1
|
Olanlokun JO, Owolabi AB, Odedeyi A, Oderinde SO, Bodede O, Steenkamp P, Koorbanally NA, Olorunsogo OO. Mechanism of antimalarial action and mitigation of infection-mediated mitochondrial dysfunction by phyto-constituents of Andrographis paniculata ((Burm f.) Wall. ex Nees) in Plasmodium berghei-infected mice. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118241. [PMID: 38670400 DOI: 10.1016/j.jep.2024.118241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Andrographis paniculata (AP) ((Burm f.) Wall. ex Nees) is a medicinal plant, documented for its folkloric use in the treatment of malaria. AIM This study was designed to determine the potency of extract and fractions of A. paniculata (AP) as a curative, both for susceptible and resistant malaria and to also determine the plant's mechanism of action. This study was also designed to determine whether AP extract and its most potent fraction will mitigate infection-mediated mitochondrial dysfunction, and to assess the phytochemical constituents of the most potent fraction. MATERIALS AND METHODS n-Hexane, dichloromethane, ethylacetate and methanol were used to partition the methanol extract of A. paniculata. Graded doses of these extract and fractions were used to treat mice infected with chloroquine-sensitive strain of P. berghei in a curative model. The most potent fraction was used to treat mice infected with resistant (ANKA strain) P. berghei. Inhibition of hemozoin formation, reversal of mitochondrial dysfunction and antiinflammatory potentials were determined. A combination of ultraperformance liquid chromatography-quadrupole time of flight-mass spectrometry and nuclear magnetic resonance spectroscopy were used for chemical analysis. RESULTS Microscopy revealed that the dichloromethane fraction decreased the parasite burden the most, and inhibition of the hemozoin formation is one of its mechanisms of action. The dichloromethane fraction reversed parasite-induced mitochondrial pore opening in the host, enzyme-dependent ATP hydrolysis and peroxidation of host mitochondrial membrane phospholipids as well as its antiinflammatory potentials. The UPLC-qTOF-MS report and NMR fingerprints of the dichloromethane fraction of A. paniculata yielded fourteen compounds of which sibiricinone C was identified from the plant for the first time. CONCLUSION Fractions of A. paniculata possess antiplasmodial effects with the dichloromethane fraction having the highest potency. The potent effect of this fraction may be attributed to the phytochemicals present because it contains terpenes implicated with antimalarial and antiinflammatory activities.
Collapse
Affiliation(s)
- John Oludele Olanlokun
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria.
| | - Adesola Bunmi Owolabi
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
| | - Aminat Odedeyi
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
| | - Solomon Obaloluwa Oderinde
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
| | - Olusola Bodede
- Department of Chemistry, University of Pretoria, Pretoria, 0028, South Africa
| | - Paul Steenkamp
- Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa
| | | | - Olufunso Olabode Olorunsogo
- Laboratories for Biomembrane Research and Biotechnology, Department of Biochemistry, University of Ibadan, Ibadan, Nigeria
| |
Collapse
|
2
|
Appetecchia F, Fabbrizi E, Fiorentino F, Consalvi S, Biava M, Poce G, Rotili D. Transmission-Blocking Strategies for Malaria Eradication: Recent Advances in Small-Molecule Drug Development. Pharmaceuticals (Basel) 2024; 17:962. [PMID: 39065810 PMCID: PMC11279868 DOI: 10.3390/ph17070962] [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: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Malaria drug research and development efforts have resurged in the last decade following the decelerating rate of mortality and malaria cases in endemic regions. The inefficiency of malaria interventions is largely driven by the spreading resistance of the Plasmodium falciparum parasite to current drug regimens and that of the malaria vector, the Anopheles mosquito, to insecticides. In response to the new eradication agenda, drugs that act by breaking the malaria transmission cycle (transmission-blocking drugs), which has been recognized as an important and additional target for intervention, are being developed. These drugs take advantage of the susceptibility of Plasmodium during population bottlenecks before transmission (gametocytes) and in the mosquito vector (gametes, zygotes, ookinetes, oocysts, sporozoites). To date, compounds targeting stage V gametocytes predominate in the chemical library of transmission-blocking drugs, and some of them have entered clinical trials. The targeting of Plasmodium mosquito stages has recently renewed interest in the development of innovative malaria control tools, which hold promise for the application of compounds effective at these stages. In this review, we highlight the major achievements and provide an update on the research of transmission-blocking drugs, with a particular focus on their chemical scaffolds, antiplasmodial activity, and transmission-blocking potential.
