartic proteinases among 10 encoded in the Plasmodium falciparum malarial genome. These have been hypothesized to initiate and contribute significantly to hemoglobin degradation, a catabolic function essential to the survival of this intraerythrocytic parasite. Because of their perceived significance, these plasmepsins have been proposed as potential targets for antimalarial drug development. To test their essentiality, knockout constructs were prepared for each corresponding gene such that homologous recombination would result in two partial, nonfunctional gene copies. Disruption of each gene was achieved, as confirmed by PCR, Southern, and Northern blot analyses. Western and two-dimensional gel analyses revealed the absence of mature or even truncated plasmepsins corresponding to the disrupted gene. Reduced growth rates were observed with PfPM1 and PfPM4 knockouts, indicating that although these plasmepsins are not essential, they are important for parasite development. Abnormal mitochondrial morphology also appeared to accompany loss of PfPM2, and an abundant accumulation of electron-dense vesicles in the digestive vacuole was observed upon disruption of PfPM4; however, those phenotypes only manifested in about a third of the disrupted cells. The ability to compensate for loss of individual plasmepsin function may be explained by close similarity in the structure and active site of these four vacuolar enzymes. Our data imply that drug discovery efforts focused on vacuolar plasmepsins must incorporate measures to develop compounds that can inhibit two or more of this enzyme family.
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Affiliation(s)
- A Levi Omara-Opyene
- Department of Pathobiology, University of Florida, Gainesville, Florida 32611-0880, USA
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Velázquez‐Campoy A, Ohtaka H, Nezami A, Muzammil S, Freire E. Isothermal Titration Calorimetry. ACTA ACUST UNITED AC 2004; Chapter 17:Unit 17.8. [DOI: 10.1002/0471143030.cb1708s23] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Na BK, Lee EG, Lee HW, Cho SH, Bae YA, Kong Y, Lee JK, Kim TS. Aspartic proteases of Plasmodium vivax are highly conserved in wild isolates. THE KOREAN JOURNAL OF PARASITOLOGY 2004; 42:61-6. [PMID: 15181345 PMCID: PMC2717343 DOI: 10.3347/kjp.2004.42.2.61] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The plasmepsins are the aspartic proteases of malaria parasites. Treatment of aspartic protease inhibitor inhibits hemoglobin hydrolysis and blocks the parasite development in vitro suggesting that these proteases might be exploited their potentials as antimalarial drug targets. In this study, we determined the genetic variations of the aspartic proteases of Plasmodium vivax (PvPMs) of wild isolates. Two plasmepsins (PvPM4 and PvPM5) were cloned and sequenced from 20 P. vivax Korean isolates and two imported isolates. The sequences of the enzymes were highly conserved except a small number of amino acid substitutions did not modify key residues for the function or the structure of the enzymes. The high sequence conservations between the plasmepsins from the isolates support the notion that the enzymes could be reliable targets for new antimalarial chemotherapeutics.
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Affiliation(s)
- Byoung-Kuk Na
- Department of Molecular Parasitology and Center for Molecular Medicine, Sungkyunkwan University School of Medicine and Samsung Biomedical Research Institute, Suwon 440-746, Korea.
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Johansson PO, Chen Y, Belfrage AK, Blackman MJ, Kvarnström I, Jansson K, Vrang L, Hamelink E, Hallberg A, Rosenquist A, Samuelsson B. Design and synthesis of potent inhibitors of the malaria aspartyl proteases plasmepsin I and II. Use of solid-phase synthesis to explore novel statine motifs. J Med Chem 2004; 47:3353-66. [PMID: 15189032 DOI: 10.1021/jm031106i] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picomolar to low nanomolar inhibitors of the two aspartic proteases plasmepsin (Plm) I and II, from the malaria parasite Plasmodium falciparum, have been identified from sets of libraries containing novel statine-like templates modified at the amino and carboxy terminus. The syntheses of the novel statine templates were carried out in solution phase using efficient synthetic routes and resulting in excellent stereochemical control. The most promising statine template was attached to solid support and diversified by use of parallel synthesis. The products were evaluated for their Plm I and II inhibitory activity as well as their selectivity over cathepsin D. Selected inhibitors were, in addition, evaluated for their inhibition of parasite growth in cultured infected human red blood cells. The most potent inhibitor in this report, compound 16, displays Ki values of 0.5 and 2.2 nM for Plm I and II, respectively. Inhibitor 16 is also effective in attenuating parasite growth in red blood cells showing 51% inhibition at a concentration of 5 microM. Several inhibitors have been identified that exhibit Ki values between 0.5 and 74 nM for both Plm I and II. Some of these inhibitors also show excellent selectivity vs cathepsin D.
