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Verma K, Lahariya AK, Verma G, Kumari M, Gupta D, Maurya N, Verma AK, Mani A, Schneider KA, Bharti PK. Screening of potential antiplasmodial agents targeting cysteine protease-Falcipain 2: a computational pipeline. J Biomol Struct Dyn 2023; 41:8121-8164. [PMID: 36218071 DOI: 10.1080/07391102.2022.2130984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/24/2022] [Indexed: 10/17/2022]
Abstract
The spread of antimalarial drug resistance is a substantial challenge in achieving global malaria elimination. Consequently, the identification of novel therapeutic candidates is a global health priority. Malaria parasite necessitates hemoglobin degradation for its survival, which is mediated by Falcipain 2 (FP2), a promising antimalarial target. In particular, FP2 is a key enzyme in the erythrocytic stage of the parasite's life cycle. Here, we report the screening of approved drugs listed in DrugBank using a computational pipeline that includes drug-likeness, toxicity assessments, oral toxicity evaluation, oral bioavailability, docking analysis, maximum common substructure (MCS) and molecular dynamics (MD) Simulations analysis to identify capable FP2 inhibitors, which are hence potential antiplasmodial agents. A total of 45 drugs were identified, which have positive drug-likeness, no toxic features and good bioavailability. Among these, six drugs showed good binding affinity towards FP2 compared to E64, an epoxide known to inhibit FP2. Notably, two of them, Cefalotin and Cefoxitin, shared the highest MCS with E64, which suggests that they possess similar biological activity as E64. In an investigation using MD for 100 ns, Cefalotin and Cefoxitin showed adequate protein compactness as well as satisfactory complex stability. Overall, these computational approach findings can be applied for designing and developing specific inhibitors or new antimalarial agents for the treatment of malaria infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanika Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ayush Kumar Lahariya
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Garima Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- School of Studies in Microbiology, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Monika Kumari
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biotechnology, St. Aloysius' (Autonomous) College, Affiliated to Rani Durgawati University, Jabalpur, Madhya Pradesh, Jabalpur, India
| | - Divanshi Gupta
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biological Sciences, Rani Durgawati University, Jabalpur, Madhya Pradesh, India
| | - Neha Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | - Anil Kumar Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | | | - Praveen Kumar Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Parasite Host Biology, National Institute of Malaria Research, Delhi, India
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Siddiqui FA, Cabrera M, Wang M, Brashear A, Kemirembe K, Wang Z, Miao J, Chookajorn T, Yang Z, Cao Y, Dong G, Rosenthal PJ, Cui L. Plasmodium falciparum Falcipain-2a Polymorphisms in Southeast Asia and Their Association With Artemisinin Resistance. J Infect Dis 2019; 218:434-442. [PMID: 29659945 DOI: 10.1093/infdis/jiy188] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/04/2018] [Indexed: 11/14/2022] Open
Abstract
Background Falcipain-2a ([FP2a] PF3D7_1115700) is a Plasmodium falciparum cysteine protease and hemoglobinase. Functional FP2a is required for potent activity of artemisinin, and in vitro selection for artemisinin resistance selected for an FP2a nonsense mutation. Methods To investigate associations between FP2a polymorphisms and artemisinin resistance and to characterize the diversity of the enzyme in parasites from the China-Myanmar border, we sequenced the full-length FP2a gene in 140 P falciparum isolates collected during 2004-2011. Results The isolates were grouped into 8 different haplotype groups. Haplotype group I appeared in samples obtained after 2008, coinciding with implementation of artemisinin-based combination therapy in this region. In functional studies, compared with wild-type parasites, the FP2a haplotypes demonstrated increased ring survival, and all haplotype groups exhibited significantly reduced FP2a activity, with group I showing the slowest protease kinetics and reduced parasite fitness. Conclusions These results suggest that altered hemoglobin digestion due to FP2a mutations may contribute to artemisinin resistance.
