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Nagar P, Bhowmick K, Chawla A, Malik MZ, Subbarao N, Kaur I, Dhar SK. Plasmodium falciparum cysteine protease Falcipain 3: A potential enzyme for proteolytic processing of histone acetyltransferase PfGCN5. Biotechnol Appl Biochem 2024. [PMID: 38924147 DOI: 10.1002/bab.2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
In spite of 150 years of studying malaria, the unique features of the malarial parasite, Plasmodium, still perplex researchers. One of the methods by which the parasite manages its gene expression is epigenetic regulation, the champion of which is PfGCN5, an essential enzyme responsible for acetylating histone proteins. PfGCN5 is a ∼170 kDa chromatin-remodeling enzyme that harbors the conserved bromodomain and acetyltransferase domain situated in its C-terminus domain. Although the PfGCN5 proteolytic processing is essential for its activity, the specific protease involved in this process still remains elusive. Identification of PfGCN5 interacting proteins through immunoprecipitation (IP) followed by LC-tandem mass spectrometry analysis revealed the presence of food vacuolar proteins, such as the cysteine protease Falcipain 3 (FP3), in addition to the typical members of the PfGCN5 complex. The direct interaction between FP3 and PfGCN5 was further validated by in vitro pull-down assay as well as IP assay. Subsequently, use of cysteine protease inhibitor E64d led to the inhibition of protease-specific processing of PfGCN5 with concomitant enrichment and co-localization of PfGCN5 and FP3 around the food vacuole as evidenced by confocal microscopy as well as electron microscopy. Remarkably, the proteolytic cleavage of the nuclear protein PfGCN5 by food vacuolar protease FP3 is exceptional and atypical in eukaryotic organisms. Targeting the proteolytic processing of GCN5 and the associated protease FP3 could provide a novel approach for drug development aimed at addressing the growing resistance of parasites to current antimalarial drugs.
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Affiliation(s)
- Poonam Nagar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Krishanu Bhowmick
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- The Institute for Bioelectronic Medicine, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York, USA
| | - Aishwarya Chawla
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Md Zubbair Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Inderjeet Kaur
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- TERI School of Advanced Studies, Vasant Kunj, New Delhi, India
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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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Chauke E, Pelle R, Coetzer THT. A single exon-encoded Theileria parva strain Muguga cysteine protease (ThpCP): Molecular modelling and characterisation. Biochimie 2023; 206:24-35. [PMID: 36198333 DOI: 10.1016/j.biochi.2022.09.018] [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: 06/24/2022] [Revised: 09/01/2022] [Accepted: 09/26/2022] [Indexed: 11/27/2022]
Abstract
The tick-transmitted apicomplexan Theileria parva causes East Coast fever, a bovine disease of great economic and veterinary importance in Africa. Papain-like cysteine proteases play important roles in protozoan parasite host cell entry and egress, nutrition and host immune evasion. This study reports the identification and characterisation of a T. parva strain Muguga cathepsin L-like (C1A subfamily) cysteine protease (ThpCP). Molecular modelling confirmed the papain-like fold of ThpCP, hydrophobic character of the S2 substrate binding pocket and non-covalent interaction between the pro- and catalytic domains preceding low pH autoactivation. ThpCP was recombinantly expressed in a protease deficient E. coli (Rosetta (DE3)pLysS strain) expression host as a 46 kDa proenzyme. Following Ni-chelate affinity chromatography and acidification, the 27 kDa mature ThpCP was purified by cation-exchange chromatography. Purified ThpCP hydrolysed typical cathepsin L substrates N-α-benzyloxycarbonyl (Z)-Phe-Arg-7-amino-4-methyl-coumarin (AMC) (kcat/Km = 4.49 × 105 s-1M-1) and Z-Leu-Arg-AMC (kcat/Km = 4.20 × 105 s-1M-1), but showed no activity against the cathepsin B-selective substrate Z-Arg-Arg-AMC. Recombinant ThpCP was active over a broad pH range from pH 4.5 to 7.5, thereby showing potential activity in the acidic parasite food vacuole and close to neutral pH of the host lymphocyte cytoplasm. Recombinant ThpCP was inhibited by the cysteine protease inhibitors E64, iodoacetate, leupeptin, chymostatin, Z-Phe-Ala-diazomethylketone (DMK) and Z-Phe-Phe-DMK and hydrolysed bovine proteins: haemoglobin, immunoglobulin G, serum albumin and fibrinogen as well as goat IgG at pH 6 and 7. Functional expression and characterisation of Theileria cysteine proteases should enable high throughput screening of cysteine protease inhibitor libraries against these proteases.
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Affiliation(s)
- Ephraim Chauke
- Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box, 30709-00100, Nairobi, Kenya
| | - Theresa H T Coetzer
- Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa.
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4
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Kwon CW, Chung B, Yoo SH, Chang PS. Heterologous expression of a papain-like protease inhibitor (SnuCalCpI17) in the E. coli and its mode of inhibition. Appl Microbiol Biotechnol 2022; 106:4563-4574. [PMID: 35748913 DOI: 10.1007/s00253-022-12032-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
The effect of the Escherichia coli (E. coli) Rosetta (DE3) system on the expression of recombinant papain-like cysteine protease inhibitors (SnuCalCpIs) was evaluated, and the inhibition mode of the expressed inhibitor was determined. SnuCalCpI08 and SnuCalCpI17, which previously had not been expressed in the E. coli BL21 (DE3) system due to rare codons of more than 10%, were successfully expressed in E. coli Rosetta (DE3) since the strain provides tRNAs for six rare codons. Initially, both inhibitors were expressed as inclusion bodies; however, the water solubility of SnuCalCpI17 could be improved by lowering the incubation temperature, reducing the IPTG concentration, and increasing the induction time. In contrast, the other inhibitor could not be solubilized in water. To validate whether the inhibitor was expressed with correct protein folding, a papain inhibition assay was performed with SnuCalCpI17. SnuCalCpI17 showed a half-maximal inhibitory concentration (IC50) of 105.671 ± 9.857 µg/mL and a slow-binding inhibition mode against papain at pH 7.0 with a Kiapp of 75.80 μg/mL. The slow-binding inhibitor has a slow dissociation from the inhibitor-target complex, resulting in a long residence time in vivo, and thus can effectively inhibit the target at doses far below the IC50 of the inhibitor. KEY POINTS: • Propeptide inhibitor (SnuCalCpI17) containing rare codons was expressed in E. coli Rosetta (DE3). • The slow-binding inhibition was shown by plotting the apparent first-order rate constant (kobs). • Protein-protein interaction between SnuCalCpIs and papain was verified by docking simulation.
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Affiliation(s)
- Chang Woo Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bokyong Chung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Ho Yoo
- Department of Food Science & Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Seoul, 05006, Republic of Korea
| | - Pahn-Shick Chang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Agricultural Microorganism and Enzyme, Seoul National University, Seoul, 08826, Republic of Korea.
