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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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Evbuomwan IO, Alejolowo OO, Elebiyo TC, Nwonuma CO, Ojo OA, Edosomwan EU, Chikwendu JI, Elosiuba NV, Akulue JC, Dogunro FA, Rotimi DE, Osemwegie OO, Ojo AB, Ademowo OG, Adeyemi OS, Oluba OM. In silico modeling revealed phytomolecules derived from Cymbopogon citratus (DC.) leaf extract as promising candidates for malaria therapy. J Biomol Struct Dyn 2024; 42:101-118. [PMID: 36974933 DOI: 10.1080/07391102.2023.2192799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
The emergence of varying levels of resistance to currently available antimalarial drugs significantly threatens global health. This factor heightens the urgency to explore bioactive compounds from natural products with a view to discovering and developing newer antimalarial drugs with novel mode of actions. Therefore, we evaluated the inhibitory effects of sixteen phytocompounds from Cymbopogon citratus leaf extract against Plasmodium falciparum drug targets such as P. falciparum circumsporozoite protein (PfCSP), P. falciparum merozoite surface protein 1 (PfMSP1) and P. falciparum erythrocyte membrane protein 1 (PfEMP1). In silico approaches including molecular docking, pharmacophore modeling and 3D-QSAR were adopted to analyze the inhibitory activity of the compounds under consideration. The molecular docking results indicated that a compound swertiajaponin from C. citratus exhibited a higher binding affinity (-7.8 kcal/mol) to PfMSP1 as against the standard artesunate-amodiaquine (-6.6 kcal/mol). Swertiajaponin also formed strong hydrogen bond interactions with LYS29, CYS30, TYR34, ASN52, GLY55 and CYS28 amino acid residues. In addition, quercetin another compound from C. citratus exhibited significant binding energies -6.8 and -8.3 kcal/mol with PfCSP and PfEMP1, respectively but slightly lower than the standard artemether-lumefantrine with binding energies of -7.4 kcal/mol against PfCSP and -8.7 kcal/mol against PfEMP1. Overall, the present study provides evidence that swertiajaponin and other phytomolecules from C. citratus have modulatory properties toward P. falciparum drug targets and thus may warrant further exploration in early drug discovery efforts against malaria. Furthermore, these findings lend credence to the folkloric use of C. citratus for malaria treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ikponmwosa Owen Evbuomwan
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Department of Food Science and Microbiology, Landmark University, Omu-Aran, Nigeria
| | - Omokolade Oluwaseyi Alejolowo
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | - Charles Obiora Nwonuma
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | - Oluwafemi Adeleke Ojo
- Phytomedicine, Molecular Toxicology and Computational Biochemistry Research Group, Department of Biochemistry, Bowen University, Iwo, Nigeria
| | - Evelyn Uwa Edosomwan
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
| | | | | | | | | | - Damilare Emmanuel Rotimi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | | | | | - Olusegun George Ademowo
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
- Drug Research Laboratory, Institute of Advanced Medical Research and Training (IMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluyomi Stephen Adeyemi
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Olarewaju Michael Oluba
- SDG #03 Group - Good Health and Well-Being Research Cluster, Landmark University, Omu-Aran, Nigeria
- Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
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3
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Faloye KO, Tripathi MK, Fakola EG, Adepiti AO, Adesida SA, Oyeleke IO, Adebayo PA, Aregbesola AE, Famuyiwa SO, Akinyele OF. Plasmepsin II inhibitory potential of phytochemicals isolated from African antimalarial plants: a computational approach. J Biomol Struct Dyn 2023:1-16. [PMID: 37968884 DOI: 10.1080/07391102.2023.2283146] [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: 04/02/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Plamepsin II has been identified as a therapeutic target in the Plasmodium falciparum's life cycle and may lead to a drastic reduction in deaths caused by malaria worldwide. Africa flora is rich in medicinal qualities and possesses both simple and complex bioactive phytochemicals. This study utilized computational approaches like molecular docking, molecular dynamics simulation, quantum chemical calculations and ADMET to evaluate the plasmepsin II inhibitory properties of phytochemicals isolated from African antimalarial plants. Molecular docking was carried out to estimate the binding affinity of 229 phytochemicals whereby ekeberin A, dichamanetin, 10-hydroxyusambaresine, chamuvaritin and diuvaretin were selected. Further, RMSD and RMSF plots from the 100 ns simulation results showed that the screened phytochemicals were stable in the enzyme's binding pocket. The quantum chemical calculation revealed that all the phytochemicals are strong electrophiles, while ekeberin A was identified as the most stable and dichamanetin as the most reactive. Also, ADMET studies established the drug candidacy of the phytochemicals. Thus, these phytochemicals could act as good antimalarial agents after extensive in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kolade O Faloye
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Manish Kumar Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Emmanuel G Fakola
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Awodayo O Adepiti
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Stephen A Adesida
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Ibukun O Oyeleke
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Praise A Adebayo
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Adeola E Aregbesola
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Samson O Famuyiwa
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Olawale F Akinyele
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