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Affiliation(s)
- Faiza A Siddiqui
- Department of Entomology, Pennsylvania State University, University Park
| | - Mynthia Cabrera
- Department of Entomology, Pennsylvania State University, University Park
| | - Meilian Wang
- College of Basic Medical Sciences, China Medical University, Shenyang
| | - Awtum Brashear
- Department of Entomology, Pennsylvania State University, University Park
| | - Karen Kemirembe
- Department of Entomology, Pennsylvania State University, University Park
| | - Zenglei Wang
- Department of Entomology, Pennsylvania State University, University Park
| | - Jun Miao
- Department of Entomology, Pennsylvania State University, University Park
| | - Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, China
| | - Yaming Cao
- College of Basic Medical Sciences, China Medical University, Shenyang
| | - Gang Dong
- Max F. Perutz Laboratories, Medical University of Vienna, Austria
| | | | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park
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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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Shah F, Mukherjee P, Gut J, Legac J, Rosenthal PJ, Tekwani BL, Avery MA. Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library. J Chem Inf Model 2011; 51:852-64. [PMID: 21428453 DOI: 10.1021/ci200029y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.
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Affiliation(s)
- Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi , University, Mississippi 38677, USA
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5
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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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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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7
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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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8
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Ramjee MK, Flinn NS, Pemberton TP, Quibell M, Wang Y, Watts JP. Substrate mapping and inhibitor profiling of falcipain-2, falcipain-3 and berghepain-2: implications for peptidase anti-malarial drug discovery. Biochem J 2006; 399:47-57. [PMID: 16776649 PMCID: PMC1570174 DOI: 10.1042/bj20060422] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 06/07/2006] [Accepted: 06/15/2006] [Indexed: 11/17/2022]
Abstract
The Plasmodium falciparum cysteine peptidases FP-2 (falcipain-2) and FP-3 (falcipain-3), members of the papain-like CAC1 family, are essential haemoglobinases and are therefore potential anti-malarial drug targets. To facilitate a rational drug discovery programme, in the current study we analysed the synthetic substrate and model inhibitor profiles of FP-2 and FP-3 as well as BP-2 (berghepain-2), an orthologue from the rodent parasite Plasmodium berghei. With respect to substrate catalysis, FP-2 exhibited a promiscuous substrate profile based around a consensus non-primeside motif, FP-3 was somewhat more restricted and BP-2 was comparatively specific. Substrate turnover for FP-2 was driven by a basic or acidic P1 residue, whereas for FP-3 turnover occurred predominately through a basic P1 residue only, and for BP-2, turnover was again mainly through a basic P1 residue for some motifs and surprisingly a glycine in the P1 position for other motifs. Within these P1 binding elements, additional recognition motifs were observed with subtle nuances that switched substrate turnover on or off through specific synergistic combinations. The peptidases were also profiled against reversible and irreversible cysteine peptidase inhibitors. The results re-iterated the contrasting kinetic behaviour of each peptidase as observed through the substrate screens. The results showed that the substrate and inhibitor preferences of BP-2 were markedly different from those of FP-2 and FP-3. When FP-2 and FP-3 were compared to each other they also displayed similarities and some significant differences. In conclusion, the in vitro data highlights the current difficulties faced by a peptidase directed anti-malarial medicinal chemistry programme where compounds need to be identified with potent activity against at least three peptidases, each of which displays distinct biochemical traits.
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Key Words
- cysteine protease
- inhibitor
- malaria
- mapping
- substrate
- abz, 2-amino benzoic acid
- amc, 7-amino-4-methyl coumarin
- bp, berghepain
- dtt, dithiothreitol
- fmoc/tbu, fluoren-9-ylmethoxycarbonyl/t-butyl
- fp, falcipain
- fret, fluorescence resonance energy transfer
- hbtu, 2-(1h-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
- hobt, 1-hydroxybenzotriazole
- nle, norleucine
- nmm, n-methylmorpholine
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Affiliation(s)
- Manoj K Ramjee
- Amura Therapeutics Limited, Horizon Park, Barton Road, Comberton, CB3 7AJ, UK.