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5
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Ariizumi T, Murata S, Fujisawa S, Isezaki M, Sato T, Oishi E, Taneno A, Ichii O, Maekawa N, Okagawa T, Konnai S, Ohashi K. In vitro evaluation of a cysteine protease from poultry red mites, Demanyssus gallinae, as a vaccine antigen for chickens. Poult Sci 2021; 101:101638. [PMID: 34986449 PMCID: PMC8743220 DOI: 10.1016/j.psj.2021.101638] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
Poultry red mites (PRMs, Dermanyssus gallinae) are hematophagous ectoparasites that negatively affect egg production, which causes serious economic losses to the poultry industry worldwide. Currently, the emergence of acaricide-resistant PRMs has impeded PRM control in poultry farms. Several alternatives for acaricide use have been described for managing PRM-caused problems. Vaccination is among the methods for controlling PRMs in poultry houses. Currently, several candidates for vaccine antigens have been identified. This study identified a cysteine protease, Deg-CPR-2, which differs from 2 other previously reported cysteine proteases in PRMs, from previously obtained data from RNA-sequencing (RNA-seq) analysis. We investigated the characteristics of Deg-CPR-2 and assessed its efficacy as a vaccine antigen in vitro. Phylogenetic analysis revealed that Deg-CPR-2 belonged to a different cluster from those of other cysteine proteases in PRMs. This cluster also included cathepsin L-like proteases, enzymes thought to be involved in hemoglobin digestion in ticks. Expression analysis revealed Deg-CPR-2 expression in midguts and all the life-stages; however, there were differences in the expression levels across the life-stages. The enzyme activity of recombinant Deg-CPR-2 was inhibited in the presence of a cysteine protease inhibitor, which suggests that Deg-CPR-2 functions as a cysteine protease in PRMs. Finally, there was an in vitro increase in the mortality of PRMs, mainly protonymphs that were artificially fed with plasma from chickens immunized with Deg-CPR-2. These findings suggest that Deg-CPR-2 may contribute to protein digestion in the midgut of PRMs and is crucially involved in physiological processes in PRMs. Additionally, immunization with Deg-CPR-2 may reduce the number of protonymphs, and Deg-CPR-2 should be considered as a candidate antigen for anti-PRM vaccine development.
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Affiliation(s)
- Takuma Ariizumi
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Shiro Murata
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
| | - Sotaro Fujisawa
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Masayoshi Isezaki
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Takumi Sato
- Vaxxinova Japan K.K., Minato-ku, Tokyo, Japan
| | - Eiji Oishi
- Vaxxinova Japan K.K., Minato-ku, Tokyo, Japan
| | | | - Osamu Ichii
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Laboratory of Agrobiomedical Science, Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Naoya Maekawa
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tomohiro Okagawa
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Satoru Konnai
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kazuhiko Ohashi
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
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Murata S, Taniguchi A, Isezaki M, Fujisawa S, Sakai E, Taneno A, Ichii O, Ito T, Maekawa N, Okagawa T, Konnai S, Ohashi K. Characterisation of a cysteine protease from poultry red mites and its potential use as a vaccine for chickens. ACTA ACUST UNITED AC 2021; 28:9. [PMID: 33544074 PMCID: PMC7863971 DOI: 10.1051/parasite/2021005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/13/2021] [Indexed: 11/15/2022]
Abstract
Poultry red mites (PRMs, Dermanyssus gallinae) are ectoparasites that negatively affect farmed chickens, leading to serious economic losses worldwide. Acaricides have been used to control PRMs in poultry houses. However, some PRMs have developed resistance to acaricides, and therefore different approaches are required to manage the problems caused by PRMs. Vaccination of chickens is one of the methods being considered to reduce the number of PRMs in poultry houses. In a previous study, a cysteine protease, Deg-CPR-1, was identified as a candidate vaccine against PRMs distributed in Europe. In this study, we investigated the characteristics of Deg-CPR-1. A phylogenetic analysis revealed that Deg-CPR-1 is closely related to the digestive cysteine proteases of other mite species, and it was classified into a cluster different from that of chicken cathepsins. Deg-CPR-1 of PRMs in Japan has an amino acid substitution compared with that of PRMs in Europe, but it showed efficacy as a vaccine, consistent with previous findings. Deg-CPR-1 exhibited cathepsin L-like enzyme activity. In addition, the Deg-CPR-1 mRNA was expressed in the midgut and in all stages of PRMs that feed on blood. These results imply that Deg-CPR-1 in the midgut may have important functions in physiological processes, and the inhibition of its expression may contribute to the efficacy of a Deg-CPR-1-based vaccine. Further research is required to fully understand the mechanisms of vaccine efficacy.
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Affiliation(s)
- Shiro Murata
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan - Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Ayaka Taniguchi
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Masayoshi Isezaki
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Sotaro Fujisawa
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Eishi Sakai
- Vaxxinova Japan K.K., 1-24-8 Hamamatsucho, Minato-ku, Tokyo 105-0013, Japan
| | - Akira Taneno
- Vaxxinova Japan K.K., 1-24-8 Hamamatsucho, Minato-ku, Tokyo 105-0013, Japan
| | - Osamu Ichii
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Takuya Ito
- Hokkaido Institute of Public Health, Kita-19, Nishi-12, Kita-ku, Sapporo 060-0819, Japan
| | - Naoya Maekawa
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Tomohiro Okagawa
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Satoru Konnai
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan - Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Kazuhiko Ohashi
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan - Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
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7
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Pritsch IC, Tikhonova IG, Jewhurst HL, Drysdale O, Cwiklinski K, Molento MB, Dalton JP, Verissimo CDM. Regulation of the Fasciola hepatica newly excysted juvenile cathepsin L3 (FhCL3) by its propeptide: a proposed 'clamp-like' mechanism of binding and inhibition. BMC Mol Cell Biol 2020; 21:90. [PMID: 33287692 PMCID: PMC7720491 DOI: 10.1186/s12860-020-00335-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/26/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The zoonotic worm parasite Fasciola hepatica secretes an abundance of cathepsin L peptidases that are associated with virulence, invasiveness, feeding and migration. The peptidases are produced as inactive zymogens that activate at low pH by autocatalytic removal of their N-terminal pro-domain or propeptide. Propeptides bind to their cognate enzyme with high specificity. Little is known, however, about the mechanism by which the propeptide of FhCL3, a cathepsin L peptidase secreted by the infective newly excysted juveniles (NEJs), regulates the inhibition and activation of the mature enzyme before it is secreted into host tissues. RESULTS Immunolocalisation/immunoblotting studies show that the FhCL3 zymogen is produced and secreted by gastrodermal cells of the NEJs gut. A recombinant propeptide of FhCL3 (ppFhCL3) was shown to be a highly potent and selective inhibitor of native and recombinant F. hepatica FhCL3 peptidase, and other members of the cathepsin L family; inhibition constant (Ki) values obtained for FhCL1, FhCL2 and FhCL3 were 0.04 nM, 0.004 nM and < 0.002 nM, respectively. These values are at least 1000-fold lower than those Ki obtained for human cathepsin L (HsCL) and human cathepsin K (HsCK) demonstrating the selectivity of the ppFhCL3 for parasite cathepsins L. By exploiting 3-D structural data we identified key molecular interactions in the specific binding between the ppFhCL3 and FhCL3 mature domain. Using recombinant variants of ppFhCL3 we demonstrated the critical importance of a pair of propeptide residues (Tyr46Lys47) for the interaction with the propeptide binding loop (PBL) of the mature enzyme and other residues (Leu66 and Glu68) that allow the propeptide to block the active site. CONCLUSIONS The FhCL3 peptidase involved in host invasion by F. hepatica is produced as a zymogen in the NEJs gut. Regulation of its activation involves specific binding sites within the propeptide that are interdependent and act as a "clamp-like" mechanism of inhibition. These interactions are disrupted by the low pH of the NEJs gut to initiate autocatalytic activation. Our enzyme kinetics data demonstrates high potency and selectivity of the ppFhCL3 for its cognate FhCL3 enzyme, information that could be utilised to design inhibitors of parasite cathepsin L peptidases.