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Marković S, Andrejević NS, Milošević J, Polović NĐ. Structural Transitions of Papain-like Cysteine Proteases: Implications for Sensor Development. Biomimetics (Basel) 2023; 8:281. [PMID: 37504169 PMCID: PMC10807080 DOI: 10.3390/biomimetics8030281] [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: 02/27/2023] [Revised: 05/03/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
The significant role of papain-like cysteine proteases, including papain, cathepsin L and SARS-CoV-2 PLpro, in biomedicine and biotechnology makes them interesting model systems for sensor development. These enzymes have a free thiol group that is suitable for many sensor designs including strong binding to gold nanoparticles or low-molecular-weight inhibitors. Focusing on the importance of the preservation of native protein structure for inhibitor-binding and molecular-imprinting, which has been applied in some efficient examples of sensor development, the aim of this work was to examine the effects of the free-thiol-group's reversible blocking on papain denaturation that is the basis of its activity loss and aggregation. To utilize biophysical methods common in protein structural transitions characterization, such as fluorimetry and high-resolution infrared spectroscopy, low-molecular-weight electrophilic thiol blocking reagent S-Methyl methanethiosulfonate (MMTS) was used in solution. MMTS binding led to a two-fold increase in 8-Anilinonaphthalene-1-sulfonic acid fluorescence, indicating increased hydrophobic residue exposure. A more in-depth analysis showed significant transitions on the secondary structure level upon MMTS binding, mostly characterized by the lowered content of α-helices and unordered structures (either for approximately one third), and the increase in aggregation-specific β-sheets (from 25 to 52%) in a dose-dependant manner. The recovery of this inhibited protein showed that reversibility of inhibition is accompanied by reversibility of protein denaturation. Nevertheless, a 100-fold molar excess of the inhibitor led to the incomplete recovery of proteolytic activity, which can be explained by irreversible denaturation. The structural stability of the C-terminal β-sheet rich domain of the papain-like cysteine protease family opens up an interesting possibility to use its foldamers as a strategy for sensor development and other multiple potential applications that rely on the great commercial value of papain-like cysteine proteases.
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Affiliation(s)
| | | | | | - Natalija Đ. Polović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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Madhav H, Patel TS, Rizvi Z, Reddy GS, Rahman A, Rahman MA, Ahmedi S, Fatima S, Saxena K, Manzoor N, Bhattacharjee S, Dixit BC, Sijwali PS, Hoda N. Development of diphenylmethylpiperazine hybrids of chloroquinoline and triazolopyrimidine using Petasis reaction as new cysteine proteases inhibitors for malaria therapeutics. Eur J Med Chem 2023; 258:115564. [PMID: 37321109 DOI: 10.1016/j.ejmech.2023.115564] [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: 05/14/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/17/2023]
Abstract
Malaria is a widespread infectious disease, causing nearly 247 million cases in 2021. The absence of a broadly effective vaccine and rapidly decreasing effectiveness of most of the currently used antimalarials are the major challenges to malaria eradication efforts. To design and develop novel antimalarials, we synthesized a series of 4,7-dichloroquinoline and methyltriazolopyrimidine analogues using a multi-component Petasis reaction. The synthesized molecules (11-31) were screened for in-vitro antimalarial activity against drug-sensitive and drug-resistant strains of Plasmodium falciparum with an IC50 value of 0.53 μM. The selected compounds were screened to evaluate in-vitro and in-silico enzyme inhibition efficacy against two cysteine proteases, PfFP2 and PfFP3. The compounds 15 and 17 inhibited PfFP2 with an IC50 = 3.5 and 4.8 μM, respectively and PfFP3 with an IC50 = 4.9 and 4.7 μM, respectively. Compounds 15 and 17 were found equipotent against the Pf3D7 strain with an IC50 value of 0.74 μM, whereas both were displayed IC50 values of 1.05 μM and 1.24 μM for the PfW2 strain, respectively. Investigation of effect of compounds on parasite development demonstrated that compounds were able to arrest the growth of the parasites at trophozoite stage. The selected compounds were screened for in-vitro cytotoxicity against mammalian lines and human red-blood-cell (RBC), which demonstrated no significant cytotoxicity associated with the molecules. In addition, in silico ADME prediction and physiochemical properties supported the drug-likeness of the synthesized molecules. Thus, the results highlighted the diphenylmethylpiperazine group cast on 4,7-dichloroquinoline and methyltriazolopyrimidine using Petasis reaction may serve as models for the development of new antimalarial agents.
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Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Tarosh S Patel
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University, Vallabh Vidyanagar, 388 120, Gujarat, India
| | - Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - G Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Abdur Rahman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Md Ataur Rahman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Saiema Ahmedi
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Sadaf Fatima
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India
| | - Kanika Saxena
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, UP, India
| | - Nikhat Manzoor
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Bharat C Dixit
- Chemistry Department, V. P. & R. P. T. P Science College, Affiliated to Sardar Patel University, Vallabh Vidyanagar, 388 120, Gujarat, India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, TS, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia, New Delhi, 110025, India.
