51
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Selected gold compounds cause pronounced inhibition of Falcipain 2 and effectively block P. falciparum growth in vitro. J Inorg Biochem 2011; 105:1576-9. [DOI: 10.1016/j.jinorgbio.2011.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 11/18/2022]
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52
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Hansen G, Heitmann A, Witt T, Li H, Jiang H, Shen X, Heussler VT, Rennenberg A, Hilgenfeld R. Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium. Structure 2011; 19:919-29. [PMID: 21742259 DOI: 10.1016/j.str.2011.03.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 11/17/2022]
Abstract
Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 Å X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.
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Affiliation(s)
- Guido Hansen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lübeck, Germany
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53
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Hansen G, Schwarzloh B, Rennenberg A, Heussler VT, Hilgenfeld R. The macromolecular complex of ICP and falcipain-2 from Plasmodium: preparation, crystallization and preliminary X-ray diffraction analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1406-10. [PMID: 22102243 DOI: 10.1107/s1744309111034592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 08/22/2011] [Indexed: 11/10/2022]
Abstract
The malaria parasite Plasmodium depends on the tight control of cysteine-protease activity throughout its life cycle. Recently, the characterization of a new class of potent inhibitors of cysteine proteases (ICPs) secreted by Plasmodium has been reported. Here, the recombinant production, purification and crystallization of the inhibitory C-terminal domain of ICP from P. berghei in complex with the P. falciparum haemoglobinase falcipain-2 is described. The 1:1 complex was crystallized in space group P4(3), with unit-cell parameters a = b = 71.15, c = 120.09 Å. A complete diffraction data set was collected to a resolution of 2.6 Å.
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Affiliation(s)
- Guido Hansen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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54
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Design and synthesis of protein-protein interaction mimics as Plasmodium falciparum cysteine protease, falcipain-2 inhibitors. Eur J Med Chem 2011; 46:2083-90. [PMID: 21429631 DOI: 10.1016/j.ejmech.2011.02.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/14/2011] [Accepted: 02/24/2011] [Indexed: 11/23/2022]
Abstract
Small peptides that mimic the protein-protein interactions between falcipain-2 and egg white cystatin, an endogenous inhibitor of cysteine proteases, were designed and synthesized and their effects on falcipain-2 activity were analyzed. The mimics are characterized by the presence of different linkers: γ-aminobutyric acid, cis-4-aminocyclohexane carboxylic acid and a macrocycle formed by GABA and two cysteines joined by a disulfide linkage. Some of these compounds showed falcipain-2 inhibition in the micromolar range and produced morphological abnormalities in the Plasmodium food vacuole. Although these peptides are less potent than cystatin, considering the reduction of amino acid residues and the capacity to cross membranes, this approach could be an interesting starting point for the development of a new class of anti-malarial drugs.
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55
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Ehmke V, Kilchmann F, Heindl C, Cui K, Huang J, Schirmeister T, Diederich F. Peptidomimetic nitriles as selective inhibitors for the malarial cysteine protease falcipain-2. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00115a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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56
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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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57
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Cloning and characterisation of novel cystatins from elapid snake venom glands. Biochimie 2010; 93:659-68. [PMID: 21172403 DOI: 10.1016/j.biochi.2010.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 12/09/2010] [Indexed: 11/20/2022]
Abstract
Snake venoms contain a complex mixture of polypeptides that modulate prey homeostatic mechanisms through highly specific and targeted interactions. In this study we have identified and characterised cystatin-like cysteine-protease inhibitors from elapid snake venoms for the first time. Novel cystatin sequences were cloned from 12 of 13 elapid snake venom glands and the protein was detected, albeit at very low levels, in a total of 22 venoms. One highly conserved isoform, which displayed close sequence identity with family 2 cystatins, was detected in each elapid snake. Crude Austrelaps superbus (Australian lowland copperhead) snake venom inhibited papain, and a recombinant form of A. superbus cystatin inhibited cathepsin L ≅ papain > cathepsin B, with no inhibition observed for calpain or legumain. While snake venom cystatins have truncated N-termini, sequence alignment and structural modelling suggested that the evolutionarily conserved Gly-11 of family 2 cystatins, essential for cysteine protease inhibition, is conserved in snake venom cystatins as Gly-3. This was confirmed by mutagenesis at the Gly-3 site, which increased the dissociation constant for papain by 10(4)-fold. These data demonstrate that elapid snake venom cystatins are novel members of the type 2 family. The widespread, low level expression of type 2 cystatins in snake venom, as well as the presence of only one highly conserved isoform in each species, imply essential housekeeping or regulatory roles for these proteins.