Collapse
Affiliation(s)
| | | | | | | | | | - Giovanna Poce
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.A.); (E.F.); (F.F.); (S.C.); (M.B.)
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; (F.A.); (E.F.); (F.F.); (S.C.); (M.B.)
| |
Collapse
|
3
|
Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
Collapse
Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| |
Collapse
|
4
|
Lisauskaitė M, Nixon GL, Woodley CM, Berry NG, Coninckx A, Qie LC, Leung SC, Taramelli D, Basilico N, Parapini S, Ward SA, Vadas O, Soldati-Favre D, Hong WD, O'Neill PM. Design, synthesis and modelling of photoreactive chemical probes for investigating target engagement of plasmepsin IX and X in Plasmodium falciparum. RSC Chem Biol 2024; 5:19-29. [PMID: 38179191 PMCID: PMC10763550 DOI: 10.1039/d3cb00109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/27/2023] [Indexed: 01/06/2024] Open
Abstract
The emergence of Plasmodium parasite resistance to current front-line antimalarial treatments poses a serious threat to global malaria control and highlights the necessity for the development of therapeutics with novel targets and mechanisms of action. Plasmepsins IX and X (PMIX/PMX) have been recognised as highly promising targets in Plasmodium due to their contribution to parasite's pathogenicity. Recent research has demonstrated that dual PMIX/PMX inhibition results in the impairment of multiple parasite's life cycle stages, which is an important feature in drug resistance prevention. Herein we report novel hydroxyethylamine photoaffinity labelling (PAL) probes, designed for PMIX/PMX target engagement and proteomics experiments in Plasmodium parasites. The prepared probes have both a photoreactive group (diazirine or benzophenone) for covalent attachment to target proteins, and a terminal alkyne handle allowing their use in bioorthogonal ligation. One of the synthesised benzophenone probes was shown to be highly promising as demonstrated by its outstanding antimalarial potency (IC50 = 15 nM versus D10 P. falciparum) and its inhibitory effect against PfPMX in an enzymatic assay. Molecular docking and molecular dynamics studies show that the inclusion of the benzophenone and alkyne handle does not alter the binding mode compared to the parent compound. The photoaffinity probe can be used in future chemical proteomics studies to allow hydroxyethylamine drug scaffold target identification and validation in Plasmodium. We expect our findings to act as a tool for future investigations on PMIX/PMX inhibition in antimalarial drug discovery.
Collapse
Affiliation(s)
| | - Gemma L Nixon
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | | | - Neil G Berry
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Andy Coninckx
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - L Charlie Qie
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Suet C Leung
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Donatella Taramelli
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DISFEB), Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Nicoletta Basilico
- Dipartimento di Scienze Biomediche, Chirurgiche e Odontoiatriche, Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Silvia Parapini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano 20133 Milano Italy
- Affiliated to Centro Interuniversitario di Ricerche sulla Malaria/Italian Malaria Network (CIRM-IMN), Università degli Studi di Camerino Italy
| | - Stephen A Ward
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine Liverpool L3 5QA UK
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet CH-1211 Genève 4 Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet CH-1211 Genève 4 Switzerland
| | - W David Hong
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| | - Paul M O'Neill
- Department of Chemistry, University of Liverpool Liverpool L69 7ZD UK
| |
Collapse
|
5
|
Sakata K, Lowe MA, Xuan M, Bruffaerts J, Stasi LP, Lallemand B, Cardenas A, Taylor RD, Vidler LR, King L, Valentin JP, Laleu B, de Haro T. Design of Novel Series of Antimalarial PMX Inhibitors with Increased Half-Life via Molecular Property Optimization. ACS Med Chem Lett 2023; 14:1582-1588. [PMID: 37974949 PMCID: PMC10641918 DOI: 10.1021/acsmedchemlett.3c00404] [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: 09/11/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023] Open
Abstract
Plasmepsin X (PMX) has been identified as a multistage antimalarial target. PMX is a malarial aspartyl protease essential for merozoite egress from infected red blood cells and invasion of the host erythrocytes. Previously, we reported the identification of PMX inhibitors by structure-based optimization of a cyclic guanidine core. Preclinical assessment of UCB7362, which displayed both in vitro and in vivo antimalarial activity, revealed a suboptimal dose paradigm (once daily dosing of 50 mg for 7 days for treatment of uncomplicated malaria) relative to current standard of care (three-dose regime). We report here the efforts toward extending the half-life (t1/2) by reducing metabolic clearance and increasing volume of distribution (Vss). Our efforts culminated in the identification of a biaryl series, with an expected longer t1/2 in human than UCB7362 while maintaining a similar in vitro off-target hit rate.