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6
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Patra J, Rana D, Arora S, Pal M, Mahindroo N. Falcipains: Biochemistry, target validation and structure-activity relationship studies of inhibitors as antimalarials. Eur J Med Chem 2023; 252:115299. [PMID: 36996716 DOI: 10.1016/j.ejmech.2023.115299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Malaria is a tropical disease with significant morbidity and mortality burden caused by Plasmodium species in Africa, the Middle East, Asia, and South America. Pathogenic Plasmodium species have lately become increasingly resistant to approved chemotherapeutics and combination therapies. Therefore, there is an emergent need for identifying new druggable targets and novel chemical classes against the parasite. Falcipains, cysteine proteases required for heme metabolism in the erythrocytic stage, have emerged as promising drug targets against Plasmodium species that infect humans. This perspective discusses the biology, biochemistry, structural features, and genetics of falcipains. The efforts to identify selective or dual inhibitors and their structure-activity relationships are reviewed to give a perspective on the design of novel compounds targeting falcipains for antimalarial activity evaluating reasons for hits and misses for this important target.
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Affiliation(s)
- Jeevan Patra
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Devika Rana
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India
| | - Smriti Arora
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Mintu Pal
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, 151001, India
| | - Neeraj Mahindroo
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India; School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, 124 Paud Road, Kothrud, Pune, Maharashtra, 411038, India.
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Lowe MA, Cardenas A, Valentin JP, Zhu Z, Abendroth J, Castro JL, Class R, Delaunois A, Fleurance R, Gerets H, Gryshkova V, King L, Lorimer DD, MacCoss M, Rowley JH, Rosseels ML, Royer L, Taylor RD, Wong M, Zaccheo O, Chavan VP, Ghule GA, Tapkir BK, Burrows JN, Duffey M, Rottmann M, Wittlin S, Angulo-Barturen I, Jiménez-Díaz MB, Striepen J, Fairhurst KJ, Yeo T, Fidock DA, Cowman AF, Favuzza P, Crespo-Fernandez B, Gamo FJ, Goldberg DE, Soldati-Favre D, Laleu B, de Haro T. Discovery and Characterization of Potent, Efficacious, Orally Available Antimalarial Plasmepsin X Inhibitors and Preclinical Safety Assessment of UCB7362. J Med Chem 2022; 65:14121-14143. [PMID: 36216349 DOI: 10.1021/acs.jmedchem.2c01336] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plasmepsin X (PMX) is an essential aspartyl protease controlling malaria parasite egress and invasion of erythrocytes, development of functional liver merozoites (prophylactic activity), and blocking transmission to mosquitoes, making it a potential multistage drug target. We report the optimization of an aspartyl protease binding scaffold and the discovery of potent, orally active PMX inhibitors with in vivo antimalarial efficacy. Incorporation of safety evaluation early in the characterization of PMX inhibitors precluded compounds with a long human half-life (t1/2) to be developed. Optimization focused on improving the off-target safety profile led to the identification of UCB7362 that had an improved in vitro and in vivo safety profile but a shorter predicted human t1/2. UCB7362 is estimated to achieve 9 log 10 unit reduction in asexual blood-stage parasites with once-daily dosing of 50 mg for 7 days. This work demonstrates the potential to deliver PMX inhibitors with in vivo efficacy to treat malaria.