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9
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Wang SX, Pandey KC, Somoza JR, Sijwali PS, Kortemme T, Brinen LS, Fletterick RJ, Rosenthal PJ, McKerrow JH. Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease. Proc Natl Acad Sci U S A 2006; 103:11503-8. [PMID: 16864794 PMCID: PMC1544199 DOI: 10.1073/pnas.0600489103] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Falcipain-2 (FP2), the major cysteine protease of the human malaria parasite Plasmodium falciparum, is a hemoglobinase and promising drug target. Here we report the crystal structure of FP2 in complex with a protease inhibitor, cystatin. The FP2 structure reveals two previously undescribed cysteine protease structural motifs, designated FP2(nose) and FP2(arm), in addition to details of the active site that will help focus inhibitor design. Unlike most cysteine proteases, FP2 does not require a prodomain but only the short FP2(nose) motif to correctly fold and gain catalytic activity. Our structure and mutagenesis data suggest a molecular basis for this unique mechanism by highlighting the functional role of two Tyr within FP2(nose) and a conserved Glu outside this motif. The FP2(arm) motif is required for hemoglobinase activity. The structure reveals topographic features and a negative charge cluster surrounding FP2(arm) that suggest it may serve as an exo-site for hemoglobin binding. Motifs similar to FP2(nose) and FP2(arm) are found only in related plasmodial proteases, suggesting that they confer malaria-specific functions.
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Affiliation(s)
- Stephanie X. Wang
- *Department of Pathology and the Sandler Center, Box 2550, Byers Hall N508, and
| | - Kailash C. Pandey
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - John R. Somoza
- Celera Genomics, 180 Kimball Way, South San Francisco, CA 94080
| | - Puran S. Sijwali
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - Tanja Kortemme
- Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, and Departments of
| | | | - Robert J. Fletterick
- Biochemistry and Biophysics, University of California, San Francisco, CA 94143; and
| | - Philip J. Rosenthal
- Department of Medicine, San Francisco General Hospital, Box 0811, University of California, San Francisco, CA 94143
| | - James H. McKerrow
- *Department of Pathology and the Sandler Center, Box 2550, Byers Hall N508, and
- Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, and Departments of
- **To whom correspondence should be addressed. E-mail:
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Hogg T, Nagarajan K, Herzberg S, Chen L, Shen X, Jiang H, Wecke M, Blohmke C, Hilgenfeld R, Schmidt CL. Structural and functional characterization of Falcipain-2, a hemoglobinase from the malarial parasite Plasmodium falciparum. J Biol Chem 2006; 281:25425-37. [PMID: 16777845 DOI: 10.1074/jbc.m603776200] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malaria is caused by protozoan erythrocytic parasites of the Plasmodium genus, with Plasmodium falciparum being the most dangerous and widespread disease-causing species. Falcipain-2 (FP-2) of P. falciparum is a papain-family (C1A) cysteine protease that plays an important role in the parasite life cycle by degrading erythrocyte proteins, most notably hemoglobin. Inhibition of FP-2 and its paralogues prevents parasite maturation, suggesting these proteins may be valuable targets for the design of novel antimalarial drugs, but lack of structural knowledge has impeded progress toward the rational discovery of potent, selective, and efficacious inhibitors. As a first step toward this goal, we present here the crystal structure of mature FP-2 at 3.1 A resolution, revealing novel structural features of the FP-2 subfamily proteases including a dynamic beta-hairpin hemoglobin binding motif, a flexible N-terminal alpha-helical extension, and a unique active-site cleft. We also demonstrate by biochemical methods that mature FP-2 can proteolytically process its own precursor in trans at neutral to weakly alkaline pH, that the binding of hemoglobin to FP-2 is strictly pH-dependent, and that FP-2 preferentially binds methemoglobin over hemoglobin. Because the specificity and proteolytic activity of FP-2 toward its multiple targets appears to be pH-dependent, we suggest that environmental pH may play an important role in orchestrating FP-2 function over the different life stages of the parasite. Moreover, it appears that selectivity of FP-2 for methemoglobin may represent an evolutionary adaptation to oxidative stress conditions within the host cell.