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Affiliation(s)
- Izanara C Pritsch
- Department of Basic Pathology, Federal University of Parana, Curitiba, 81531-970, Brazil.,School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Heather L Jewhurst
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK.,Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Orla Drysdale
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Krystyna Cwiklinski
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK.,Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Marcelo B Molento
- Department of Basic Pathology, Federal University of Parana, Curitiba, 81531-970, Brazil.,Department of Veterinary Medicine, Federal University of Parana, Curitiba, Paraná, Brazil
| | - John P Dalton
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK.,Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Carolina De M Verissimo
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK. .,Centre for One Health and Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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8
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Smith NA, Clarke OB, Lee M, Hodder AN, Smith BJ. Structure of the Plasmodium falciparum PfSERA5 pseudo-zymogen. Protein Sci 2020; 29:2245-2258. [PMID: 32955133 PMCID: PMC7586913 DOI: 10.1002/pro.3956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022]
Abstract
PfSERA5, a significantly abundant protein present within the parasitophorous vacuole (PV) and essential for normal growth during the blood-stage life cycle of the malaria parasite Plasmodium falciparum, displays structural similarity to many other cysteine proteases. However, PfSERA5 does not exhibit any detectable protease activity and therefore the role of the PfSERA5 papain-like domain (PfSERA5E), thought to remain bound to its cognate prodomain, remains unknown. In this study, we present a revised structure of the central PfSERA5E domain at a resolution of 1.2 Å, and the first structure of the "zymogen" of this papain-like domain including its cognate prodomain (PfSERA5PE) to 2.2 Å resolution. PfSERA5PE is somewhat structurally similar to that of other known proenzymes, retaining the conserved overall folding and orientation of the prodomain through, and occluding, the archetypal papain-like catalytic triad "active-site" cleft, in the same reverse direction as conventional prodomains. Our findings are congruent with previously identified structures of PfSERA5E and of similar "zymogens" and provide a foundation for further investigation into the function of PfSERA5.
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Affiliation(s)
- Nicholas A. Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
| | - Oliver B. Clarke
- Department of AnesthesiologyColumbia UniversityNew YorkNew YorkUSA
- Department of Physiology and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
| | - Anthony N. Hodder
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
| | - Brian J. Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVictoriaAustralia
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9
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Zhu L, Shan L, Zhu J, Li L, Li S, Wang L, Wang J, Zhang S, Zhou H, Zhang W, Li H. Discovery of a natural fluorescent probe targeting the Plasmodium falciparum cysteine protease falcipain-2. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1016-1025. [PMID: 32048162 DOI: 10.1007/s11427-019-1581-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/26/2019] [Indexed: 01/19/2023]
Abstract
The Plasmodium falciparum cysteine protease falcipain-2 (FP-2) is an attractive antimalarial target. Here, we discovered that the natural compound NP1024 is a nonpeptidic inhibitor of FP-2 with an IC50 value of 0.44 μmol L-1. The most exciting finding is that both in vitro and in vivo, NP1024 directly targets FP-2 in malaria parasite-infected erythrocytes as a natural fluorescent probe, thereby paving the way for an integration of malaria diagnosis and treatment.
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Affiliation(s)
- Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lei Shan
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Junsheng Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Li Li
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Liyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiawei Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Shoude Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Hongchang Zhou
- School of Medicine, Huzhou University, Huzhou Central Hospital, Huzhou, 313000, China
| | - Weidong Zhang
- Department of Natural Product Chemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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10
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Rosenthal PJ. Falcipain cysteine proteases of malaria parasites: An update. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140362. [DOI: 10.1016/j.bbapap.2020.140362] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
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11
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Helton LG, Kennedy EJ. Targeting Plasmodium with constrained peptides and peptidomimetics. IUBMB Life 2020; 72:1103-1114. [PMID: 32037730 DOI: 10.1002/iub.2244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/24/2020] [Indexed: 01/04/2023]
Abstract
Malaria remains a worldwide health concern with an estimated quarter of a billion people infected and nearly half a million deaths annually. Malaria is caused by a parasite infection from Plasmodium strains which are transmitted from mosquitoes into the human host. Although several small molecule inhibitors have been found to target the early stages of transmission and prevent parasite proliferation, multiple drug resistant parasite strains have emerged and drug resistance remains a major hurdle. As an alternative to small molecule inhibition, several peptide-based therapeutics have been explored for their potential as antimalarial compounds. Chemically constrained peptides or peptidomimetics were developed to target large binding interfaces of parasite-based proteins that have historically been difficult to selectively inhibit using small molecules. Here, we review ongoing research aimed at developing constrained peptides targeting protein-protein interactions pertinent to malaria pathogenesis. These targets include Falcipain-2, the J domain of CDPK1, myosin A tail domain interacting protein, the PKA signaling pathway, and an unclear signaling pathway involving angiotensin-derived peptides. Diverse synthetic methods were also used for each target. Merging parasite biology with synthetic strategies may provide new opportunities to develop alternative methods for uncovering novel antimalarials and may offer an alternate source for targeting drug-resistant parasite strains.
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Affiliation(s)
- Leah G Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
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12
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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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Musyoka TM, Njuguna JN, Tastan Bishop Ö. Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide based inhibitor design. Malar J 2019; 18:159. [PMID: 31053072 PMCID: PMC6500056 DOI: 10.1186/s12936-019-2790-2] [Citation(s) in RCA: 12] [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: 08/29/2018] [Accepted: 04/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Falcipains are major cysteine proteases of Plasmodium falciparum involved in haemoglobin degradation and remain attractive anti-malarial drug targets. Several inhibitors against these proteases have been identified, yet none of them has been approved for malaria treatment. Other Plasmodium species also possess highly homologous proteins to falcipains. For selective therapeutic targeting, identification of sequence and structure differences with homologous human cathepsins is necessary. The substrate processing activity of these proteins is tightly controlled via a prodomain segment occluding the active site which is chopped under low pH conditions exposing the catalytic site. Current work characterizes these proteases to identify residues mediating the prodomain regulatory function for the design of peptide based anti-malarial inhibitors. METHODS Sequence and structure variations between prodomain regions of plasmodial proteins and human cathepsins were determined using in silico approaches. Additionally, evolutionary clustering of these proteins was evaluated using phylogenetic analysis. High quality partial zymogen protein structures were modelled using homology modelling and residue interaction analysis performed between the prodomain segment and mature domain to identify key interacting residues between these two domains. The resulting information was used to determine short peptide sequences which could mimic the inherent regulatory function of the prodomain regions. Through flexible docking, the binding affinity of proposed peptides on the proteins studied was evaluated. RESULTS Sequence, evolutionary and motif analyses showed important differences between plasmodial and human proteins. Residue interaction analysis identified important residues crucial for maintaining prodomain integrity across the different proteins as well as the pro-segment responsible for inhibitory mechanism. Binding affinity of suggested peptides was highly dependent on their residue composition and length. CONCLUSIONS Despite the conserved structural and catalytic mechanism between human cathepsins and plasmodial proteases, current work revealed significant differences between the two protein groups which may provide valuable information for selective anti-malarial inhibitor development. Part of this study aimed to design peptide inhibitors based on endogenous inhibitory portions of protease prodomains as a novel aspect. Even though peptide inhibitors may not be practical solutions to malaria at this stage, the approach followed and results offer a promising means to find new malarial inhibitors.
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Affiliation(s)
- Thommas Mutemi Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
| | - Joyce Njoki Njuguna
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown, 6140, South Africa.