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Affiliation(s)
| | | | | | - Zhaoning Zhu
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Jan Abendroth
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | | | - Reiner Class
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | | | - Helga Gerets
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Lloyd King
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Donald D Lorimer
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Malcolm MacCoss
- Bohicket Pharma Consulting LLC, 2556 Seabrook Island Road, Seabrook Island, South Carolina 29455, United States
| | | | | | - Leandro Royer
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Melanie Wong
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | | | - Vishal P Chavan
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Gokul A Ghule
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Bapusaheb K Tapkir
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Jeremy N Burrows
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Maëlle Duffey
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Iñigo Angulo-Barturen
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - Josefine Striepen
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paola Favuzza
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | | | | | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8051, St. Louis, Missouri 63110, United States
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet, CH-1211 Genève 4, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
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Lê HG, Kang JM, Võ TC, Yoo WG, Lee KH, Na BK. Biochemical Properties of Two Plasmodium malariae Cysteine Proteases, Malapain-2 and Malapain-4. Microorganisms 2022; 10:microorganisms10010193. [PMID: 35056641 PMCID: PMC8780100 DOI: 10.3390/microorganisms10010193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
Cysteine proteases belonging to the falcipain (FP) family play a pivotal role in the biology of malaria parasites and have been extensively investigated as potential antimalarial drug targets. Three paralogous FP-family cysteine proteases of Plasmodium malariae, termed malapains 2–4 (MP2–4), were identified in PlasmoDB. The three MPs share similar structural properties with the FP-2/FP-3 subfamily enzymes and exhibit a close phylogenetic lineage with vivapains (VXs) and knowpains (KPs), FP orthologues of P. vivax and P. knowlesi. Recombinant MP-2 and MP-4 were produced in a bacterial expression system, and their biochemical properties were characterized. Both recombinant MP-2 and MP-4 showed enzyme activity across a broad range of pH values with an optimum activity at pH 5.0 and relative stability at neutral pHs. Similar to the FP-2/FP-3 subfamily enzymes in other Plasmodium species, recombinant MP-2 and MP-4 effectively hydrolyzed hemoglobin at acidic pHs. They also degraded erythrocyte cytoskeletal proteins, such as spectrin and band 3, at a neutral pH. These results imply that MP-2 and MP-4 are redundant hemoglobinases of P. malariae and may also participate in merozoite egression by degrading erythrocyte cytoskeletal proteins. However, compared with other FP-2/FP-3 enzymes, MP-2 showed a strong preference for arginine at the P2 position. Meanwhile, MP-4 showed a primary preference for leucine at the P2 position but a partial preference for phenylalanine. These different substrate preferences of MPs underscore careful consideration in the design of optimized inhibitors targeting the FP-family cysteine proteases of human malaria parasites.
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Affiliation(s)
- Hương Giang Lê
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Tuấn Cường Võ
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Won Gi Yoo
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Kon Ho Lee
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
- Department of Microbiology, Gyeongsang National University College of Medicine, Jinju 52727, Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
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9
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Rojas L, Cabrera-Muñoz A, Gil Pradas D, González JB, Alonso-Del-Rivero M, González-González Y. Arginine substitution by alanine at the P1 position increases the selectivity of CmPI-II, a non-classical Kazal inhibitor. Biochem Biophys Rep 2021; 26:101008. [PMID: 34027134 PMCID: PMC8131977 DOI: 10.1016/j.bbrep.2021.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/28/2022] Open
Abstract
CmPI-II is a Kazal-type tight-binding inhibitor isolated from the Caribbean snail Cenchritis muricatus. This inhibitor has an unusual specificity in the Kazal family, as it can inhibit subtilisin A (SUBTA), elastases and trypsin. An alanine in CmPI-II P1 site could avoid trypsin inhibition while improving/maintaining SUBTA and elastases inhibition. Thus, an alanine mutant of this position (rCmPI-II R12A) was obtained by site-directed mutagenesis. The gene cmpiR12A was expressed in P. pastoris KM71H yeast. The recombinant protein (rCmPI-II R12A) was purified by the combination of two ionic exchange chromatography (1:cationic, 2 anionic) followed by and size exclusion chromatography. The N-terminal sequence obtained as well as the experimental molecular weight allowed verifying the identity of the recombinant protein, while the correct folding was confirmed by CD experiments. rCmPI-II R12A shows a slightly increase in potency against SUBTA and elastases. The alanine substitution at P1 site on CmPI-II abolishes the trypsin inhibition, confirming the relevance of an arginine residue at P1 site in CmPI-II for trypsin inhibition and leading to a molecule with more potentialities in biomedicine.
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Affiliation(s)
- Laritza Rojas
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
| | - Aymara Cabrera-Muñoz
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
| | - Dayrom Gil Pradas
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
| | - Jessica B González
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
| | - Maday Alonso-Del-Rivero
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
| | - Yamile González-González
- Centro de Estudio de Proteínas, Universidad de La Habana, Calle 25 # 455, Plaza de La Revolución, CP 10400, La Habana, Cuba
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10
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Rawat A, Roy M, Jyoti A, Kaushik S, Verma K, Srivastava VK. Cysteine proteases: Battling pathogenic parasitic protozoans with omnipresent enzymes. Microbiol Res 2021; 249:126784. [PMID: 33989978 DOI: 10.1016/j.micres.2021.126784] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023]
Abstract
Millions of people worldwide lie at the risk of parasitic protozoic infections that kill over a million people each year. The rising inefficacy of conventional therapeutics to combat these diseases, mainly due to the development of drug resistance to a handful of available licensed options contributes substantially to the rising burden of these ailments. Cysteine proteases are omnipresent enzymes that are critically implicated in the pathogenesis of protozoic infections. Despite their significance and druggability, cysteine proteases as therapeutic targets have not yet been translated into the clinic. The review presents the significance of cysteine proteases of members of the genera Plasmodium, Entamoeba, and Leishmania, known to cause Malaria, Amoebiasis, and Leishmaniasis, respectively, the protozoic diseases with the highest morbidity and mortality. Further, projecting them as targets for molecular tools like the CRISPR-Cas technology for favorable manipulation, exploration of obscure genomes, and achieving a better insight into protozoic functioning. Overcoming the hurdles that prevent us from gaining a better insight into the functioning of these enzymes in protozoic systems is a necessity. Managing the burden of parasitic protozoic infections pivotally depends upon the betterment of molecular tools and therapeutic concepts that will pave the path to an array of diagnostic and therapeutic applications.