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Affiliation(s)
- Tanis Hogg
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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11
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Chan C, Goh LL, Sim TS. Differences in biochemical properties of the Plasmodial falcipain-2 and berghepain-2 orthologues: implications for in vivo screens of inhibitors. FEMS Microbiol Lett 2005; 249:315-21. [PMID: 16019160 DOI: 10.1016/j.femsle.2005.06.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/13/2005] [Accepted: 06/13/2005] [Indexed: 11/17/2022] Open
Abstract
Falcipain-2A, the cysteine protease of Plasmodium falciparum has been proposed as a good drug target. This study evaluated the suitability of Plasmodium berghei as the animal model and reports the first functional expression and characterization of the falcipain-2A orthologue, berghepain-2. Comparative studies revealed that the orthologues exhibited different biochemical properties. Berghepain-2 demonstrated optimal activity at a narrower pH optima of 5.5-6 and a lack of preference for substrates with leucine at position 2. Mutagenesis studies revealed roles for residues Val63 and Arg230 of berghepain-2 in contributing to its distinctive biochemical properties. This warrants re-evaluation of employing P. berghei as the murine model for the in vivo screening of falcipain-2A inhibitors. More importantly, these findings stress the underlying importance of establishing the functionality of relevant genes of P. falciparum with concomitant relevance to its murine counterpart prior to its use as the animal model for the screening of potential antimalarials.
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Affiliation(s)
- Cheryl Chan
- Department of Microbiology, National University of Singapore, 5 Science Drive 2, MD4A, Singapore 117597, Singapore
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12
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Goh LL, Sim TS. Characterization of amino acid variation at strategic positions in parasite and human proteases for selective inhibition of falcipains in Plasmodium falciparum. Biochem Biophys Res Commun 2005; 335:762-70. [PMID: 16095562 DOI: 10.1016/j.bbrc.2005.07.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
Falcipains (FP) of Plasmodium falciparum are important virulence factors marked as potential targets for antimalarial drug discovery. In this study, the previously uncharacterized fp2B (PF11_0161) was shown to be highly expressed as an active enzyme during the erythrocytic stage. With three related proteases in the FP family and the existence of human homologues, it is prudent to identify clusters of residues unique to the parasite proteases that can be targeted selectively for drug design. Using bioinformatic tools, we have carefully mapped out a highly conserved and unique region constituted by I85, S149, and A151 in the plasmodial proteases that can influence the development of compounds capable of inhibiting the entire FP family. Taking drug interactions with the human homologues into consideration, these residues in FP2B were replaced with the cognate residues found in human cathepsin L (catL) for evaluation. Despite the high sequence similarity between the FP2 isozymes (97.5%), FP2B is found to be more tolerant to amino acid substitution at position 149 than FP2A. This structural disparity implied that residues mediating peptide substrate interactions are not fully conserved across the FP family and warrant attention in the design and evaluation of protease inhibitors focused on the FPs. The simultaneous substitution of the neighboring residues (I85 or A151) rendered the double mutants (S149A/I85M and S149A/A151D) completely inactive. Significantly, the mutations did not result in 'catL-like' specificity, suggesting that substrate-based inhibitors could be rationally designed against these important parasite-specific structural determinants.
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Affiliation(s)
- Liuh Ling Goh
- Department of Microbiology, Faculty of Medicine, National University of Singapore, MD4A, 5 Science Drive 2, Singapore 117597, Singapore
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