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Guo P, Wang Z, Wang Q, Liu H, Zhang Y, Xu H, Zhao P. Fibroinase and its physiological inhibitors involved in the regulation of silk gland development in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 106:19-27. [PMID: 30639702 DOI: 10.1016/j.ibmb.2019.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/22/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
Fibroinase, a cathepsin L-like cysteine protease, was previously identified in the silk gland of the silkworm, Bombyx mori. It shows high degradation activity during the pre-pupa period, when the silk gland undergoes apoptosis and remodeling. Here, we recombinantly expressed pro-fibroinase and activated it in vitro. Fibroinase showed optimal hydrolytic activity at pH 4.0 and its optimum temperature was about 42 °C. One physiological inhibitor, B. mori cysteine protease inhibitor (BCPI) was found, which showed strong inhibitory activity against fibroinase. The inhibitory reaction was caused by the formation of a non-covalent complex; this is in contrast to a previously reported mode of fibroinase inhibition by Serpin18. Expression profiles and immunolocalization analysis demonstrated that fibroinase was involved in silk gland development by degrading silk proteins and apoptosis/remodeling of silk glands at specific points. Furthermore, the comparison of the temporal expression of fibroinase and its inhibitors, BCPI and Serpin18, indicated that these inhibitors were involved in the silk gland development by regulating the activity of fibroinase from the fifth instar until the early spinning stage. These findings improve our understanding of the mechanism of protease regulation and its inhibitors in silk gland development.
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Affiliation(s)
- Pengchao Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China
| | - Zhan Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Qian Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Huawei Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Yunshi Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Haiyang Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400715, China.
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15
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Crucial residues in falcipains that mediate hemoglobin hydrolysis. Exp Parasitol 2019; 197:43-50. [PMID: 30648557 DOI: 10.1016/j.exppara.2019.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/03/2018] [Accepted: 01/11/2019] [Indexed: 02/08/2023]
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16
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Pant A, Kumar R, Wani NA, Verma S, Sharma R, Pande V, Saxena AK, Dixit R, Rai R, Pandey KC. Allosteric Site Inhibitor Disrupting Auto-Processing of Malarial Cysteine Proteases. Sci Rep 2018; 8:16193. [PMID: 30385827 PMCID: PMC6212536 DOI: 10.1038/s41598-018-34564-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 10/16/2018] [Indexed: 02/08/2023] Open
Abstract
Falcipains are major haemoglobinases of Plasmodium falciparum required for parasite growth and development. They consist of pro- and mature domains that interact via 'hot-spot' interactions and maintain the structural integrity of enzyme in zymogen state. Upon sensing the acidic environment, these interactions dissociate and active enzyme is released. For inhibiting falcipains, several active site inhibitors exist, however, compounds that target via allosteric mechanism remains uncharacterized. Therefore, we designed and synthesized six azapeptide compounds, among which, NA-01 & NA-03 arrested parasite growth by specifically blocking the auto-processing of falcipains. Inhibitors showed high affinity for enzymes in presence of the prodomain without affecting the secondary structure. Binding of NA-03 at the interface induced rigidity in the prodomain preventing structural reorganization. We further reported a histidine-dependent activation of falcipain. Collectively, for the first time we provide a framework for blocking the allosteric site of crucial haemoglobinases of the human malaria parasite. Targeting the allosteric site could provide high selectivity and less vulnerable to drug resistance.
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Affiliation(s)
- A Pant
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - R Kumar
- Integrated Science Lab, Umeå University, Umeå, Sweden
| | - N A Wani
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - S Verma
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - R Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - V Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - A K Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - R Dixit
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
| | - R Rai
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - K C Pandey
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India.
- Department of Biochemistry, ICMR-National Institute for Research in Environmental Health, Bhopal, MP - 462001, India.
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17
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Meno KH, Kastrup JS, Kuo IC, Chua KY, Gajhede M. The structure of the mite allergen Blo t 1 explains the limited antibody cross-reactivity to Der p 1. Allergy 2017; 72:665-670. [PMID: 27997997 DOI: 10.1111/all.13111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
Abstract
The Blomia tropicalis (Blo t) mite species is considered a storage mite in temperate climate zones and an important source of indoor allergens causing allergic asthma and rhinitis in tropical and subtropical regions. Here, we report the crystal structure of one of the allergens from Blo t, recombinant proBlo t 1 (rproBlo t 1), determined at 2.1 Å resolution. Overall, the fold of rproBlo t 1 is characteristic for the pro-form of cysteine proteases from the C1A class. Structural comparison of experimentally mapped Der f 1/Der p1 IgG epitopes to the same surface patch on Blo t 1, as well as of sequence identity of surface-exposed residues, suggests limited cross-reactivity between these allergens and Blo t 1. This is in agreement with ELISA inhibition results showing that, although cross-reactive human IgE epitopes exist, there are unique IgE epitopes for both Blo t 1 and Der p 1.
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Affiliation(s)
- K. H. Meno
- Global Research; ALK-Abelló A/S; Hørsholm Denmark
| | - J. S. Kastrup
- Biostructural Research; Department of Drug Design and Pharmacology; University of Copenhagen; Copenhagen Denmark
| | - I.-C. Kuo
- Departments of Paediatrics; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Khoo Teck Puat-National University Children's Medical Institute; The National University Health System; Singapore
| | - K. Y. Chua
- Departments of Paediatrics; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Immunology Programme; Centre for Life Sciences; National University of Singapore; Singapore
| | - M. Gajhede
- Biostructural Research; Department of Drug Design and Pharmacology; University of Copenhagen; Copenhagen Denmark
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18
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Yoonuan T, Nuamtanong S, Dekumyoy P, Phuphisut O, Adisakwattana P. Molecular and immunological characterization of cathepsin L-like cysteine protease of Paragonimus pseudoheterotremus. Parasitol Res 2016; 115:4457-4470. [PMID: 27562899 DOI: 10.1007/s00436-016-5232-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/12/2016] [Indexed: 11/29/2022]
Abstract
Cathepsin L is a cysteine protease belonging to the papain family. In parasitic trematodes, cathepsin L plays essential roles in parasite survival and host-parasite interactions. In this study, cathepsin L of the lung fluke Paragonimus pseudoheterotremus (PpsCatL) was identified and its molecular biological and immunological features characterized. A sequence analysis of PpsCatL showed that the gene encodes a 325-amino-acid protein that is most similar to P. westermani cathepsin L. The in silico three-dimensional structure suggests that PpsCatL is a pro-enzyme that becomes active when the propeptide is cleaved. A recombinant pro-PpsCatL lacking the signal peptide (rPpsCatL), with a molecular weight of 35 kDa, was expressed in E. coli and reacted with P. pseudoheterotremus-infected rat sera. The native protein was detected in crude worm antigens and excretory-secretory products and was localized in the cecum and in the lamellae along the intestinal tract of the adult parasite. Enzymatic activity of rPpsCatL showed that the protein could cleave the fluorogenic substrate Z-Phe-Arg-AMC after autocatalysis but was inhibited with E64. The immunodiagnostic potential of the recombinant protein was evaluated with an enzyme-linked immunosorbent assay (ELISA) and suggested that rPpsCatL can detect paragonimiasis with high sensitivity and specificity (100 and 95.6 %, respectively). This supports the further development of an rPpsCatL-ELISA as an immunodiagnostic tool.
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Affiliation(s)
- Tippayarat Yoonuan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Supaporn Nuamtanong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Paron Dekumyoy
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Orawan Phuphisut
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, 10400, Thailand.