Collapse
Affiliation(s)
- Komei Sakata
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | | | | | | | | | | | | | | | | | - Lloyd King
- UCB, 216 Bath Road, Slough SL1 3WE, United
Kingdom
| | | | - Benoît Laleu
- Medicines
for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | | |
Collapse
|
6
|
Sulyman AO, Aje OO, Ajani EO, Abdulsalam RA, Balogun FO, Sabiu S. Bioprospection of Selected Plant Secondary Metabolites as Modulators of the Proteolytic Activity of Plasmodium falciparum Plasmepsin V. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6229503. [PMID: 37388365 PMCID: PMC10307063 DOI: 10.1155/2023/6229503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Malaria is a devastating disease, and its management is only achieved through chemotherapy. However, resistance to available medication is still a challenge; therefore, there is an urgent need for the discovery and development of therapeutics with a novel mechanism of action to counter the resistance scourge consistent with the currently available antimalarials. Recently, plasmepsin V was validated as a therapeutic target for the treatment of malaria. The pepsin-like aspartic protease anchored in the endoplasmic reticulum is responsible for the trafficking of parasite-derived proteins to the erythrocytic surface of the host cells. In this study, a small library of compounds was preliminarily screened in vitro to identify novel modulators of Plasmodium falciparum plasmepsin V (PfPMV). The results obtained revealed kaempferol, quercetin, and shikonin as possible PfPMV inhibitors, and these compounds were subsequently probed for their inhibitory potentials using in vitro and in silico methods. Kaempferol and shikonin noncompetitively and competitively inhibited the specific activity of PfPMV in vitro with IC50 values of 22.4 and 43.34 μM, respectively, relative to 62.6 μM obtained for pepstatin, a known aspartic protease inhibitor. Further insight into the structure-activity relationship of the compounds through a 100 ns molecular dynamic (MD) simulation showed that all the test compounds had a significant affinity for PfPMV, with quercetin (-36.56 kcal/mol) being the most prominent metabolite displaying comparable activity to pepstatin (-35.72 kcal/mol). This observation was further supported by the compactness and flexibility of the resulting complexes where the compounds do not compromise the structural integrity of PfPMV but rather stabilized and interacted with the active site amino acid residues critical to PfPMV modulation. Considering the findings in this study, quercetin, kaempferol, and shikonin could be proposed as novel aspartic protease inhibitors worthy of further investigation in the treatment of malaria.
Collapse
Affiliation(s)
- Abdulhakeem Olarewaju Sulyman
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Oluwapelumi Oluwaseun Aje
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Emmanuel Oladipo Ajani
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| |
Collapse
|
7
|
Chen S, Liang C, Li H, Yu W, Prothiwa M, Kopczynski D, Loroch S, Fransen M, Verhelst SHL. Pepstatin-Based Probes for Photoaffinity Labeling of Aspartic Proteases and Application to Target Identification. ACS Chem Biol 2023; 18:686-692. [PMID: 36920024 DOI: 10.1021/acschembio.2c00946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Aspartic proteases are a small class of proteases implicated in a wide variety of human diseases. Covalent chemical probes for photoaffinity labeling (PAL) of these proteases are underdeveloped. We here report a full on-resin synthesis of clickable PAL probes based on the natural product inhibitor pepstatin incorporating a minimal diazirine reactive group. The position of this group in the inhibitor determines the labeling efficiency. The most effective probes sensitively detect cathepsin D, a biomarker for breast cancer, in cell lysates. Moreover, through chemical proteomics experiments and deep learning algorithms, we identified sequestosome-1, an important player in autophagy, as a direct interaction partner and substrate of cathepsin D.