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58
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Ehmke V, Heindl C, Rottmann M, Freymond C, Schweizer WB, Brun R, Stich A, Schirmeister T, Diederich F. Potent and selective inhibition of cysteine proteases from Plasmodium falciparum and Trypanosoma brucei. ChemMedChem 2010; 6:273-8. [PMID: 21275051 PMCID: PMC7162187 DOI: 10.1002/cmdc.201000449] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Veronika Ehmke
- Laboratory of Organic Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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59
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Na BK, Bae YA, Zo YG, Choe Y, Kim SH, Desai PV, Avery MA, Craik CS, Kim TS, Rosenthal PJ, Kong Y. Biochemical properties of a novel cysteine protease of Plasmodium vivax, vivapain-4. PLoS Negl Trop Dis 2010; 4:e849. [PMID: 20967286 PMCID: PMC2953480 DOI: 10.1371/journal.pntd.0000849] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 09/14/2010] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multiple cysteine proteases of malaria parasites are required for maintenance of parasite metabolic homeostasis and egress from the host erythrocyte. In Plasmodium falciparum these proteases appear to mediate the processing of hemoglobin and aspartic proteases (plasmepsins) in the acidic food vacuole and the hydrolysis of erythrocyte structural proteins at neutral pH. Two cysteine proteases, vivapain (VX)-2 and VX-3 have been characterized in P. vivax, but comprehensive studies of P. vivax cysteine proteases remain elusive. FINDINGS We characterized a novel cysteine protease of P. vivax, VX-4, of which orthologs appears to have evolved differentially in primate plasmodia with strong cladistic affinity toward those of rodent Plasmodium. Recombinant VX-4 demonstrated dual substrate specificity depending on the surrounding micro-environmental pH. Its hydrolyzing activity against benzyloxycarbonyl-Leu-Arg-4-methyl-coumaryl-7-amide (Z-Leu-Arg-MCA) and Z-Phe-Arg-MCA was highest at acidic pH (5.5), whereas that against Z-Arg-Arg-MCA was maximal at neutral pH (6.5-7.5). VX-4 preferred positively charged amino acids and Gln at the P1 position, with less strict specificity at P3 and P4. P2 preferences depended on pH (Leu at pH 5.5 and Arg at pH 7.5). Three amino acids that delineate the S2 pocket were substituted in VX-4 compared to VX-2 and VX-3 (Ala90, Gly157 and Glu180). Replacement of Glu180 abolished activity against Z-Arg-Arg-MCA at neutral pH, indicating the importance of this amino acid in the pH-dependent substrate preference. VX-4 was localized in the food vacuoles and cytoplasm of the erythrocytic stage of P. vivax. VX-4 showed maximal activity against actin at neutral pH, and that against P. vivax plasmepsin 4 and hemoglobin was detected at neutral/acidic and acidic pH, respectively. CONCLUSION VX-4 demonstrates pH-dependent substrate switching, which might offer an efficient mechanism for the specific cleavage of different substrates in different intracellular environments. VX-4 might function as a hemoglobinase in the acidic parasite food vacuole, a maturase of P. vivax plasmepsin 4 at neutral or acidic pH, and a cytoskeleton-degrading protease in the neutral erythrocyte cytosol.
