scholarly journals In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Jelili Oyelade ◽  
Itunuoluwa Isewon ◽  
Efosa Uwoghiren ◽  
Olufemi Aromolaran ◽  
Olufunke Oladipupo
Keyword(s):  
Infectious Disease ◽  
Plasmodium Falciparum ◽  
Metabolic Network ◽  
Antimalarial Drug ◽  
Drug Target ◽  
Drug Targets ◽  
New Drugs ◽  
Biological Evidence ◽  
Essential Reactions ◽  
Extensive List

Malaria is an infectious disease that affects close to half a million individuals every year and Plasmodium falciparum is a major cause of malaria. The treatment of this disease could be done effectively if the essential enzymes of this parasite are specifically targeted. Nevertheless, the development of the parasite in resisting existing drugs now makes discovering new drugs a core responsibility. In this study, a novel computational model that makes the prediction of new and validated antimalarial drug target cheaper, easier, and faster has been developed. We have identified new essential reactions as potential targets for drugs in the metabolic network of the parasite. Among the top seven (7) predicted essential reactions, four (4) have been previously identified in earlier studies with biological evidence and one (1) has been with computational evidence. The results from our study were compared with an extensive list of seventy-seven (77) essential reactions with biological evidence from a previous study. We present a list of thirty-one (31) potential candidates for drug targets in Plasmodium falciparum which includes twenty-four (24) new potential candidates for drug targets.

scholarly journals A specific non-bisphosphonate inhibitor of the bifunctional farnesyl/geranylgeranyl diphosphate synthase in malaria parasites

2017 ◽  
Author(s):  
Jolyn E. Gisselberg ◽  
Zachary Herrera ◽  
Lindsey Orchard ◽  
Manuel Llinás ◽  
Ellen Yeh
Keyword(s):  
Plasmodium Falciparum ◽  
Physicochemical Properties ◽  
Small Molecule ◽  
Antimalarial Drug ◽  
Drug Target ◽  
Drug Targets ◽  
Geranylgeranyl Diphosphate Synthase ◽  
Geranylgeranyl Diphosphate ◽  
Malaria Parasites ◽  
Starting Point

SummaryIsoprenoid biosynthesis is essential for Plasmodium falciparum (malaria) parasites and contains multiple validated antimalarial drug targets, including a bifunctional farnesyl and geranylgeranyl diphosphate synthase (FPPS/GGPPS). We identified MMV019313 as an inhibitor of PfFPPS/GGPPS. Though PfFPPS/GGPPS is also inhibited by a class of bisphosphonate drugs, MMV019313 has significant advantages for antimalarial drug development. MMV019313 has superior physicochemical properties compared to charged bisphosphonates that have poor bioavailability and strong bone affinity. We also show that it is highly selective for PfFPPS/GGPPS and showed no activity against human FPPS or GGPPS. Inhibition of PfFPPS/GGPPS by MMV019313, but not bisphosphonates, was disrupted in an S228T variant, demonstrating that MMV019313 and bisphosphonates have distinct modes-of-inhibition against PfFPPS/GGPPS. Altogether MMV019313 is the first specific, non-bisphosphonate inhibitor of PfFPPS/GGPPS. Our findings uncover a new small molecule binding site in this important antimalarial drug target and provide a promising starting point for development of Plasmodium-specific FPPS/GGPPS inhibitors.

scholarly journals Identification of Plasmodium falciparum Mitochondrial Malate: Quinone Oxidoreductase Inhibitors from the Pathogen Box

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 471 ◽  
Author(s):  
Xinying Wang ◽  
Yukiko Miyazaki ◽  
Daniel Ken Inaoka ◽  
Endah Dwi Hartuti ◽  
Yoh-Ichi Watanabe ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Antimalarial Drug ◽  
Drug Target ◽  
Drug Targets ◽  
Tricarboxylic Acid Cycle ◽  
Drug Resistant ◽  
Quinone Oxidoreductase ◽  
Mitochondrial Inner Membrane ◽  
Transport Chain ◽  
Urgent Task

Malaria is one of the three major global health threats. Drug development for malaria, especially for its most dangerous form caused by Plasmodium falciparum, remains an urgent task due to the emerging drug-resistant parasites. Exploration of novel antimalarial drug targets identified a trifunctional enzyme, malate quinone oxidoreductase (MQO), located in the mitochondrial inner membrane of P. falciparum (PfMQO). PfMQO is involved in the pathways of mitochondrial electron transport chain, tricarboxylic acid cycle, and fumarate cycle. Recent studies have shown that MQO is essential for P. falciparum survival in asexual stage and for the development of experiment cerebral malaria in the murine parasite P. berghei, providing genetic validation of MQO as a drug target. However, chemical validation of MQO, as a target, remains unexplored. In this study, we used active recombinant protein rPfMQO overexpressed in bacterial membrane fractions to screen a total of 400 compounds from the Pathogen Box, released by Medicines for Malaria Venture. The screening identified seven hit compounds targeting rPfMQO with an IC50 of under 5 μM. We tested the activity of hit compounds against the growth of 3D7 wildtype strain of P. falciparum, among which four compounds showed an IC50 from low to sub-micromolar concentrations, suggesting that PfMQO is indeed a potential antimalarial drug target.