Collapse
Affiliation(s)
- Suyuan Chen
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Chunguang Liang
- Bioinformatik, Biozentrum, Universität Würzburg, 97074 Würzburg, Germany.,Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Hongli Li
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Peroxisome Biology and Intracellular Communication, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Weimeng Yu
- Bioinformatik, Biozentrum, Universität Würzburg, 97074 Würzburg, Germany
| | - Michaela Prothiwa
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Stefan Loroch
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Ruhr-Universität Bochum, Medizinisches Proteom-Center, Building ProDi E2.240, Gesundheitscampus 4, D-44801 Bochum, Germany.,ProtiFi LLC, 1000 Turk Hill Road, Suite 180, 2nd Floor, Fairport, New York 14450, United States
| | - Marc Fransen
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Peroxisome Biology and Intracellular Communication, Herestraat 49 box 901b, 3000 Leuven, Belgium
| | - Steven H L Verhelst
- Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, 3000 Leuven, Belgium
| |
Collapse
|
8
|
Elsworth B, Keroack C, Rezvani Y, Paul A, Barazorda K, Tennessen J, Sack S, Moreira C, Gubbels MJ, Meyers M, Zarringhalam K, Duraisingh M. Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases. RESEARCH SQUARE 2023:rs.3.rs-2553721. [PMID: 36909484 PMCID: PMC10002801 DOI: 10.21203/rs.3.rs-2553721/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Apicomplexan egress from host cells is fundamental to the spread of infection and is poorly characterized in Babesia spp., parasites of veterinary importance and emerging zoonoses. Through the use of video microscopy, transcriptomics and chemical genetics, we have implicated signaling, proteases and gliding motility as key drivers of egress by Babesia divergens. We developed reverse genetics to perform a knockdown screen of putative mediators of egress, identifying kinases and proteases involved in distinct steps of egress (ASP3, PKG and CDPK4) and invasion (ASP2, ASP3 and PKG). Inhibition of egress leads to continued intracellular replication, indicating exit from the replication cycle is uncoupled from egress. Chemical genetics validated PKG, ASP2 and ASP3 as druggable targets in Babesia spp. All taken together, egress in B. divergens more closely resembles T. gondii than the more evolutionarily-related Plasmodium spp. We have established a molecular framework for biological and translational studies of B. divergens egress.
Collapse
|
9
|
Bridging the Gap in Malaria Parasite Resistance, Current Interventions, and the Way Forward from in Silico Perspective: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227915. [PMID: 36432016 PMCID: PMC9692793 DOI: 10.3390/molecules27227915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
The past decade has seen most antimalarial drugs lose their clinical potency stemming from parasite resistance. Despite immense efforts by researchers to mitigate this global scourge, a breakthrough is yet to be achieved, as most current malaria chemotherapies suffer the same fate. Though the etiology of parasite resistance is not well understood, the parasite's complex life has been implicated. A drug-combination therapy with artemisinin as the central drug, artemisinin-based combination therapy (ACT), is currently the preferred malaria chemotherapy in most endemic zones. The emerging concern of parasite resistance to artemisinin, however, has compromised this treatment paradigm. Membrane-bound Ca2+-transporting ATPase and endocytosis pathway protein, Kelch13, among others, are identified as drivers in plasmodium parasite resistance to artemisinin. To mitigate parasite resistance to current chemotherapy, computer-aided drug design (CADD) techniques have been employed in the discovery of novel drug targets and the development of small molecule inhibitors to provide an intriguing alternative for malaria treatment. The evolution of plasmepsins, a class of aspartyl acid proteases, has gained tremendous attention in drug discovery, especially the non-food vacuole. They are expressed at multi-stage of the parasite's life cycle and involve in hepatocytes' egress, invasion, and dissemination of the parasite within the human host, further highlighting their essentiality. In silico exploration of non-food vacuole plasmepsin, PMIX and PMX unearthed the dual enzymatic inhibitory mechanism of the WM382 and 49c, novel plasmepsin inhibitors presently spearheading the search for potent antimalarial. These inhibitors impose structural compactness on the protease, distorting the characteristic twist motion. Pharmacophore modeling and structure activity of these compounds led to the generation of hits with better affinity and inhibitory prowess towards PMIX and PMX. Despite these headways, the major obstacle in targeting PM is the structural homogeneity among its members and to human Cathepsin D. The incorporation of CADD techniques described in the study at early stages of drug discovery could help in selective inhibition to augment malaria chemotherapy.
Collapse
|
10
|
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.