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Affiliation(s)
- Byoung-Kuk Na
- Department of Molecular Parasitology and Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
- Department of Parasitology and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Korea
| | - Young-An Bae
- Department of Molecular Parasitology and Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Young-Gun Zo
- Department of Molecular Parasitology and Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Youngchool Choe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Seon-Hee Kim
- Department of Molecular Parasitology and Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Prashant V. Desai
- Department of Medicinal Chemistry, National Center for Natural Products Research, University of Mississippi, University, Mississippi, United States of America
| | - Mitchell A. Avery
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, Unites States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Tong-Soo Kim
- Department of Parasitology, Inha University College of Medicine, Incheon, Korea
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Yoon Kong
- Department of Molecular Parasitology and Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
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60
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Coterón JM, Catterick D, Castro J, Chaparro MJ, Díaz B, Fernández E, Ferrer S, Gamo FJ, Gordo M, Gut J, de las Heras L, Legac J, Marco M, Miguel J, Muñoz V, Porras E, de la Rosa JC, Ruiz JR, Sandoval E, Ventosa P, Rosenthal PJ, Fiandor JM. Falcipain inhibitors: optimization studies of the 2-pyrimidinecarbonitrile lead series. J Med Chem 2010; 53:6129-52. [PMID: 20672841 DOI: 10.1021/jm100556b] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Falcipain-2 and falcipain-3 are papain-family cysteine proteases of the malaria parasite Plasmodium falciparum that are responsible for host hemoglobin hydrolysis to provide amino acids for parasite protein synthesis. Different heteroarylnitrile derivatives were studied as potential falcipain inhibitors and therefore potential antiparasitic lead compounds, with the 5-substituted-2-cyanopyrimidine chemical class emerging as the most potent and promising lead series. Through a sequential lead optimization process considering the different positions present in the initial scaffold, nanomolar and subnanomolar inhibitors at falcipains 2 and 3 were identified, with activity against cultured parasites in the micromolar range. Introduction of protonable amines within lead molecules led to marked improvements of up to 1000 times in activity against cultured parasites without noteworthy alterations in other SAR tendencies. Optimized compounds presented enzymatic activities in the picomolar to low nanomolar range and antiparasitic activities in the low nanomolar range.
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Affiliation(s)
- Jose M Coterón
- Department of Drug Discovery Chemistry, GlaxoSmithKline, Madrid, Spain
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61
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Wanare G, Aher R, Kawathekar N, Ranjan R, Kaushik NK, Sahal D. Synthesis of novel α-pyranochalcones and pyrazoline derivatives as Plasmodium falciparum growth inhibitors. Bioorg Med Chem Lett 2010; 20:4675-8. [PMID: 20576433 DOI: 10.1016/j.bmcl.2010.05.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 05/04/2010] [Accepted: 05/18/2010] [Indexed: 11/15/2022]
Affiliation(s)
- Gajanan Wanare
- Department of Pharmacy, Shri G.S. Institute of Technology and Science, Indore, MP 452003, India.
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62
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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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63
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Kerr ID, Lee JH, Farady CJ, Marion R, Rickert M, Sajid M, Pandey KC, Caffrey CR, Legac J, Hansell E, McKerrow JH, Craik CS, Rosenthal PJ, Brinen LS. Vinyl sulfones as antiparasitic agents and a structural basis for drug design. J Biol Chem 2009; 284:25697-703. [PMID: 19620707 DOI: 10.1074/jbc.m109.014340] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine proteases of the papain superfamily are implicated in a number of cellular processes and are important virulence factors in the pathogenesis of parasitic disease. These enzymes have therefore emerged as promising targets for antiparasitic drugs. We report the crystal structures of three major parasite cysteine proteases, cruzain, falcipain-3, and the first reported structure of rhodesain, in complex with a class of potent, small molecule, cysteine protease inhibitors, the vinyl sulfones. These data, in conjunction with comparative inhibition kinetics, provide insight into the molecular mechanisms that drive cysteine protease inhibition by vinyl sulfones, the binding specificity of these important proteases and the potential of vinyl sulfones as antiparasitic drugs.