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Affiliation(s)
- Aadish Rawat
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Mrinalini Roy
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India
| | - Kuldeep Verma
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, India
| | - Vijay Kumar Srivastava
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, NH-11C, Jaipur-Delhi Highway, Jaipur, India.
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11
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Kayamba F, Malimabe T, Ademola IK, Pooe OJ, Kushwaha ND, Mahlalela M, van Zyl RL, Gordon M, Mudau PT, Zininga T, Shonhai A, Nyamori VO, Karpoormath R. Design and synthesis of quinoline-pyrimidine inspired hybrids as potential plasmodial inhibitors. Eur J Med Chem 2021; 217:113330. [PMID: 33744688 DOI: 10.1016/j.ejmech.2021.113330] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 01/16/2023]
Abstract
Presently, artemisinin-based combination therapy (ACT) is the first-line therapy of Plasmodium falciparum malaria. With the emergence of malaria parasites that are resistant to ACT, alternative antimalarial therapies are urgently needed. In line with this, we designed and synthesised a series of novel N-(7-chloroquinolin-4-yl)-N'-(4,6-diphenylpyrimidin-2-yl)alkanediamine hybrids (6a-7c) and evaluated their inhibitory activity against the NF54 chloroquine-susceptible strain as a promising class of antimalarial compounds. The antiplasmodial screening revealed that seven analogues showed promising to good activity with half-maximal inhibitory concentration (IC50) = 0.32 μM-4.30 μM. Compound 7a with 1,4-diamine butyl linker and 4-hydroxyl phenyl on fourth and sixth position of pyrimidine core showed the most prominent activity with an IC50 value of 0.32 ± 0.06 μM, with a favourable safety profile of 9.79 to human kidney epithelial (HEK293) cells. The remaining six analogues showed moderate activity with IC50 values ranging from 7.50 μM to 83.01 μM. We further investigated the binding affinities of the molecules to two essential cytosolic P. falciparum heat shock protein 70 homologues; PfHsp70-1 and PfHsp70-z. Compound 7a exhibited the highest binding affinity for both PfHsp70s with KD in a lower nanomolar range (4.4-11.4 nM). Furthermore, molecular docking revealed that compounds 6, 6k, 7b and 7a exhibited better fitness in PfHsp70-1 with compound 7a showing the highest and lowest binding scores of -9.8 kcal/mol. Therefore, we speculate that PfHsp70-1 is one of the targets of these inhibitors. The bioisoteric replacement of the groups at phenyl ring at the fourth and sixth position of the pyrimidine core had a constructive association with antiplasmodial activity. The promising antiplasmodial activity of the synthesised analogues illustrates how crucial molecular hybridisation is as a strategy in the development of quinoline-pyrimidine hybrids as prospective antiprotozoal agents.
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Affiliation(s)
- Francis Kayamba
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Teboho Malimabe
- Pharmacology Division, Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2193, South Africa; WITS Research Institute for Malaria (WRIM), Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2193, South Africa
| | - Idowu Kehinde Ademola
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Ofentse Jacob Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Mavela Mahlalela
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Robyn L van Zyl
- Pharmacology Division, Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2193, South Africa; WITS Research Institute for Malaria (WRIM), Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2193, South Africa
| | - Michelle Gordon
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Pertunia T Mudau
- Department of Biochemistry University of Venda, School of Mathematical and Natural Sciences, Thohoyandou, 0950, South Africa
| | - Tawanda Zininga
- Department of Biochemistry University of Venda, School of Mathematical and Natural Sciences, Thohoyandou, 0950, South Africa; Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Vincent O Nyamori
- School of Chemistry and Physics, University of KwaZulu-Natal, Westville Campus, Durban, 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa.