Collapse
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
| | | |
Collapse
|
11
|
Abugri J, Ayariga J, Sunwiale SS, Wezena CA, Gyamfi JA, Adu-Frimpong M, Agongo G, Dongdem JT, Abugri D, Dinko B. Targeting the Plasmodium falciparum proteome and organelles for potential antimalarial drug candidates. Heliyon 2022; 8:e10390. [PMID: 36033316 PMCID: PMC9398786 DOI: 10.1016/j.heliyon.2022.e10390] [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: 09/12/2021] [Revised: 01/12/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022] Open
Abstract
There is an unmet need to unearth alternative treatment options for malaria, wherein this quest is more pressing in recent times due to high morbidity and mortality data arising mostly from the endemic countries coupled with partial diversion of attention from the disease in view of the SARS-Cov-2 pandemic. Available therapeutic options for malaria have been severely threatened with the emergence of resistance to almost all the antimalarial drugs by the Plasmodium falciparum parasite in humans, which is a worrying situation. Artemisinin combination therapies (ACT) that have so far been the mainstay of malaria have encountered resistance by malaria parasite in South East Asia, which is regarded as a notorious ground zero for the emergence of resistance to antimalarial drugs. This review analyzes a few key druggable targets for the parasite and the potential of specific inhibitors to mitigate the emerging antimalarial drug resistance problem by providing a concise assessment of the essential proteins of the malaria parasite that could serve as targets. Moreover, this work provides a summary of the advances made in malaria parasite biology and the potential to leverage these findings for antimalarial drug production.
Collapse
Affiliation(s)
- James Abugri
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Joseph Ayariga
- The Biomedical Engineering Programme, Alabama State University, Montgomery, AL, 36104, USA
| | - Samuel Sunyazi Sunwiale
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Cletus Adiyaga Wezena
- Department of Microbiology, School of Biosciences, University for Development Studies (UDS), Nyankpala Campus, Tamale, Ghana
| | - Julien Agyemang Gyamfi
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Michael Adu-Frimpong
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C. K. Tedam University of Technology and Applied Sciences (CKT-UTAS), Navrongo, Ghana
| | - Julius Tieroyaare Dongdem
- Department of Biochemistry and Molecular Medicine. School of Medicine. University for Development Studies (UDS), Tamale-Campus, Ghana
| | - Daniel Abugri
- Department of Biological Sciences, Microbiology PhD Programme, Laboratory of Ethnomedicine, Parasitology, and Drug Discovery, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, USA
| | - Bismarck Dinko
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho. Ghana
| |
Collapse
|
12
|
In Silico and In Vitro Antimalarial Screening and Validation Targeting Plasmodium falciparum Plasmepsin V. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092670. [PMID: 35566023 PMCID: PMC9102085 DOI: 10.3390/molecules27092670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022]
Abstract
Malaria chemotherapy is greatly threatened by the recent emergence and spread of resistance in the Plasmodium falciparum parasite against artemisinins and their partner drugs. Therefore, it is an urgent priority to develop new antimalarials. Plasmepsin V (PMV) is regarded as a superior drug target for its essential role in protein export. In this study, we performed virtual screening based on homology modeling of PMV structure, molecular docking and pharmacophore model analysis against a library with 1,535,478 compounds, which yielded 233 hits. Their antimalarial activities were assessed amongst four non-peptidomimetic compounds that demonstrated the promising inhibition of parasite growth, with mean IC50 values of 6.67 μM, 5.10 μM, 12.55 μM and 8.31 μM. No significant affection to the viability of L929 cells was detected in these candidates. These four compounds displayed strong binding activities with the PfPMV model through H-bond, hydrophobic, halogen bond or π-π interactions in molecular docking, with binding scores under −9.0 kcal/mol. The experimental validation of molecule-protein interaction identified the binding of four compounds with multiple plasmepsins; however, only compound 47 showed interaction with plasmepsin V, which exhibited the potential to be developed as an active PfPMV inhibitor.
Collapse
|
13
|
Hai Y, Cai ZM, Li PJ, Wei MY, Wang CY, Gu YC, Shao CL. Trends of antimalarial marine natural products: progresses, challenges and opportunities. Nat Prod Rep 2022; 39:969-990. [DOI: 10.1039/d1np00075f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review provides an overview of the antimalarial marine natural products, focusing on their chemistry, malaria-related targets and mechanisms, and highlighting their potential for drug development.