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Affiliation(s)
- Iain D Kerr
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2550, USA
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64
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Li H, Huang J, Chen L, Liu X, Chen T, Zhu J, Lu W, Shen X, Li J, Hilgenfeld R, Jiang H. Identification of Novel Falcipain-2 Inhibitors as Potential Antimalarial Agents through Structure-Based Virtual Screening. J Med Chem 2009; 52:4936-40. [DOI: 10.1021/jm801622x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jin Huang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaofeng Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tong Chen
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jin Zhu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weiqiang Lu
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck 23538, Germany
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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65
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Pandey KC, Barkan DT, Sali A, Rosenthal PJ. Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. PLoS One 2009; 4:e5694. [PMID: 19479029 PMCID: PMC2682653 DOI: 10.1371/journal.pone.0005694] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 03/24/2009] [Indexed: 11/18/2022] Open
Abstract
Falcipain-2, a papain family cysteine protease of the malaria parasite Plasmodium falciparum, plays a key role in parasite hydrolysis of hemoglobin and is a potential chemotherapeutic target. As with many proteases, falcipain-2 is synthesized as a zymogen, and the prodomain inhibits activity of the mature enzyme. To investigate the mechanism of regulation of falcipain-2 by its prodomain, we expressed constructs encoding different portions of the prodomain and tested their ability to inhibit recombinant mature falcipain-2. We identified a C-terminal segment (Leu155–Asp243) of the prodomain, including two motifs (ERFNIN and GNFD) that are conserved in cathepsin L sub-family papain family proteases, as the mediator of prodomain inhibitory activity. Circular dichroism analysis showed that the prodomain including the C-terminal segment, but not constructs lacking this segment, was rich in secondary structure, suggesting that the segment plays a crucial role in protein folding. The falcipain-2 prodomain also efficiently inhibited other papain family proteases, including cathepsin K, cathepsin L, cathepsin B, and cruzain, but it did not inhibit cathepsin C or tested proteases of other classes. A structural model of pro-falcipain-2 was constructed by homology modeling based on crystallographic structures of mature falcipain-2, procathepsin K, procathepsin L, and procaricain, offering insights into the nature of the interaction between the prodomain and mature domain of falcipain-2 as well as into the broad specificity of inhibitory activity of the falcipain-2 prodomain.
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Affiliation(s)
- Kailash C. Pandey
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - David T. Barkan
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Graduate Group in Bioinformatics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Andrej Sali
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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66
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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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67
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Subramanian S, Hardt M, Choe Y, Niles RK, Johansen EB, Legac J, Gut J, Kerr ID, Craik CS, Rosenthal PJ. Hemoglobin cleavage site-specificity of the Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3. PLoS One 2009; 4:e5156. [PMID: 19357776 PMCID: PMC2663817 DOI: 10.1371/journal.pone.0005156] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/10/2009] [Indexed: 11/18/2022] Open
Abstract
The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 degrade host hemoglobin to provide free amino acids for parasite protein synthesis. Hemoglobin hydrolysis has been described as an ordered process initiated by aspartic proteases, but cysteine protease inhibitors completely block the process, suggesting that cysteine proteases can also initiate hemoglobin hydrolysis. To characterize the specific roles of falcipains, we used three approaches. First, using random P1 – P4 amino acid substrate libraries, falcipain-2 and falcipain-3 demonstrated strong preference for cleavage sites with Leu at the P2 position. Second, with overlapping peptides spanning α and β globin and proteolysis-dependent 18O labeling, hydrolysis was seen at many cleavage sites. Third, with intact hemoglobin, numerous cleavage products were identified. Our results suggest that hemoglobin hydrolysis by malaria parasites is not a highly ordered process, but rather proceeds with rapid cleavage by falcipains at multiple sites. However, falcipain-2 and falcipain-3 show strong specificity for P2 Leu in small peptide substrates, in agreement with the specificity in optimized small molecule inhibitors that was identified previously. These results are consistent with a principal role of falcipain-2 and falcipain-3 in the hydrolysis of hemoglobin by P. falciparum and with the possibility of developing small molecule inhibitors with optimized specificity as antimalarial agents.
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Affiliation(s)
- Shoba Subramanian
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Markus Hardt
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Youngchool Choe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Richard K. Niles
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Eric B. Johansen
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, United States of America
| | - Jennifer Legac
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Jiri Gut
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Iain D. Kerr
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Philip J. Rosenthal
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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68
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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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69
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Nissen MS, Kumar GNM, Youn B, Knowles DB, Lam KS, Ballinger WJ, Knowles NR, Kang C. Characterization of Solanum tuberosum multicystatin and its structural comparison with other cystatins. THE PLANT CELL 2009; 21:861-75. [PMID: 19304935 PMCID: PMC2671694 DOI: 10.1105/tpc.108.064717] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/02/2009] [Accepted: 03/05/2009] [Indexed: 05/23/2023]
Abstract
Potato (Solanum tuberosum) multicystatin (PMC) is a crystalline Cys protease inhibitor present in the subphellogen layer of potato tubers. It consists of eight tandem domains of similar size and sequence. Our in vitro results showed that the pH/PO(4)(-)-dependent oligomeric behavior of PMC was due to its multidomain nature and was not a characteristic of the individual domains. Using a single domain of PMC, which still maintains inhibitor activity, we identified a target protein of PMC, a putative Cys protease. In addition, our crystal structure of a representative repeating unit of PMC, PMC-2, showed structural similarity to both type I and type II cystatins. The N-terminal trunk, alpha-helix, and L2 region of PMC-2 were most similar to those of type I cystatins, while the conformation of L1 more closely resembled that of type II cystatins. The structure of PMC-2 was most similar to the intensely sweet protein monellin from Dioscorephyllum cumminisii (serendipity berry), despite a low level of sequence similarity. We present a model for the possible molecular organization of the eight inhibitory domains in crystalline PMC. The unique molecular properties of the oligomeric PMC crystal are discussed in relation to its potential function in regulating the activity of proteases in potato tubers.