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19
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Verma S, Dixit R, Pandey KC. Cysteine Proteases: Modes of Activation and Future Prospects as Pharmacological Targets. Front Pharmacol 2016; 7:107. [PMID: 27199750 PMCID: PMC4842899 DOI: 10.3389/fphar.2016.00107] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/08/2016] [Indexed: 02/05/2023] Open
Abstract
Proteolytic enzymes are crucial for a variety of biological processes in organisms ranging from lower (virus, bacteria, and parasite) to the higher organisms (mammals). Proteases cleave proteins into smaller fragments by catalyzing peptide bonds hydrolysis. Proteases are classified according to their catalytic site, and distributed into four major classes: cysteine proteases, serine proteases, aspartic proteases, and metalloproteases. This review will cover only cysteine proteases, papain family enzymes which are involved in multiple functions such as extracellular matrix turnover, antigen presentation, processing events, digestion, immune invasion, hemoglobin hydrolysis, parasite invasion, parasite egress, and processing surface proteins. Therefore, they are promising drug targets for various diseases. For preventing unwanted digestion, cysteine proteases are synthesized as zymogens, and contain a prodomain (regulatory) and a mature domain (catalytic). The prodomain acts as an endogenous inhibitor of the mature enzyme. For activation of the mature enzyme, removal of the prodomain is necessary and achieved by different modes. The pro-mature domain interaction can be categorized as protein-protein interactions (PPIs) and may be targeted in a range of diseases. Cysteine protease inhibitors are available that can block the active site but no such inhibitor available yet that can be targeted to block the pro-mature domain interactions and prevent it activation. This review specifically highlights the modes of activation (processing) of papain family enzymes, which involve auto-activation, trans-activation and also clarifies the future aspects of targeting PPIs to prevent the activation of cysteine proteases.
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Affiliation(s)
- Sonia Verma
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research New Delhi, India
| | - Rajnikant Dixit
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research New Delhi, India
| | - Kailash C Pandey
- Department of Biochemistry, National Institute for Research in Environmental Health, Indian Council of Medical Research Bhopal, India
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20
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Rahul CN, Shiva Krishna K, Pawar AP, Rajesh V. In silico approach to ascertain the calcium dependent role of Plasmodium falciparum SERA5. J Biomol Struct Dyn 2016; 35:17-25. [PMID: 26725489 DOI: 10.1080/07391102.2015.1129988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The P. falciparum serine repeat antigen (PfSERA5) is the most abundantly expressed protein in the parasitophorous vacuole during the asexual blood stage and serves as both drug and vaccine target. The processed central fragment (56 KDa) of PfSERA5 is implicated to play an important role in parasite exit (egress) during schizont rupture from erythrocytes. Structural characterization of its enzymatic domain supports protease-like function for this central domain. The understanding of exact functional role of PfSERA5 in parasite egress remains unconfirmed as recent studies also indicate an indispensable non-catalytic role for PfSERA5 putative enzyme domain in the blood stage. No structural insight into PfSERA5 prodomain is available. Structure prediction of PfSERA5 prodomain using in silico approach in our study, showed it to have structural similarity with calcium-binding proteins. An earlier observation of steep rise in intracellular calcium concentration as an important factor in egress makes the prodomain calcium-binding role significant. The implication of calcium on structure and activity of PfSERA5 putative enzyme domain is also unknown, and such information would aid to substantiating any calcium-dependent effects on PfSERA5. To understand this, we performed molecular dynamic (MD) simulation both in the presence and absence of calcium. MD results show secondary structure conformational differences in local regions of protein structure. Our results support calcium to be an important parameter for stability and function of PfSERA5. This computational assessment suggest a need to design future experiments like calcium-dependent inhibition studies to reveal exact functional role of PfSERA5 in parasite egress.
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Affiliation(s)
- C N Rahul
- a Department of Biological Sciences, Birla Institute of Technology and Science, Pilani , Hyderabad Campus , Andhra Pradesh , India
| | - K Shiva Krishna
- a Department of Biological Sciences, Birla Institute of Technology and Science, Pilani , Hyderabad Campus , Andhra Pradesh , India
| | - Atul P Pawar
- a Department of Biological Sciences, Birla Institute of Technology and Science, Pilani , Hyderabad Campus , Andhra Pradesh , India
| | - Vidya Rajesh
- a Department of Biological Sciences, Birla Institute of Technology and Science, Pilani , Hyderabad Campus , Andhra Pradesh , India
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21
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Santamaria ME, Arnaiz A, Diaz-Mendoza M, Martinez M, Diaz I. Inhibitory properties of cysteine protease pro-peptides from barley confer resistance to spider mite feeding. PLoS One 2015; 10:e0128323. [PMID: 26039069 PMCID: PMC4454591 DOI: 10.1371/journal.pone.0128323] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/26/2015] [Indexed: 11/26/2022] Open
Abstract
C1A plant cysteine proteases are synthesized as pre-pro-enzymes that need to be processed to become active by the pro-peptide claves off from its cognate enzyme. These pro-sequences play multifunctional roles including the capacity to specifically inhibit their own as well as other C1A protease activities from diverse origin. In this study, it is analysed the potential role of C1A pro-regions from barley as regulators of cysteine proteases in target phytophagous arthropods (coleopteran and acari). The in vitro inhibitory action of these pro-sequences, purified as recombinant proteins, is demonstrated. Moreover, transgenic Arabidopsis plants expressing different fragments of HvPap-1 barley gene containing the pro-peptide sequence were generated and the acaricide function was confirmed by bioassays conducted with the two-spotted spider mite Tetranychus urticae. Feeding trials resulted in a significant reduction of leaf damage in the transgenic lines expressing the pro-peptide in comparison to non-transformed control and strongly correlated with an increase in mite mortality. Additionally, the analysis of the expression levels of a selection of potential mite targets (proteases and protease inhibitors) revealed a mite strategy to counteract the inhibitory activity produced by the C1A barley pro-prodomain. These findings demonstrate that pro-peptides can control mite pests and could be applied as defence proteins in biotechnological systems.
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Affiliation(s)
- M. Estrella Santamaria
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid, Autovia M40 (km 38), Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Ana Arnaiz
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid, Autovia M40 (km 38), Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Mercedes Diaz-Mendoza
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid, Autovia M40 (km 38), Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid, Autovia M40 (km 38), Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid, Autovia M40 (km 38), Pozuelo de Alarcon, 28223 Madrid, Spain
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Demidyuk IV, Shubin AV, Gasanov EV, Kostrov SV. Propeptides as modulators of functional activity of proteases. Biomol Concepts 2015; 1:305-22. [PMID: 25962005 DOI: 10.1515/bmc.2010.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Most proteases are synthesized in the cell as precursor-containing propeptides. These structural elements can determine the folding of the cognate protein, function as an inhibitor/activator peptide, mediate enzyme sorting, and mediate the protease interaction with other molecules and supramolecular structures. The data presented in this review demonstrate modulatory activity of propeptides irrespective of the specific mechanism of action. Changes in propeptide structure, sometimes minor, can crucially alter protein function in the living organism. Modulatory activity coupled with high variation allows us to consider propeptides as specific evolutionary modules that can transform biological properties of proteases without significant changes in the highly conserved catalytic domains. As the considered properties of propeptides are not unique to proteases, propeptide-mediated evolution seems to be a universal biological mechanism.