Collapse
Affiliation(s)
- Yang Hai
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Zi-Mu Cai
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Peng-Jie Li
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Mei-Yan Wei
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| |
Collapse
|
14
|
Tallei TE, Kepel BJ, Alorabi M, El-Shehawi AM, Bodhi W, Tumilaar SG, Celik I, Mostafa-Hedeab G, Mohamed AAR, Emran TB. Appraisal of Bioactive Compounds of Betel Fruit as Antimalarial Agents by Targeting Plasmepsin 1 and 2: A Computational Approach. Pharmaceuticals (Basel) 2021; 14:ph14121285. [PMID: 34959685 PMCID: PMC8707617 DOI: 10.3390/ph14121285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
In many countries, the fruit of betel (Piper betle Linn) is traditionally used as medicine for treating malaria. It is a fatal disease, and existing medications are rapidly losing potency, necessitating the development of innovative pharmaceutics. The current study attempted to determine the compounds in the n-hexane fraction of betel fruit extract and investigate the potential inhibition of bioactive compounds against aspartic protease plasmepsin 1 (PDB ID: 3QS1) and plasmepsin 2 (PDB ID: 1LEE) of Plasmodium falciparum using a computational approach. The ethanol extract was fractionated into n-hexane and further analyzed using gas chromatography-mass spectrometry (GC-MS) to obtain information regarding the compounds contained in betel fruit. Each compound's potential antimalarial activity was evaluated using AutoDock Vina and compared to artemisinin, an antimalarial drug. Molecular dynamics simulations (MDSs) were performed to evaluate the stability of the interaction between the ligand and receptors. Results detected 20 probable compounds in the n-hexane extract of betel fruit based on GC-MS analysis. The docking study revealed that androstan-17-one,3-ethyl-3-hydroxy-, (5 alpha)- has the highest binding affinity for plasmepsin 1 and plasmepsin 2. The compound exhibits a similar interaction with artemisinin at the active site of the receptors. The compound does not violate Lipinski's rules of five. It belongs to class 5 toxicity with an LD50 of 3000 mg/kg. MDS results showed stable interactions between the compound and the receptors. Our study concluded that androstan-17-one,3-ethyl-3-hydroxy-, (5 alpha)- from betel fruit has the potential to be further investigated as a potential inhibitor of the aspartic protease plasmepsin 1 and plasmepsin 2 of Plasmodium falciparum.
Collapse
Affiliation(s)
- Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
- Correspondence: (F.); (T.E.T.); (T.B.E.); Tel.: +62-812-4408-855 (F.); +62-811-4314-880 (T.E.T.); +880-01819-942214 (T.B.E.)
| | - Billy Johnson Kepel
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia; (B.J.K.); (W.B.)
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (M.A.); (A.M.E.-S.)
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia; (M.A.); (A.M.E.-S.)
| | - Widdhi Bodhi
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia; (B.J.K.); (W.B.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department, Health Sciences Research Unit, Medical College, Jouf University, Sakaka 72446, Saudi Arabia;
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef 62521, Egypt
| | | | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Correspondence: (F.); (T.E.T.); (T.B.E.); Tel.: +62-812-4408-855 (F.); +62-811-4314-880 (T.E.T.); +880-01819-942214 (T.B.E.)
| |
Collapse
|
15
|
Patent highlights June-July 2021. Pharm Pat Anal 2021; 10:237-244. [PMID: 34753317 DOI: 10.4155/ppa-2021-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
Collapse
|
16
|
Sharma N, Kashif M, Singh V, Fontinha D, Mukherjee B, Kumar D, Singh S, Prudencio M, Singh AP, Rathi B. Novel Antiplasmodial Compounds Leveraged with Multistage Potency against the Parasite Plasmodium falciparum: In Vitro and In Vivo Evaluations and Pharmacokinetic Studies. J Med Chem 2021; 64:8666-8683. [PMID: 34124905 DOI: 10.1021/acs.jmedchem.1c00659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyethylamine (HEA)-based novel compounds were synthesized and their activity against Plasmodium falciparum 3D7 was assessed, identifying a few hits without any apparent toxicity. Hits 5c and 5d also exhibited activity against resistant field strains, PfRKL-9 and PfC580Y. A single dose, 50 mg/Kg, of hits administered to the rodent parasite Plasmodium berghei ANKA exhibited up to 70% reduction in the parasite load. Compound 5d tested in combination with artesunate produced an additional antiparasitic effect with a prolonged survival period. Additionally, compound 5d showed 50% inhibition against hepatic P. berghei infection at 1.56 ± 0.56 μM concentration. This compound also considerably delayed the progression of transmission stages, ookinete and oocyst. Furthermore, the toxicity of 5d assessed in mice supported the normal liver and kidney functions. Altogether, HEA analogues (5a-m), particularly 5d, are nontoxic multistage antiplasmodial agents with therapeutic and transmission-blocking efficacy, along with favorable preliminary pharmacokinetic properties.