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Affiliation(s)
- Mark S Nissen
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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70
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Zhu J, Chen T, Liu J, Ma R, Lu W, Huang J, Li H, Li J, Jiang H. 2-(3,4-dihydro-4-oxothieno[2,3-d]pyrimidin-2-ylthio) acetamides as a new class of falcipain-2 inhibitors. 3. design, synthesis and biological evaluation. Molecules 2009; 14:785-97. [PMID: 19223827 PMCID: PMC6253991 DOI: 10.3390/molecules14020785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/18/2009] [Accepted: 02/13/2009] [Indexed: 12/04/2022] Open
Abstract
The cysteine protease falcipain-2 (FP-2) of Plasmodium falciparum is a principal cysteine protease and an essential hemoglobinase of erythrocytic P. falciparum trophozoites, making it become an attractive target enzyme for developing anti-malarial drugs. In this study, a series of novel small molecule FP-2 inhibitors have been designed and synthesized based on compound 1, which was identified by using structure-based virtual screening in conjunction with an enzyme inhibition assay. All compounds showed high inhibitory effect against FP-2 with IC(50)s of 1.46-11.38 microM, and the inhibitory activity of compound 2a was ~2 times greater than that of prototype compound 1. The preliminary SARs are summarized and should be helpful for future inhibitor design, and the novel scaffold presented here, with its potent inhibitory activity against FP-2, also has potential application in discovery of new anti-malarial drugs.
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Affiliation(s)
- Jin Zhu
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Tong Chen
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Jie Liu
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Ruoqun Ma
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Weiqiang Lu
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Jin Huang
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China
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71
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Zhu J, Chen T, Chen L, Lu W, Che P, Huang J, Li H, Li J, Jiang H. 2-amido-3-(1H-indol-3-yl)-N-substituted-propanamides as a new class of falcipain-2 inhibitors. 1. Design, synthesis, biological evaluation and binding model studies. Molecules 2009; 14:494-508. [PMID: 19158658 PMCID: PMC6253880 DOI: 10.3390/molecules14010494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 01/11/2009] [Accepted: 01/13/2009] [Indexed: 11/16/2022] Open
Abstract
The Plasmodium falciparum cysteine protease falcipain-2 (FP-2) is an important cysteine protease and an essential hemoglobinase of erythrocytic P. falciparum trophozoites. The discovery of new FP-2 inhibitors is now a hot topic in the search for potential malaria treatments. In this study, a series of novel small molecule FP-2 inhibitors have been designed and synthesized based on three regional optimizations of the lead (R)-2-phenoxycarboxamido-3-(1H-indol-3-yl)-N-benzylpropanamide(1), which was identified using structure-based virtual screening in conjunction with surface plasmon resonance (SPR)-based binding assays. Four compounds--1, 2b, 2k and 2l--showed moderate FP-2 inhibition activity, with IC(50) values of 10.0-39.4 microM, and the inhibitory activity of compound 2k was approximately 3-fold better than that of the prototype compound 1 and may prove useful for the development of micromolar level FP-2 inhibitors. Preliminary SAR data was obtained, while molecular modeling revealed that introduction of H-bond donor or/and acceptor atoms to the phenyl ring moiety in the C region would be likely to produce some additional H-bond interactions, which should consequently enhance molecular bioactivity.
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Affiliation(s)
- Jin Zhu
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Tong Chen
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Lili Chen
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China; E-Mail: (L. C.)
| | - Weiqiang Lu
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Peng Che
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Jin Huang
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, P.R. China. E-Mails: (J. Z.); (T. C.); (W. L.); (P. C.); (H. J.)
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P.R. China; E-Mail: (L. C.)