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The recombinant prepro region of TvCP4 is an inhibitor of cathepsin L-like cysteine proteinases of Trichomonas vaginalis that inhibits trichomonal haemolysis. Int J Biochem Cell Biol 2015; 59:73-83. [DOI: 10.1016/j.biocel.2014.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/24/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022]
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Omotuyi IO. Ebola virus envelope glycoprotein derived peptide in human Furin-bound state: computational studies. J Biomol Struct Dyn 2014; 33:461-70. [PMID: 25347780 DOI: 10.1080/07391102.2014.981207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ebola virus (EboV) is currently ravaging West Africa with estimated case fatality rate of 52%. Currently, no drug treatment is available and immunoglobulin therapy is still at the rudimentary stage. For anti-EboV drug development, druggable viral and host protein targets, including human Furin are under intense investigation. Here, molecular dynamics simulation was performed on Apo-Furin, meta-guanidinomethyl-Phac-RVR-Amba-bound, and two EboV glycoprotein (GP) 494-TGGRRTRREA-503/Furin complexes (Accurate and one amino acid shift alignment). The results of the simulation established ligand-induced desolvation of Furin active site and structural compactness. Accurately aligned EboV-GP peptide exhibited a tighter binding mode with Furin and showed 1.5- and 3.0-fold MMPBSA binding free energy estimate compared with the displaced peptide and inhibitor, respectively. The difference in free energy was traced to the difference in contribution of threonine residues of the peptides. Furthermore, Furin subsites I conferred substrate specificity and ligand binding accuracy. Accurately aligned peptide trapped active site His194 side chain into gauche (-) (+60(o)) χ1-dihedral compared with gauche+ (-60(o)) in other biosystems while Asp153 is trapped in gauche+ (-60(o)) in ligand bound not Apo state. Ramachandran plot showed that the scissile Arg8 of the accurately aligned peptide showed β conformation distribution as apposed to 310R, αL, and 310L. Finally, the active site proximal Na(+) binding is dependent on substrate peptide occupancy of the active site but detaches in the absence of a ligand. In conclusion, Furin might represent candidate drug target for Ebola virus disease treatment via therapeutic target of the active site and Na(+) binding pocket.
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Affiliation(s)
- I Olaposi Omotuyi
- a Department of Pharmacology and Therapeutic Innovation , Graduate School of Biomedical Science, Nagasaki University , Nagasaki , Japan
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Omotuyi OI. Methyl-methoxylpyrrolinone and flavinium nucleus binding signatures on falcipain-2 active site. J Mol Model 2014; 20:2386. [PMID: 25096811 DOI: 10.1007/s00894-014-2386-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/17/2014] [Indexed: 01/18/2023]
Abstract
Following the increasing reports of human toxicity and plasmodium resistance to artemisinin and its derivatives, falcipain-2 (FP-2) is now emerging as the choice antimalarial drug target. Coincidentally, FP-2 is the in vivo target of naturally occurring, therapeutically safe flavonoids (stenopalustroside, myricetin, and fisetin) and symplostatin (symplostatin 4) compounds known to exhibit potent in vitro and in vivo antiplasmodial actions. Here, the structural bases for their inhibitory actions have been studied using molecular dynamics simulation. Myricetin and fisetin act as proton transfer tunnel breakers by inserting between His174 and Cys42, which are key active site residues of FP-2, stenopalustroside inhibits the polarization of His174 by Asn173; a major preparatory step for Cys42/His174 proton transfer process. The roles of flavonoids are favored by T-shaped pi-pi interactions with His174. Symplostatin 4 inserts its methyl-methoxylpyrrolinone moiety into the active site where its proton acceptor function prepares Cys42 for nucleophilic attack on the Michael α,β-unsaturated bonds on its 4(S)-amino-2(E)-pentenoate moiety. Further analyses of the structures identified a unique bridge formed on FP-2 active site groove by stenopalustroside and symplostatin 4 during interaction with the sub-site I of FP-2, whereas fisetin preferentially interacts with sub-site II and myricetin interacts with sub-site III residues. Ultimately, symplostatin-4, myricetin, and fisetin were better than stenopalustroside at trapping FP-2 in its inactive state as revealed by comparative RSMD plots with X-ray structures of FP-2 co-crystallized with inhibitors. Comparative estimates of free energy of binding using the Molecular Mechanics-Poisson Boltzmann Surface Area (MMPBSA) method suggested that His174 protonation may further enhance stenopalustroside-FP-2 interaction. The unique binding signatures of the ligands within the FP-2 active site groove and its sub-sites may explain the subtle differences in their IC50 values and their mechanism of inhibition.
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Affiliation(s)
- Olaposi I Omotuyi
- Center for Drug Discovery and Therapeutic Innovation, Nagasaki University, Nagasaki, Japan,
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26
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Omotuyi IO, Hamada T. Dynamical footprint of falcipain-2 catalytic triad in hemoglobin-β-bound state. J Biomol Struct Dyn 2014; 33:1027-36. [PMID: 24943200 DOI: 10.1080/07391102.2014.924878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malaria epidemic. Here, a theoretical FP-2/hemoglobin complex has been proposed and the dynamical footprint and energetics of binding have been investigated using molecular and quantum mechanics approaches. The mapped interaction interface comprises residues 34-51 of hemoglobin and cysteine-42/histidine-174/glutamine-36/asparagine-173/204 and subsites S1, S1', and S3 of FP-2. In hemoglobin-bound FP-2, asparagine-173 preferentially partners histidine-174, while glutamine-36 is preferred in ligand-free state. Cysteine-42 exhibits dihedral switch from 110° to 30° in free and bound states, respectively, with exclusion of water from the binding core upon hemoglobin binding. Hemoglobin similarly exhibits high occupancy within .2 nm distance with charged amido acid-rich subsites S1 and S3 of FP-2 functioning in tandem to reduce conformational flexibility of hemoglobin and facilitate the formation of a stabilizing anti-parallel β-sheet between Leucine-172-valine-176 of FP-2 and phenylalanine-45-asparate-47 of hemoglobin and to overcome the + 1.13e + 5 eV activation energy required to optimize the FP-2/hemoglobin-β conformation that precedes hydrolysis.
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Affiliation(s)
- I O Omotuyi
- a Department of Molecular Pharmacology and Neuroscience , Nagasaki University , Nagasaki , Japan
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Cross-talk between malarial cysteine proteases and falstatin: the BC loop as a hot-spot target. PLoS One 2014; 9:e93008. [PMID: 24699522 PMCID: PMC3974720 DOI: 10.1371/journal.pone.0093008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/27/2014] [Indexed: 02/05/2023] Open
Abstract
Cysteine proteases play a crucial role in the development of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Our earlier studies demonstrated that these enzymes are equipped with specific domains for defined functions and further suggested the mechanism of activation of cysteine proteases. The activities of these proteases are regulated by a new class of endogenous inhibitors of cysteine proteases (ICPs). Structural studies of the ICPs of Trypanosoma cruzi (chagasin) and Plasmodium berghei (PbICP) indicated that three loops (termed BC, DE, and FG) are crucial for binding to target proteases. Falstatin, an ICP of P. falciparum, appears to play a crucial role in invasion of erythrocytes and hepatocytes. However, the mechanism of inhibition of cysteine proteases by falstatin has not been established. Our study suggests that falstatin is the first known ICP to function as a multimeric protein. Using site-directed mutagenesis, hemoglobin hydrolysis assays and peptide inhibition studies, we demonstrate that the BC loop, but not the DE or FG loops, inhibits cysteine proteases of P. falciparum and P. vivax via hydrogen bonds. These results suggest that the BC loop of falstatin acts as a hot-spot target for inhibiting malarial cysteine proteases. This finding suggests new strategies for the development of anti-malarial agents based on protease-inhibitor interactions.