Collapse
Affiliation(s)
- Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Mohammad Kashif
- Infectious Diseases Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa 1649-028, Portugal
| | - Budhaditya Mukherjee
- School of Medical Science and Technology, IIT Kharagpur, Kharagpur 721302, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida 201301, Uttar Pradesh, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Miguel Prudencio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa 1649-028, Portugal
| | - Agam P Singh
- Infectious Diseases Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| |
Collapse
|
17
|
Sharma PP, Kumar S, Kaushik K, Singh A, Singh IK, Grishina M, Pandey KC, Singh P, Potemkin V, Poonam, Singh G, Rathi B. In silico validation of novel inhibitors of malarial aspartyl protease, plasmepsin V and antimalarial efficacy prediction. J Biomol Struct Dyn 2021; 40:8352-8364. [PMID: 33870856 DOI: 10.1080/07391102.2021.1911855] [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: 10/21/2022]
Abstract
Plasmepsin V (Plm V) is an essential aspartic protease required for survival of the malaria parasite, Plasmodium falciparum (Pf). Plm V is required for cleaving the PEXEL motifs of many Pf proteins and its inhibition leads to a knockout effect, indicating its suitability as potential drug target. To decipher new inhibitors of PfPlm V, molecular docking of four HIV-1 protease inhibitors active against PfPlmV was performed on Glide module of Schrödinger suite that supported saquinavir as a lead drug, and therefore, selected as a control. Saquinavir contains an important hydroxyethylamine (HEA) pharmacophore, which was utilized as backbone coupled with piperazine scaffold to build new library of compounds. Newly designed HEA compounds were screened virtually against Plm V. Molecular docking led to a few hits (1 and 3) with higher docking score over the control drug. Notably, compound 1 showed the highest docking score (-11.90 kcal/mol) and XP Gscore (-11.948 kcal/mol). The Prime MMGBSA binding free energy for compound 1 (-60.88 kcal/mol) and 3 (-50.96 kcal/mol) was higher than saquinavir (-37.51 kcal/mol). The binding free energy for the last frame of molecular dynamic simulation supported compound 1 (-92.88 kcal/mol) as potent inhibitor of PfPlm V over saquinavir (-72.77 kcal/mol), and thus, deserves experimental validations in culture and subsequently in animal models.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Prem Prakash Sharma
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India.,Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Kumar Kaushik
- Centre for Fire, Explosives & Environment Safety, Fire Chemistry Group, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab., Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Kailash C Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, New Delhi, India
| | | | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Geeta Singh
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India.,Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| |
Collapse
|
18
|
Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
Collapse
Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
| |
Collapse
|
19
|
Alebachew Y, Bisrat D, Tadesse S, Asres K. In vivo anti-malarial activity of the hydroalcoholic extract of rhizomes of Kniphofia foliosa and its constituents. Malar J 2021; 20:3. [PMID: 33386079 PMCID: PMC7777528 DOI: 10.1186/s12936-020-03552-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kniphofia foliosa is a flamboyant robust perennial herb which has dense clumps and tick upright rhizomes with leaves at the base. In Ethiopia, it has several vernacular names including Abelbila, Ashenda, Amelmela, Yeznjero Ageda, Shemetmetie and Yezinjero Ageda. The plant is endemic to Ethiopian highlands, where its rhizomes are traditionally used for the treatment of malaria, abdominal cramps and wound healing. In the present study, the 80% methanol extract of K. foliosa rhizomes and its constituents are tested against Plasmodium berghei in mice. METHODS Isolation was carried out using column and preparative thin layer chromatography (PTLC). The chemical structures of the compounds were elucidated by spectroscopic methods (ESI-MS, 1D and 2D-NMR). Peters' 4-day suppressive test against P. berghei in mice was utilized for in vivo anti-malarial evaluation of the test substances. RESULTS Two compounds, namely knipholone and dianellin were isolated from the 80% methanolic extract of K. foliosa rhizomes, and characterized. The hydroalcoholic extract (400 mg/kg) and knipholone (200 mg/kg) showed the highest activity with chemosuppression values of 61.52 and 60.16%, respectively. From the dose-response plot, the median effective (ED50) doses of knipholone and dianellin were determined to be 81.25 and 92.31 mg/kg, respectively. Molecular docking study revealed that knipholone had a strong binding affinity to Plasmodium falciparum l-lactate dehydrogenase (pfLDH) target. CONCLUSION Results of the current study support the traditional use of the plant for the treatment of malaria.