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72
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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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73
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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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74
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Is dihydrolipoic acid among the reductive activators of parasite CysHis proteases? Exp Parasitol 2007; 118:604-13. [PMID: 18068706 DOI: 10.1016/j.exppara.2007.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 10/19/2007] [Accepted: 11/02/2007] [Indexed: 11/23/2022]
Abstract
Activities of mature CysHis proteases depend upon relative rates of oxidations vs. reductions of catalytic sulfur by multiple enzymatic and non-enzymatic reactions. CysHis peptidolysis is inhibited by Fe3+ but not Fe2+. Others report the paradox that malarial parasites require exogenous free lipoic acid (LA) from human host, although the apicoplast organelle produces it. Extra-cellular LA disulfide can be taken up and reduced to dihydrolipoic acid (DHLA) by reductases of any cell type. Here, the opposing effects of DHLA vs. Fe3+ on the falcipain-2 hemoglobinase were investigated employing Z-Phe-Arg-AMC substrate. Despite limited solubility, non-regenerated DHLA (10 microM, threshold 2 microM) was found to be the most potent activator of the air-inactivated (sulfoxygenated) protease discovered thus far. Activation was preemptively opposed by Fe3+, but not Fe2+. However, cruzain from T. cruzi, and cathepsin B from mammal were indistinguishable in their responsiveness to DHLA and Fe redox. Thus, DHLA activation vs. Fe3+ inhibition is not unique to falcipain-2 or apicomplexans but is rather a primordial feature of CysHis peptidolysis. Free LA and/or unassociated lipoylated enzyme subunits could be among multiple pathways shuttling reducing equivalents to reduction of proteins, including CysHis proteases. It is discussed that opposing DHLA-Fe3+ modification of plasmodial proteolysis might be a specialized adaptation to intra-erythrocytic growth.
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75
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Gayathri P, Balaram H, Murthy MRN. Structural biology of plasmodial proteins. Curr Opin Struct Biol 2007; 17:744-54. [PMID: 17875391 DOI: 10.1016/j.sbi.2007.08.001] [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] [Received: 07/12/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/29/2022]
Abstract
Malaria is a global disease infecting several million individuals annually. Malarial infection is particularly severe in the poorest parts of the world and is a major drain on their limited resources. Development of drug resistance and absence of a preventive vaccine have led to an immediate necessity for identifying new drug targets to combat malaria. Understanding the intricacies of parasite biology is essential to design novel intervention strategies that can prevent the growth of the parasite. The structural biology approach towards this goal involves the identification of key differences in the structures of the human and parasite enzymes and the determination of unique protein structures essential for parasite survival. This review covers the work on structural biology of plasmodial proteins carried out during the period of January 2006 to June 2007.
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Affiliation(s)
- P Gayathri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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76
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Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Sci 2007; 16:2585-96. [PMID: 17965183 DOI: 10.1110/ps.073228407] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The vast majority of host-pathogen interactions involve protein-protein recognition, yet our current understanding of these interactions is limited. Here, we present and apply a computational whole-genome protocol that generates testable predictions of host-pathogen protein interactions. The protocol first scans the host and pathogen genomes for proteins with similarity to known protein complexes, then assesses these putative interactions, using structure if available, and, finally, filters the remaining interactions using biological context, such as the stage-specific expression of pathogen proteins and tissue expression of host proteins. The technique was applied to 10 pathogens, including species of Mycobacterium, apicomplexa, and kinetoplastida, responsible for "neglected" human diseases. The method was assessed by (1) comparison to a set of known host-pathogen interactions, (2) comparison to gene expression and essentiality data describing host and pathogen genes involved in infection, and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host-pathogen interactions. We present several specific predictions that warrant experimental follow-up, including interactions from previously characterized mechanisms, such as cytoadhesion and protease inhibition, as well as suspected interactions in hypothesized networks, such as apoptotic pathways. Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions.
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Affiliation(s)
- Fred P Davis
- Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, California 94158, USA.