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Identification of diverse natural products as falcipain-2 inhibitors through structure-based virtual screening. Bioorg Med Chem Lett 2014; 24:1261-4. [DOI: 10.1016/j.bmcl.2014.01.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/01/2014] [Accepted: 01/23/2014] [Indexed: 11/21/2022]
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29
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Rathi B, Singh AK, Kishan R, Singh N, Latha N, Srinivasan S, Pandey KC, Tiwari HK, Singh BK. Functionalized hydroxyethylamine based peptide nanostructures as potential inhibitors of falcipain-3, an essential proteases of Plasmodium falciparum. Bioorg Med Chem 2013; 21:5503-9. [DOI: 10.1016/j.bmc.2013.05.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
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30
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Kang JM, Ju HL, Sohn WM, Na BK. Defining the regulatory and inhibitory elements within the prodomain of CsCF-6, a cathepsin F cysteine protease of Clonorchis sinensis. Mol Biochem Parasitol 2013; 190:92-6. [DOI: 10.1016/j.molbiopara.2013.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/11/2013] [Accepted: 07/11/2013] [Indexed: 10/26/2022]
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31
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Pandey KC. Macromolecular inhibitors of malarial cysteine proteases —An invited review. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jbise.2013.69108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Expression, characterization, and cellular localization of knowpains, papain-like cysteine proteases of the Plasmodium knowlesi malaria parasite. PLoS One 2012; 7:e51619. [PMID: 23251596 PMCID: PMC3520923 DOI: 10.1371/journal.pone.0051619] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 11/02/2012] [Indexed: 01/09/2023] Open
Abstract
Papain-like cysteine proteases of malaria parasites degrade haemoglobin in an acidic food vacuole to provide amino acids for intraerythrocytic parasites. These proteases are potential drug targets because their inhibitors block parasite development, and efforts are underway to develop chemotherapeutic inhibitors of these proteases as the treatments for malaria. Plasmodium knowlesi has recently been shown to be an important human pathogen in parts of Asia. We report expression and characterization of three P. knowlesi papain-like proteases, termed knowpains (KP2-4). Recombinant knowpains were produced using a bacterial expression system, and tested for various biochemical properties. Antibodies against recombinant knowpains were generated and used to determine their cellular localization in parasites. Inhibitory effects of the cysteine protease inhibitor E64 were assessed on P. knowlesi culture to validate drug target potential of knowpains. All three knowpains were present in the food vacuole, active in acidic pH, and capable of degrading haemoglobin at the food vacuolar pH (≈5.5), suggesting roles in haemoglobin degradation. The proteases showed absolute (KP2 and KP3) to moderate (KP4) preference for peptide substrates containing leucine at the P2 position; KP4 preferred arginine at the P2 position. While the three knowpains appear to have redundant roles in haemoglobin degradation, KP4 may also have a role in degradation of erythrocyte cytoskeleton during merozoite egress, as it displayed broad substrate specificity and was primarily localized at the parasite periphery. Importantly, E64 blocked erythrocytic development of P. knowlesi, with enlargement of food vacuoles, indicating inhibition of haemoglobin hydrolysis and supporting the potential for inhibition of knowpains as a strategy for the treatment of malaria. Functional expression and characterization of knowpains should enable simultaneous screening of available cysteine protease inhibitor libraries against knowpains for developing broadly effective compounds active against multiple human malaria parasites.
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Sundararaj S, Singh D, Saxena AK, Vashisht K, Sijwali PS, Dixit R, Pandey KC. The Ionic and hydrophobic interactions are required for the auto activation of cysteine proteases of Plasmodium falciparum. PLoS One 2012; 7:e47227. [PMID: 23077573 PMCID: PMC3473063 DOI: 10.1371/journal.pone.0047227] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/11/2012] [Indexed: 02/05/2023] Open
Abstract
The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 are major hemoglobinases and potential antimalarial drug targets. Our previous studies demonstrated that these enzymes are equipped with specific domains for specific functions. Structural and functional analysis of falcipains showed that they have unique domains including a refolding domain and a hemoglobin binding domain. As with many proteases, falcipain-2 and falcipain-3 are synthesized as inactive zymogens. However, it is not known how these enzymes get activated for hemoglobin hydrolysis. In this study, we are presenting the first evidence that salt bridges and hydrophobic interactions are required for the auto activation of cysteine proteases of P.falciparum. To investigate the mechanism of activation of these enzymes, we expressed the wild type protein as well as different mutants in E.coli. Refolding was assessed by circular dichroism. Both CD and trans activation data showed that the wild type enzymes and mutants are rich in secondary structures with similar folds. Our study revealed that prodomain-mature domain of falcipain-2 and falcipain-3 interacts via salt bridges and hydrophobic interactions. We mutated specific residues of falcipain-2 and falcipain-3, and evaluated their ability to undergo auto processing. Mutagenesis result showed that two salt bridges (Arg¹⁸⁵- Glu²²¹, Glu²¹⁰- Lys⁴⁰³) in falcipain-2, and one salt bridge (Arg²⁰²-Glu²³⁸) in falcipain-3, play crucial roles in the activation of these enzymes. Further study revealed that hydrophobic interactions present both in falcipain-2 (Phe²¹⁴ Trp⁴⁴⁹ Trp⁴⁵³) and falcipain-3 (Phe²³¹ Trp⁴⁵⁷ Trp⁴⁶¹) also play important roles in the activation of these enzymes. Our results revealed the interactions involved in auto processing of two major hemoglobinases of malaria parasite.
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Affiliation(s)
- Srinivasan Sundararaj
- Host–Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | - Deepak Singh
- Host–Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | - Ajay K. Saxena
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kapil Vashisht
- Host–Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | | | - Rajnikant Dixit
- Host–Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
| | - Kailash C. Pandey
- Host–Parasite Interaction Biology Group, National Institute of Malaria Research, Indian Council of Medical Research, Dwarka, New Delhi, India
- * E-mail:
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Cai H, Kuang R, Gu J, Wang Y. Proteases in malaria parasites - a phylogenomic perspective. Curr Genomics 2012; 12:417-27. [PMID: 22379395 PMCID: PMC3178910 DOI: 10.2174/138920211797248565] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/17/2011] [Accepted: 07/20/2011] [Indexed: 12/21/2022] Open
Abstract
Malaria continues to be one of the most devastating global health problems due to the high morbidity and mortality it causes in endemic regions. The search for new antimalarial targets is of high priority because of the increasing prevalence of drug resistance in malaria parasites. Malarial proteases constitute a class of promising therapeutic targets as they play important roles in the parasite life cycle and it is possible to design and screen for specific protease inhibitors. In this mini-review, we provide a phylogenomic overview of malarial proteases. An evolutionary perspective on the origin and divergence of these proteases will provide insights into the adaptive mechanisms of parasite growth, development, infection, and pathogenesis.B
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Cambra I, Hernández D, Diaz I, Martinez M. Structural basis for specificity of propeptide-enzyme interaction in barley C1A cysteine peptidases. PLoS One 2012; 7:e37234. [PMID: 22615948 PMCID: PMC3355106 DOI: 10.1371/journal.pone.0037234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 04/18/2012] [Indexed: 11/30/2022] Open
Abstract
C1A cysteine peptidases are synthesized as inactive proenzymes. Activation takes place by proteolysis cleaving off the inhibitory propeptide. The inhibitory capacity of propeptides from barley cathepsin L and B-like peptidases towards commercial and barley cathepsins has been characterized. Differences in selectivity have been found for propeptides from L-cathepsins against their cognate and non cognate enzymes. Besides, the propeptide from barley cathepsin B was not able to inhibit bovine cathepsin B. Modelling of their three-dimensional structures suggests that most propeptide inhibitory properties can be explained from the interaction between the propeptide and the mature cathepsin structures. Their potential use as biotechnological tools is discussed.