Collapse
Affiliation(s)
- Yonatan Alebachew
- Department of Pharmaceutical Chemistry and Pharmacognosy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Bisrat
- Department of Pharmaceutical Chemistry and Pharmacognosy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Tadesse
- Department of Pharmaceutical Chemistry and Pharmacognosy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kaleab Asres
- Department of Pharmaceutical Chemistry and Pharmacognosy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
| |
Collapse
|
20
|
Manhas A, Kumar S, Jha PC. Identification of the natural compound inhibitors against Plasmodium falciparum plasmepsin-II via common feature based screening and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:31-43. [PMID: 32794426 DOI: 10.1080/07391102.2020.1806110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Malaria is counted amongst the deadly disease caused by Plasmodium falciparum. Recently, plasmepsin-II enzyme has gained much importance as an attractive drug target for the exploration of antimalarials. Therefore, the common feature pharmacophore models were generated from the crystallized complexes of the plasmepsin-II proteome. These models were subjected to a series of validation procedures, i.e. test set and Güner Henry studies to enlist the representative models. The selected representative hypotheses incorporating the most essential chemical features (common ZHHA) were screened against the natural product database to retrieve the potential candidates. To ensure the selection of the drug-like candidates, prior to screening, filtering steps (Drug-likeness and ADMET filters) were employed on the selected database. To study the interaction pattern of the candidates within the protein, these molecules were advanced to the molecular docking studies. Subsequently, based on the selected cut-off criteria obtained via redocking of the reference (4Z22), 15 compounds showed higher docking score (> -16.05 kcal/mol), and displayed the presence of hydrogen bonding with the crucial amino acids, i.e. Asp34 and Asp214. Further, the stability of the docked molecules was scrutinized via molecular dynamics simulations, and the results were compared with the reference compound 4Z22. All the docked compounds showed stable dynamics behaviour. Thus, in the present contribution, the combination of screening and stability procedures resulted in the identification of 15 hits that can serve as a new chemical space in the designing of the novel antimalarials.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Anu Manhas
- Department of Chemistry, Pandit Deendayal Petroleum University, Gujarat, India.,School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
| | - Sujeet Kumar
- School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
| |
Collapse
|
21
|
Nasamu AS, Polino AJ, Istvan ES, Goldberg DE. Malaria parasite plasmepsins: More than just plain old degradative pepsins. J Biol Chem 2020; 295:8425-8441. [PMID: 32366462 PMCID: PMC7307202 DOI: 10.1074/jbc.rev120.009309] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Plasmepsins are a group of diverse aspartic proteases in the malaria parasite Plasmodium Their functions are strikingly multifaceted, ranging from hemoglobin degradation to secretory organelle protein processing for egress, invasion, and effector export. Some, particularly the digestive vacuole plasmepsins, have been extensively characterized, whereas others, such as the transmission-stage plasmepsins, are minimally understood. Some (e.g. plasmepsin V) have exquisite cleavage sequence specificity; others are fairly promiscuous. Some have canonical pepsin-like aspartic protease features, whereas others have unusual attributes, including the nepenthesin loop of plasmepsin V and a histidine in place of a catalytic aspartate in plasmepsin III. We have learned much about the functioning of these enzymes, but more remains to be discovered about their cellular roles and even their mechanisms of action. Their importance in many key aspects of parasite biology makes them intriguing targets for antimalarial chemotherapy. Further consideration of their characteristics suggests that some are more viable drug targets than others. Indeed, inhibitors of invasion and egress offer hope for a desperately needed new drug to combat this nefarious organism.
Collapse
Affiliation(s)
- Armiyaw S Nasamu
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alexander J Polino
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel E Goldberg
- Division of Infectious Diseases, Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
22
|
Molecular docking and dynamics studies on plasmepsin V of malarial parasite Plasmodium vivax. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|