Antimalarial Drug Targets and Drugs Targeting Dolichol Metabolic Pathway of Plasmodium falciparum

2014 ◽  
Vol 15 (4) ◽  
pp. 374-409 ◽  
Author(s):  
Tabish Qidwai ◽  
Avantika Priya ◽  
Nihal Khan ◽  
Himanshu Tripathi ◽  
Feroz Khan ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Metabolic Pathway ◽  
Antimalarial Drug ◽  
Drug Targets

scholarly journals A Chemical Rescue Screen Identifies a Plasmodium falciparum Apicoplast Inhibitor Targeting MEP Isoprenoid Precursor Biosynthesis

2014 ◽  
Vol 59 (1) ◽  
pp. 356-364 ◽  
Author(s):  
Wesley Wu ◽  
Zachary Herrera ◽  
Danny Ebert ◽  
Katie Baska ◽  
Seok H. Cho ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Antimalarial Drug ◽  
Drug Targets ◽  
Specific Activity ◽  
Drug Candidate ◽  
Content Type ◽  
Chemical Rescue ◽  
Growth Inhibitory ◽  
Parasite Populations

ABSTRACTThe apicoplast is an essential plastid organelle found inPlasmodiumparasites which contains several clinically validated antimalarial-drug targets. A chemical rescue screen identified MMV-08138 from the “Malaria Box” library of growth-inhibitory antimalarial compounds as having specific activity against the apicoplast. MMV-08138 inhibition of blood-stagePlasmodium falciparumgrowth is stereospecific and potent, with the most active diastereomer demonstrating a 50% effective concentration (EC50) of 110 nM. Whole-genome sequencing of 3 drug-resistant parasite populations from two independent selections revealed E688Q and L244I mutations inP. falciparumIspD, an enzyme in the MEP (methyl-d-erythritol-4-phosphate) isoprenoid precursor biosynthesis pathway in the apicoplast. The active diastereomer of MMV-08138 directly inhibited PfIspD activityin vitrowith a 50% inhibitory concentration (IC50) of 7.0 nM. MMV-08138 is the first PfIspD inhibitor to be identified and, together with heterologously expressed PfIspD, provides the foundation for further development of this promising antimalarial drug candidate lead. Furthermore, this report validates the use of the apicoplast chemical rescue screen coupled with target elucidation as a discovery tool to identify specific apicoplast-targeting compounds with new mechanisms of action.

scholarly journals Computational Identification of Metabolic Pathways ofPlasmodium falciparumusing thek-Shortest Path Algorithm

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Jelili Oyelade ◽  
Itunuoluwa Isewon ◽  
Olufemi Aromolaran ◽  
Efosa Uwoghiren ◽  
Titilope Dokunmu ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Shortest Path ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Poor Response ◽  
Metabolic Model ◽  
Pentose Phosphate ◽  
Shortest Path Algorithm ◽  
Alternative Pathways ◽  
Essential Reactions

Plasmodium falciparum, a malaria pathogen, has shown substantial resistance to treatment coupled with poor response to some vaccines thereby requiring urgent, holistic, and broad approach to prevent this endemic disease. Understanding the biology of the malaria parasite has been identified as a vital approach to overcome the threat of malaria. This study is aimed at identifying essential proteins unique to malaria parasites using a reconstructediPfagenome-scale metabolic model (GEM) of the 3D7 strain ofPlasmodium falciparumby filling gaps in the model with nineteen (19) metabolites and twenty-three (23) reactions obtained from the MetaCyc database. Twenty (20) currency metabolites were removed from the network because they have been identified to produce shortcuts that are biologically infeasible. The resulting modifiediPfaGEM was a model using thek-shortest path algorithm to identify possible alternative metabolic pathways in glycolysis and pentose phosphate pathways ofPlasmodium falciparum. Heuristic function was introduced for the optimal performance of the algorithm. To validate the prediction, the essentiality of the reactions in the reconstructed network was evaluated using betweenness centrality measure, which was applied to every reaction within the pathways considered in this study. Thirty-two (32) essential reactions were predicted among which our method validated fourteen (14) enzymes already predicted in the literature. The enzymatic proteins that catalyze these essential reactions were checked for homology with the host genome, and two (2) showed insignificant similarity, making them possible drug targets. In conclusion, the application of the intelligent search technique to the metabolic network ofP. falciparumpredicts potential biologically relevant alternative pathways using graph theory-based approach.