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77
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Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH. The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family. Structure 2007; 15:535-43. [PMID: 17502099 DOI: 10.1016/j.str.2007.03.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 03/01/2007] [Accepted: 03/20/2007] [Indexed: 11/19/2022]
Abstract
Protein inhibitors of proteolytic enzymes regulate proteolysis and prevent the pathological effects of excess endogenous or exogenous proteases. Cysteine proteases are a large family of enzymes found throughout the plant and animal kingdoms. Disturbance of the equilibrium between cysteine proteases and natural inhibitors is a key event in the pathogenesis of cancer, rheumatoid arthritis, osteoporosis, and emphysema. A family (I42) of cysteine protease inhibitors (http://merops.sanger.ac.uk) was discovered in protozoan parasites and recently found widely distributed in prokaryotes and eukaryotes. We report the 2.2 A crystal structure of the signature member of the I42 family, chagasin, in complex with a cysteine protease. Chagasin has a unique variant of the immunoglobulin fold with homology to human CD8alpha. Interactions of chagasin with a target protease are reminiscent of the cystatin family inhibitors. Protein inhibitors of cysteine proteases may have evolved more than once on nonhomologous scaffolds.
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Affiliation(s)
- Stephanie X Wang
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
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78
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Singh A, Walker KJ, Sijwali PS, Lau AL, Rosenthal PJ. A chimeric cysteine protease of Plasmodium berghei engineered to resemble the Plasmodium falciparum protease falcipain-2. Protein Eng Des Sel 2007; 20:171-7. [PMID: 17430972 DOI: 10.1093/protein/gzm009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cysteine proteases falcipain-2 and falcipain-3 are hemoglobinases and potential targets for chemotherapy directed against Plasmodium falciparum, the most important human malaria parasite. Most in vivo evaluations of candidate antimalarials are conducted in murine malaria models, and falcipain homologs from rodent malaria parasites differ importantly from falcipain-2 and falcipain-3. We expressed berghepain-2, the single homolog of falcipain-2 and falcipain-3 of the rodent parasite P. berghei, in Escherichia coli, and characterized the refolded active enzyme. Berghepain-2 was biochemically very similar to the previously characterized rodent plasmodial protease vinckepain-2, but differed from falcipain-2 and falcipain-3 in its fine substrate and inhibitor specificity. We then used homology modeling and evolutionary trace analysis to predict key amino acids that mediate functional differences between falcipain-2 and berghepain-2. Thirteen amino acids were sequentially altered to replace berghepain-2 residues with those in falcipain-2. Mutant enzymes varied in activity and sensitivity to inhibitors. A berghepain-2 mutant with eight substitutions retained good activity and demonstrated fine substrate and inhibitor sensitivity more similar to that of falcipain-2 than berghepain-2. These results suggest that, to facilitate drug discovery, we can produce mutant animal model malaria parasites with biochemical properties more like those of the key drug target, P. falciparum.
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Affiliation(s)
- Ajay Singh
- Department of Medicine, San Francisco General Hospital, University of California, CA 94143, USA
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79
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Mittl PR, Grütter MG. Opportunities for structure-based design of protease-directed drugs. Curr Opin Struct Biol 2006; 16:769-75. [PMID: 17112720 DOI: 10.1016/j.sbi.2006.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/06/2006] [Accepted: 10/25/2006] [Indexed: 01/09/2023]
Abstract
As a result of the recent enormous technological progress, experimental structure determination has become an integral part of the development of drugs against disease-related target proteins. The post-translational modification of proteins is an important regulatory process in living organisms; one such example is lytic processing by peptidases. Many different peptidases represent disease targets and are being used in structure-based drug design approaches. The development of drugs such as aliskiren and tipranavir, which inhibit renin and HIV protease, respectively, testifies to the success of this approach.
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Affiliation(s)
- Peer Re Mittl
- Institute for Biochemistry, University of Zürich, Winterthurer Strasse 190, 8057 Zürich, Switzerland
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80
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Abstract
A family of aspartic proteases called plasmepsins is important for hemoglobin degradation in intraerythrocytic Plasmodium parasites. Plasmepsin II (PM II) is the best studied member of this family. PM II and its close orthologs and paralogs form homodimers with extensive interfaces in all known crystal structures. This raised the question whether the homodimer is the functional subunit of plasmepsins in solution. We have used gel filtration chromatography, site-directed mutagenesis, and analytical ultracentrifugation to study the oligomeric status of PM II in solution. Our results reveal that PM II exists mainly as a monomer in solution and that the monomer is fully functional for catalysis. A hydrophobic loop at the PM II monomer surface, which would be buried in a PM II dimer, is shown to be essential for the hemoglobin degradation capability of PM II.
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Affiliation(s)
- Jun Liu
- Departments of Molecular Microbiology and Medicine, Washington University School of Medicine, Howard Hughes Medical Institute, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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