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Affiliation(s)
| | | | | | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
- * E-mail:
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Sarduy ES, Muñoz AC, Trejo SA, Chavéz Planes MDLA. High-level expression of Falcipain-2 in Escherichia coli by codon optimization and auto-induction. Protein Expr Purif 2012; 83:59-69. [DOI: 10.1016/j.pep.2012.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/08/2012] [Accepted: 03/10/2012] [Indexed: 01/11/2023]
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Nicoll-Griffith DA. Use of cysteine-reactive small molecules in drug discovery for trypanosomal disease. Expert Opin Drug Discov 2012; 7:353-66. [PMID: 22458506 DOI: 10.1517/17460441.2012.668520] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The roles of cysteine protease (CP) enzymes in the biochemistry and infectivity of the three trypanosomal parasitic infections, Chagas' disease, leishmaniasis and human African trypanosomiasis, which have been elucidated over the last three decades are summarized. Inhibitors of these enzymes, which act through trapping the active site cysteine with an electrophilic warhead, hold huge potential as therapeutic agents but the promise of these has yet to be realized in clinical studies. The article addresses aspects that ought to be considered in order to develop orally active CP inhibitors that are safe and effective therapies for trypanosomiasis. AREAS COVERED This article reviews learnings from CP research in the trypanosomal field and recent advances in developing cysteine protease inhibitors (CPIs) of human cathepsin K, a related enzyme. Considerations such as intra- and extracellular localization of the CPs, off-target activities against human cathepsin enzymes, basic versus neutral and potential pro-drug inhibitors are reviewed. A description of odanacatib, a cathepsin K inhibitor currently in late stage development, is made to illustrate the attributes of a clinically viable CPI. EXPERT OPINION The emerging role of CPs in a wide array of parasitic diseases is highlighted with the vision that CP inhibitors could become the 'β-lactams' of anti-parasitic treatments in the coming decades. New CPI research will see the optimization of intra- and extracellular enzyme targeting, reduction of off-target activities and better understanding of pharmacokinetic-pharmacodynamic interactions which will all lead to compounds with much improved efficacy and viability as clinical therapies.
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Affiliation(s)
- Deborah A Nicoll-Griffith
- Infectious Diseases Franchise, Discovery and Pre-clinical Sciences, Merck and Co., Office K11-2047B, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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Structure-function of falcipains: malarial cysteine proteases. J Trop Med 2012; 2012:345195. [PMID: 22529862 PMCID: PMC3317066 DOI: 10.1155/2012/345195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/12/2011] [Accepted: 10/27/2011] [Indexed: 02/05/2023] Open
Abstract
Evidence indicates that cysteine proteases play essential role in malaria parasites; therefore an obvious area of investigation is the inhibition of these enzymes to treat malaria. Studies with cysteine protease inhibitors and manipulating cysteine proteases genes have suggested a role for cysteine proteases in hemoglobin hydrolysis. The best characterized Plasmodium cysteine proteases are falcipains, which are papain family enzymes. Falcipain-2 and falcipain-3 are major hemoglobinases of P. falciparum. Structural and functional analysis of falcipains showed that they have unique domains including a refolding domain and a hemoglobin binding domain. Overall, the complexes of falcipain-2 and falcipain-3 with small and macromolecular inhibitors provide structural insight to facilitate the design or modification of effective drug treatment against malaria. Drug development targeting falcipains should be aided by a strong foundation of biochemical and structural studies.
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Lilburn TG, Cai H, Zhou Z, Wang Y. Protease-associated cellular networks in malaria parasite Plasmodium falciparum. BMC Genomics 2011; 12 Suppl 5:S9. [PMID: 22369208 PMCID: PMC3287505 DOI: 10.1186/1471-2164-12-s5-s9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species [1-3], providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database [4], and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system [5], blood stage microarray experiments [6-8], proteomics [9-12], literature text mining, and sequence homology analysis. Seventy-seven (77) out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs). These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins), range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide processing, cell cycle progression, transcriptional regulation, and signal transduction networks. Conclusions Our network analysis of proteases from P. falciparum uses a so-called guilt-by-association approach to extract sets of proteins from the proteome that are candidates for further study. Novel protease targets and previously unrecognized members of the protease-associated sub-systems provide new insights into the mechanisms underlying parasitism, pathogenesis and virulence.
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Affiliation(s)
- Timothy G Lilburn
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Centenary celebrations article: Cysteine proteases of human malaria parasites. J Parasit Dis 2011; 35:94-103. [PMID: 23024488 DOI: 10.1007/s12639-011-0084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/09/2011] [Indexed: 01/07/2023] Open
Abstract
There is an urgent need for new drugs against malaria, which takes millions of lives annually. Cysteine proteases are potential new drug targets, especially when current drugs are showing resistance. Falcipains and vivapains are well characterized cysteine proteases of P. falciparum and P. vivax, respectively. Studies with cysteine protease inhibitors and manipulating cysteine proteases specific genes have suggested their roles in hemoglobin hydrolysis. In P. falciparum, falcipain-2 and falcipain-3 are major hemoglobinases that hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. It is confirmed that disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis, and disruption of falcipain-3 gene was not possible, suggesting that protease is essential for erythrocytic parasites. On the other hand, vivapain-2, vivapain-3 and vivapain-4 are important cysteine proteases of P. vivax, which shared a number of features with falcipain-2 and falcipain-3. A recent study indicates that vivapains and aspartic protease of P. vivax works collaboratively to enhance the parasites' ability to hydrolyze host erythrocyte hemoglobin. Studies also indicate that falcipains and vivapains also hydrolyse the erythrocyte cytoskeleton proteins and involved in rupture of red blood cell. Structural and biochemical analysis of falcipains and vivapains showed that they have unique domains for specific functions. Overall, the complexes of cysteine proteases with small and macromolecular inhibitors provide structural insight to facilitate the drug design. Therefore, giving due importance to the cysteine proteases, this review will briefly focus the recent advancement in the field of cysteine proteases of human malaria parasites.
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Horn M, Jílková A, Vondrášek J, Marešová L, Caffrey CR, Mareš M. Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: modulation of inhibition by heparin and design of mimetic inhibitors. ACS Chem Biol 2011; 6:609-17. [PMID: 21375333 DOI: 10.1021/cb100411v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Blood flukes of the genus Schistosoma cause the disease schistosomiasis that infects over 200 million people worldwide. Treatment relies on just one drug, and new therapies are needed should drug resistance emerge. Schistosoma mansoni cathepsin B1 (SmCB1) is a gut-associated protease that digests host blood proteins as source of nutrients. It is under evaluation as a therapeutic target. Enzymatic activity of the SmCB1 zymogen is prevented by the pro-peptide that sterically blocks the active site until activation of the zymogen to the mature enzyme. We investigated the structure-inhibition relationships of how the SmCB1 pro-peptide interacts with the enzyme core using a SmCB1 zymogen model and pro-peptide-derived synthetic fragments. Two regions were identified within the pro-peptide that govern its inhibitory interaction with the enzyme core: an "active site region" and a unique "heparin-binding region" that requires heparin. The latter region is apparently only found in the pro-peptides of cathepsins B associated with the gut of trematode parasites. Finally, using the active site region as a template and a docking model of SmCB1, we designed a series of inhibitors mimicking the pro-peptide structure, the best of which yielded low micromolar inhibition constants. Overall, we identify a novel glycosaminoglycan-mediated mechanism of inhibition by the pro-peptide that potentially regulates zymogen activation and describe a promising design strategy to develop antischistosomal drugs.
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Affiliation(s)
- Martin Horn
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Adéla Jílková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Lucie Marešová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Conor R. Caffrey
- Sandler Center for Drug Discovery, California Institute for Quantitative Biosciences (QB3), University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
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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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