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12
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Vásquez-Ocmín PG, Gadea A, Cojean S, Marti G, Pomel S, Van Baelen AC, Ruiz-Vásquez L, Ruiz Mesia W, Figadère B, Ruiz Mesia L, Maciuk A. Metabolomic approach of the antiprotozoal activity of medicinal Piper species used in Peruvian Amazon. JOURNAL OF ETHNOPHARMACOLOGY 2021; 264:113262. [PMID: 32818574 DOI: 10.1016/j.jep.2020.113262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/24/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In the Peruvian Amazon as in the tropical countries of South America, the use of medicinal Piper species (cordoncillos) is common practice, particularly against symptoms of infection by protozoal parasites. However, there is few documented information about the practical aspects of their use and few scientific validation. The starting point of this work was a set of interviews of people living in six rural communities from the Peruvian Amazon (Alto Amazonas Province) about their uses of plants from Piper genus: one community of Amerindian native people (Shawi community) and five communities of mestizos. Infections caused by parasitic protozoa take a huge toll on public health in the Amazonian communities, who partly fight it using traditional remedies. Validation of these traditional practices contributes to public health care efficiency and may help to identify new antiprotozoal compounds. AIMS OF STUDY To record and validate the use of medicinal Piper species by rural people of Alto Amazonas Province (Peru) and annotate active compounds using a correlation study and a data mining approach. MATERIALS AND METHODS Rural communities were interviewed about traditional medication against parasite infections with medicinal Piper species. Ethnopharmacological surveys were undertaken in five mestizo villages, namely: Nueva Arica, Shucushuyacu, Parinari, Lagunas and Esperanza, and one Shawi community (Balsapuerto village). All communities belong to the Alto Amazonas Province (Loreto region, Peru). Seventeen Piper species were collected according to their traditional use for the treatment of parasitic diseases, 35 extracts (leaves or leaves and stems) were tested in vitro on P. falciparum (3D7 chloroquine-sensitive strain and W2 chloroquine-resistant strain), Leishmania donovani LV9 strain and Trypanosoma brucei gambiense. Assessments were performed on HUVEC cells and RAW 264.7 macrophages. The annotation of active compounds was realized by metabolomic analysis and molecular networking approach. RESULTS Nine extracts were active (IC50 ≤ 10 μg/mL) on 3D7 P. falciparum and only one on W2 P. falciparum, six on L. donovani (axenic and intramacrophagic amastigotes) and seven on Trypanosoma brucei gambiense. Only one extract was active on all three parasites (P. lineatum). After metabolomic analyses and annotation of compounds active on Leishmania, P. strigosum and P. pseudoarboreum were considered as potential sources of leishmanicidal compounds. CONCLUSIONS This ethnopharmacological study and the associated in vitro bioassays corroborated the relevance of use of Piper species in the Amazonian traditional medicine, especially in Peru. A series of Piper species with few previously available phytochemical data have good antiprotozoal activity and could be a starting point for subsequent promising work. Metabolomic approach appears to be a smart, quick but still limited methodology to identify compounds with high probability of biological activity.
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Affiliation(s)
- Pedro G Vásquez-Ocmín
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France; UMR152 PHARMADEV, IRD, UPS, Université de Toulouse, Toulouse, France.
| | - Alice Gadea
- Université de Paris, CiTCoM, UMR CNRS 8038, Paris, France
| | - Sandrine Cojean
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France; CNR du Paludisme, AP-HP, Hôpital Bichat - Claude Bernard, F-75018, Paris, France
| | - Guillaume Marti
- Laboratoire de Recherche en Sciences Végétales UMR 5546 UPS/CNRS, Plateforme MetaboHUB - MetaToul - Métabolites Végétaux, Auzeville-Tolosan, France
| | - Sébastien Pomel
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | | | - Liliana Ruiz-Vásquez
- Laboratorio de Investigación de Productos Naturales Antiparasitarios de la Amazonia (LIPNAA), Universidad Nacional de la Amazonía Peruana (UNAP), AA. HH. "Nuevo San Lorenzo", Pasaje Paujiles S/N, San Juan, Iquitos, Peru
| | - Wilfredo Ruiz Mesia
- Laboratorio de Investigación de Productos Naturales Antiparasitarios de la Amazonia (LIPNAA), Universidad Nacional de la Amazonía Peruana (UNAP), AA. HH. "Nuevo San Lorenzo", Pasaje Paujiles S/N, San Juan, Iquitos, Peru
| | - Bruno Figadère
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France
| | - Lastenia Ruiz Mesia
- Laboratorio de Investigación de Productos Naturales Antiparasitarios de la Amazonia (LIPNAA), Universidad Nacional de la Amazonía Peruana (UNAP), AA. HH. "Nuevo San Lorenzo", Pasaje Paujiles S/N, San Juan, Iquitos, Peru
| | - Alexandre Maciuk
- Université Paris-Saclay, CNRS, BioCIS, 92290, Châtenay-Malabry, France.
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13
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Dousti M, Manzano-Román R, Rashidi S, Barzegar G, Ahmadpour NB, Mohammadi A, Hatam G. A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets. Pathog Dis 2021; 79:ftaa071. [PMID: 33202000 DOI: 10.1093/femspd/ftaa071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
There is no effective vaccine against malaria; therefore, chemotherapy is to date the only choice to fight against this infectious disease. However, there is growing evidences of drug-resistance mechanisms in malaria treatments. Therefore, the identification of new drug targets is an urgent need for the clinical management of the disease. Proteomic approaches offer the chance of determining the effects of antimalarial drugs on the proteome of Plasmodium parasites. Accordingly, we reviewed the effects of antimalarial drugs on the Plasmodium falciparum proteome pointing out the relevance of several proteins as possible drug targets in malaria treatment. In addition, some of the P. falciparum stage-specific altered proteins and parasite-host interactions might play important roles in pathogenicity, survival, invasion and metabolic pathways and thus serve as potential sources of drug targets. In this review, we have identified several proteins, including thioredoxin reductase, helicases, peptidyl-prolyl cis-trans isomerase, endoplasmic reticulum-resident calcium-binding protein, choline/ethanolamine phosphotransferase, purine nucleoside phosphorylase, apical membrane antigen 1, glutamate dehydrogenase, hypoxanthine guanine phosphoribosyl transferase, heat shock protein 70x, knob-associated histidine-rich protein and erythrocyte membrane protein 1, as promising antimalarial drugs targets. Overall, proteomic approaches are able to partially facilitate finding possible drug targets. However, the integration of other 'omics' and specific pharmaceutical techniques with proteomics may increase the therapeutic properties of the critical proteins identified in the P. falciparum proteome.