scholarly journals The Effect of Aqueous Extract of Cinnamon on the Metabolome ofPlasmodium falciparumUsing1HNMR Spectroscopy

2016 ◽  
Vol 2016 ◽  
pp. 1-5 ◽  
Author(s):  
Shirin Parvazi ◽  
Sedigheh Sadeghi ◽  
Mehri Azadi ◽  
Maryam Mohammadi ◽  
Mohammad Arjmand ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Aqueous Extract ◽  
Drug Targets ◽  
Inhibitory Concentration ◽  
Biological Fluids ◽  
Medicinal Herbs ◽  
New Drugs ◽  
Lysine Biosynthesis ◽  
Glutathione Metabolism

Malaria is responsible for estimated 584,000 deaths in 2013. Researchers are working on new drugs and medicinal herbs due to drug resistance that is a major problem facing them; the search is on for new medicinal herbs. Cinnamon is the bark of a tree with reported antiparasitic effects. Metabonomics is the simultaneous study of all the metabolites in biological fluids, cells, and tissues detected by high throughput technology. It was decided to determine the mechanism of the effect of aqueous extract of cinnamon on the metabolome ofPlasmodium falciparum in vitrousing1HNMR spectroscopy. Prepared aqueous extract of cinnamon was added to a culture ofPlasmodium falciparum3D7 and its 50% inhibitory concentration determined, and, after collection, their metabolites were extracted and1HNMR spectroscopy by NOESY method was done. The spectra were analyzed by chemometric methods. The differentiating metabolites were identified using Human Metabolome Database and the metabolic cycles identified by Metaboanalyst. 50% inhibitory concentration of cinnamon onPlasmodium falciparumwas 1.25 mg/mL withp<0.001. The metabolites were identified as succinic acid, glutathione, L-aspartic acid, beta-alanine, and 2-methylbutyryl glycine. The main metabolic cycles detected were alanine and aspartame and glutamate pathway and pantothenate and coenzyme A biosynthesis and lysine biosynthesis and glutathione metabolism, which are all important as drug targets.

scholarly journals Assessment of biological role and insight into druggability of the Plasmodium falciparum protease plasmepsin V

2018 ◽  
Author(s):  
Alexander J. Polino ◽  
S. Nasamu Armiyaw ◽  
Jacquin C. Niles ◽  
Daniel E. Goldberg
Keyword(s):  
Plasmodium Falciparum ◽  
Host Cell ◽  
Drug Targets ◽  
Parasite Growth ◽  
Aspartic Protease ◽  
Protein Export ◽  
New Drugs ◽  
Functional Studies ◽  
Parasite Survival ◽  
Post Transcriptional Regulation

AbstractUpon infection of a red blood cell (RBC), the malaria parasite Plasmodium falciparum drastically remodels its host by exporting hundreds of proteins into the RBC cytosol. This program of protein export is essential for parasite survival, hence there is interest in export-related proteins as potential drug targets. One proposed target is plasmepsin V (PMV), an aspartic protease that cleaves export-destined proteins in the parasite ER at a motif called the Plasmodium export element (PEXEL). This cleavage is essential for effector export across the vacuolar membrane. Despite long-standing interest in PMV, functional studies have been hindered by the failure of current technologies to produce a regulatable lethal depletion of PMV. To overcome this technical barrier, we designed a facile system for stringent post-transcriptional regulation, allowing a tightly controlled, tunable knockdown of PMV. Under maximal knockdown conditions, parasite growth was arrested, validating PMV as essential for parasite survival in RBCs. We found that PMV levels had to be dramatically depleted to affect parasite growth, suggesting that the parasite maintains this enzyme in substantial excess. This has important implications for antimalarial development. Additionally, we found that PMV-depleted parasites arrest immediately after invasion of the host cell, suggesting that PMV has an unappreciated role in early development that is distinct from its previously reported role in protein export in later-stage parasites.ImportanceMalaria is endemic to large swaths of the developing world, causing nearly 500,000 deaths each year. While infection can be treated with antimalarial drugs, resistance continues to emerge to frontline antimalarials, spurring calls for new drugs and targets to feed the drug development pipeline. One proposed target is the aspartic protease plasmepsin V (PMV) that processes exported proteins, enabling the export program that remodels the host cell. This work uses facile genetic tools to produce lethal depletion of PMV, validating it as a drug target and showing that PMV is made in substantial excess in blood-stage parasites. Unexpectedly, PMV depletion leads to parasite death immediately after invasion of RBCs, distinct from other disruptions of the export pathway. This suggests that PMV inhibitors could lead to relatively rapid parasite death, and that PMV has additional unexplored role(s) during RBC infection.

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