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Affiliation(s)
- Per-Ola Johansson
- Department of Chemistry, Linköping University, S-581 83 Linköping, Sweden
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Fontaine F, Pastor M, Sanz F. Incorporating Molecular Shape into the Alignment-free GRid-INdependent Descriptors. J Med Chem 2004; 47:2805-15. [PMID: 15139758 DOI: 10.1021/jm0311240] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently introduced GRid-INdependent Descriptors (GRIND) were designed to provide a suitable description of a series of ligands for 3D-QSAR studies not requiring the spatial superimposition of their structures. Despite the proven usefulness of the method, it was recognized that the original GRIND failed to describe appropriately the shape of the ligand molecules, which in some cases plays a major role in ligand-receptor binding. For this reason, the original descriptors have been enhanced with the addition of a molecular shape description based on the local curvature of the molecular surface. The integration of this description into the GRIND allows the generation of 3D-QSAR models able to identify both favorable and unfavorable shape complementarity in a simple and alignment-independent way. The usefulness of the new GRIND-shape description in 3D-QSAR is illustrated using two structure-activity studies: one performed on a set of xanthine-like antagonists of the A(1) adenosine receptor; another performed on a series of Plasmodium falciparum plasmepsin II inhibitors.
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Affiliation(s)
- Fabien Fontaine
- Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, C/Dr. Aiguader, 80, E-08003 Barcelona, Spain
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Salas E, Ramírez A, Otero-Bilbao A, Vázquez R, Reyes O, Mendiola J, Duarte CA, Otero-González A, Gutiérrez OA, Chávez MA. A heterogeneous enzymatic assay for quantification of Plasmepsin II activity and the evaluation of its inhibitors. J Pharm Biomed Anal 2004; 34:833-40. [PMID: 15019062 DOI: 10.1016/s0731-7085(03)00566-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2003] [Indexed: 10/26/2022]
Abstract
The emergence and worldwide spreading of Plasmodium falciparum strains that shown to be resistant to traditional drugs is considered a very serious health problem, given the high mortality and morbidity rate of Malaria. In the search for new drugs against this parasite, Hb hydrolyzing enzymes, such as Plasmepsin II (Plm II), have been classified as very promising targets for therapeutic attacks. In this work, it is developed a cheap and high-throughput heterogeneous enzymatic assay for measuring Plasmepsin II activity in order to use it as a tool in the discovery of new inhibitors of this enzyme. In this assay, Plasmepsin II acts upon a solid-phase bound synthetic peptide (DU2) whose sequence comprises the cleavage site F(33)-L(34) present in Hb alpha-chain. The peptide surface density is quantified by means of a classical ELISA-based procedure. In order to estimate the kinetic constants of the system and to quantify both, enzymatic and inhibitory activity, it was used a model for the kinetics of enzyme quasi-saturable systems previously developed by our group, that fitted very well to the experimental data. It was used Pepstatin as a model inhibitor of Plasmepsin II and the resulting dose-response relation agreed with the expected behavior for the Pepstatin-Plasmepsin II pair under the employed experimental conditions.
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Affiliation(s)
- Emir Salas
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, Calle 25 # 455 Entre J e I, Vedado, CP 10400, Havana City, Cuba.
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Kiso A, Hidaka K, Kimura T, Hayashi Y, Nezami A, Freire E, Kiso Y. Search for substrate-based inhibitors fitting the S2? space of malarial aspartic protease plasmepsin II. J Pept Sci 2004; 10:641-7. [PMID: 15568678 DOI: 10.1002/psc.609] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Plasmepsin (Plm) has been identified as an important target for the development of new antimalarial drugs, since its inhibition leads to the starvation of Plasmodium falciparum. A series of substrate-based dipeptide-type Plm II inhibitors containing the hydroxymethylcarbonyl isostere as a transition-state mimic were synthesized. The general design principle was provision of a conformationally restrained hydroxyl group (corresponding to the set residue at the P2' position in native substrates) and a bulky unit to fit the S2' pocket.
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Affiliation(s)
- Aiko Kiso
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.
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Ersmark K, Feierberg I, Bjelic S, Hamelink E, Hackett F, Blackman MJ, Hultén J, Samuelsson B, Aqvist J, Hallberg A. Potent Inhibitors of the Plasmodium falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity. J Med Chem 2003; 47:110-22. [PMID: 14695825 DOI: 10.1021/jm030933g] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hemoglobin-degrading aspartic proteases plasmepsin I (Plm I) and plasmepsin II (Plm II) of the malaria parasite Plasmodium falciparum have lately emerged as putative drug targets. A series of C(2)-symmetric compounds encompassing the 1,2-dihydroxyethylene scaffold and a variety of elongated P1/P1' side chains were synthesized via microwave-assisted palladium-catalyzed coupling reactions. Binding affinity calculations with the linear interaction energy method and molecular dynamics simulations reproduced the experimental binding data obtained in a Plm II assay with very good accuracy. Bioactive conformations of the elongated P1/P1' chains were predicted and agreed essentially with a recent X-ray structure. The compounds exhibited picomolar to nanomolar inhibition constants for the plasmepsins and no measurable affinity to the human enzyme cathepsin D. Some of the compounds also demonstrated significant inhibition of parasite growth in cell culture. To the best of our knowledge, these plasmepsin inhibitors represent the most selective reported to date and constitute promising lead compounds for further optimization.
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Affiliation(s)
- Karolina Ersmark
- Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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