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Affiliation(s)
- Majid Dousti
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Barzegar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Alireza Mohammadi
- Department of Disease Control, Komijan Treatment and Health Network, Arak University of Medical Science, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Mishra M, Singh V, Tellis MB, Joshi RS, Singh S. Repurposing the McoTI-II Rigid Molecular Scaffold in to Inhibitor of 'Papain Superfamily' Cysteine Proteases. Pharmaceuticals (Basel) 2020; 14:ph14010007. [PMID: 33374547 PMCID: PMC7822474 DOI: 10.3390/ph14010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 01/19/2023] Open
Abstract
Clan C1A or ‘papain superfamily’ cysteine proteases are key players in many important physiological processes and diseases in most living systems. Novel approaches towards the development of their inhibitors can open new avenues in translational medicine. Here, we report a novel design of a re-engineered chimera inhibitor Mco-cysteine protease inhibitor (CPI) to inhibit the activity of C1A cysteine proteases. This was accomplished by grafting the cystatin first hairpin loop conserved motif (QVVAG) onto loop 1 of the ultrastable cyclic peptide scaffold McoTI-II. The recombinantly expressed Mco-CPI protein was able to bind with micromolar affinity to papain and showed remarkable thermostability owing to the formation of multi-disulphide bonds. Using an in silico approach based on homology modelling, protein–protein docking, the calculation of the free-energy of binding, the mechanism of inhibition of Mco-CPI against representative C1A cysteine proteases (papain and cathepsin L) was validated. Furthermore, molecular dynamics simulation of the Mco-CPI–papain complex validated the interaction as stable. To conclude, in this McoTI-II analogue, the specificity had been successfully redirected towards C1A cysteine proteases while retaining the moderate affinity. The outcomes of this study pave the way for further modifications of the Mco-CPI design for realizing its full potential in therapeutics. This study also demonstrates the relevance of ultrastable peptide-based scaffolds for the development of novel inhibitors via grafting.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar 201314, India;
- Correspondence: (M.M.); (S.S.)
| | - Vigyasa Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar 201314, India;
- Special Centre for Molecular Medicine, Jawahar Lal Nehru University, New Delhi 110067, India
| | - Meenakshi B. Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; (M.B.T.); (R.S.J.)
| | - Rakesh S. Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; (M.B.T.); (R.S.J.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar 201314, India;
- Special Centre for Molecular Medicine, Jawahar Lal Nehru University, New Delhi 110067, India
- Correspondence: (M.M.); (S.S.)
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15
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Mishra M, Singh V, Tellis MB, Joshi RS, Pandey KC, Singh S. Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial. J Biomol Struct Dyn 2020; 40:3642-3654. [PMID: 33292080 DOI: 10.1080/07391102.2020.1848629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded cyclic peptide (CYS-cIHL) and linear peptide (CYS-IHL), using the conserved inhibitory hairpin loop amino acid sequence. Using an in silico approach based on modeling, protein-peptide docking, molecular dynamics simulations and calculation of free energy of binding, we designed and validated inhibitory peptides against falcipain-2 (FP-2) and -3 (FP-3), cysteine proteases from the malarial parasite Plasmodium falciparum. Falcipains are critical hemoglobinases of P. falciparum that are validated targets for the development of antimalarial therapies. CYS-cIHL was able to bind with micromolar affinity to FP-2 and modulate its binding with its substrate, hemoglobin in in vitro and in vivo assays. CYS-cIHL could effectively block parasite growth and displayed antimalarial activity in culture assays with no cytotoxicity towards human cells. These results indicated that cyclization can substantially increase the peptide affinity to the target. Furthermore, this can be applied as an effective strategy for engineering peptide inhibitory potency against proteases.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi B Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Rakesh S Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kailash C Pandey
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, Dwarka, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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16
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Lechuga GC, Napoleão-Pêgo P, Bottino CCG, Pinho RT, Provance-Jr DW, De-Simone SG. Trypanosoma cruzi Presenilin-Like Transmembrane Aspartyl Protease: Characterization and Cellular Localization. Biomolecules 2020; 10:biom10111564. [PMID: 33212923 PMCID: PMC7698364 DOI: 10.3390/biom10111564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
The increasing detection of infections of Trypanosoma cruzi, the etiological agent of Chagas disease, in non-endemic regions beyond Latin America has risen to be a major public health issue. With an impact in the millions of people, current treatments rely on antiquated drugs that produce severe side effects and are considered nearly ineffective for the chronic phase. The minimal progress in the development of new drugs highlights the need for advances in basic research on crucial biochemical pathways in T. cruzi to identify new targets. Here, we report on the T. cruzi presenilin-like transmembrane aspartyl enzyme, a protease of the aspartic class in a unique phylogenetic subgroup with T. vivax separate from protozoans. Computational analyses suggest it contains nine transmembrane domains and an active site with the characteristic PALP motif of the A22 family. Multiple linear B-cell epitopes were identified by SPOT-synthesis analysis with Chagasic patient sera. Two were chosen to generate rabbit antisera, whose signal was primarily localized to the flagellar pocket, intracellular vesicles, and endoplasmic reticulum in parasites by whole-cell immunofluorescence. The results suggest that the parasitic presenilin-like enzyme could have a role in the secretory pathway and serve as a target for the generation of new therapeutics specific to the T. cruzi.
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Affiliation(s)
- Guilherme C. Lechuga
- Center for Technological Development in Health/National Institute of Science and Technology for Innovation on Diseases of Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (C.C.G.B.); (D.W.P.-J.)
- Cellular Ultrastructure Laboratory, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | - Paloma Napoleão-Pêgo
- Center for Technological Development in Health/National Institute of Science and Technology for Innovation on Diseases of Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (C.C.G.B.); (D.W.P.-J.)
| | - Carolina C. G. Bottino
- Center for Technological Development in Health/National Institute of Science and Technology for Innovation on Diseases of Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (C.C.G.B.); (D.W.P.-J.)
| | - Rosa T. Pinho
- Clinical Immunology Laboratory, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil;
| | - David W. Provance-Jr
- Center for Technological Development in Health/National Institute of Science and Technology for Innovation on Diseases of Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (C.C.G.B.); (D.W.P.-J.)
- Interdisciplinary Medical Research Laboratory, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | - Salvatore G. De-Simone
- Center for Technological Development in Health/National Institute of Science and Technology for Innovation on Diseases of Neglected Population (INCT-IDPN), FIOCRUZ, Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (C.C.G.B.); (D.W.P.-J.)
- Department of Molecular and Cellular Biology, Federal Fluminense University, Niterói 24220-008, Brazil
- Correspondence: ; Tel.: +55-21-3865-8183
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Aminobenzosuberone derivatives as PfA-M1 inhibitors: Molecular recognition and antiplasmodial evaluation. Bioorg Chem 2020; 98:103750. [DOI: 10.1016/j.bioorg.2020.103750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/27/2020] [Accepted: 03/09/2020] [Indexed: 12/16/2022]
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Identifying miltefosine-resistant key genes in protein-protein interactions network and experimental verification in Iranian Leishmania major. Mol Biol Rep 2019; 46:5371-5388. [PMID: 31385238 DOI: 10.1007/s11033-019-04992-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/19/2019] [Indexed: 12/23/2022]
Abstract
Drug resistance is a complex phenomenon during leishmaniasis chemotherapy. In this study, the genes and pathways involved in miltefosine (MIL)-resistant Leishmania were identified using microarray data and in silico approaches. GSE30685 and GSE45496 were obtained from GEO database and analyzed with GEO2R tool to identify genes involved in MIL-resistant Leishmania. 177 differentially expressed genes (DEGs) were selected from these GSEs, which about half of them were uncharacterized/hypothetical proteins. The interactions between DEGs were investigated using STRING database and protein-protein interaction (PPI) networks. Five hub nodes were found in the PPI network. The gene ontology (GO) analysis of the resulting network revealed that DNA replication (GO:0006260) and ATP hydrolysis coupled proton transport (GO:0015991) were the most enriched GO term. Iranian MIL-resistant Leishmania major (L. major) parasites were generated by exposure of wild-type isolates to the increasing concentrations of MIL over a period of 5 months. Proof of mRNA expression levels of the obtained hub genes was assessed in Iranian wild-type and acquired resistant L. major parasites by real-time PCR. A significant higher expression level of LDBPK_150170 (encoding protein phosphatase 2C, PP2C), was only observed in Iranian L. major parasites resistance to MIL. Moreover, the RT-PCR results showed that the expression of metacyclic marker (small hydrophilic endoplasmic reticulum-associated protein, SHERP) and MIL-resistant marker (Leishmania MIL-transporter, LMT) was significantly increased and decreased, respectively, in Iranian MIL-resistant L. major parasites. Taken together, these data suggested that PP2C as well as SHERP and LMT genes may be prospective targets for the treatment of MIL-resistant Leishmania.
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