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Predictive modeling of anti-malarial molecules inhibiting apicoplast formation

Salma Jamal, Vinita Periwal, Vinod Scaria
2013 BMC Bioinformatics  
Results: In the present study, we have used high-throughput screen datasets for the discovery of apicoplast inhibitors of the malarial pathogen as assayed from the delayed death response.  ...  We employed machine learning approach and developed computational predictive models to predict the biological activity of new antimalarial compounds.  ...  This work was funded by the Council of Scientific and Industrial Research (CSIR), India for funding through the Open Source Drug Discovery Project (HCP001).  ... 
doi:10.1186/1471-2105-14-55 pmid:23419172 pmcid:PMC3599641 fatcat:xvehkyac75a65ehyzauqf6mdmu

Recent advances in the biology and drug targeting of malaria parasite aminoacyl-tRNA synthetases

Sameena Khan
2016 Malaria Journal  
Escalating drug resistance in malaria parasites and lack of vaccine entails the discovery of novel drug targets and inhibitor molecules.  ...  Malaria parasites contain three translational compartments: the cytoplasm, apicoplast and mitochondrion, of which the latter two are of the prokaryotic type.  ...  Reported anti-malarials that target aaRSs are listed in Table 2 and key targets and their inhibition are discussed below.  ... 
doi:10.1186/s12936-016-1247-0 pmid:27068331 pmcid:PMC4828885 fatcat:iqtoj6idvjaa3lqash6ar7v2gu

Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase [article]

Supreet Kaur, Nicholas Nieto, Peter McDonald, Josh R. Beck, Richard B. Honzatko, Anuradha Roy, Scott W Nelson
2022 bioRxiv   pre-print
The apicoplast genome is replicated by a single DNA polymerase (apPOL), which is an attractive target for anti-malarial drugs.  ...  We screened small-molecule libraries (206,504 compounds) using a fluorescence-based high-throughput DNA polymerase assay.  ...  J Chem Inf Model. 2015 Feb 23;55(2):460-73. mechanisms of DNA polymerase inhibition or as lead compounds for further optimization into anti-malaria drugs.  ... 
doi:10.1101/2022.03.04.482688 fatcat:w3kpc2rf5zexxe6ebv46bheqgm

QSAR based predictive modeling for anti-malarial molecules

Deepak R. Bharti, Andrew M. Lynn
2017 Bioinformation  
Keywords: Malaria, apicoplast, predictive model building, R statistical package Background: Malaria is endemic in many tropical and subtropical regions causing high mortality and morbidity.  ...  In the present work, we describe a standard protocol to develop molecular descriptor based predictive models (QSAR models), which can be further utilized for the screening of large chemical libraries.  ...  The workflow is applied in the predictive model building of biologically active inhibitor molecules against apicoplast formation.  ... 
doi:10.6026/97320630013154 pmid:28690382 pmcid:PMC5498782 fatcat:5a5mq6bxu5gwfbs6aahhhht22y

The apicoplast as an antimalarial drug target

Stuart A. Ralph, Marthe C. D'Ombrain, Geoffrey I. McFadden
2001 Drug resistance updates  
The apicoplast contains a range of metabolic pathways and housekeeping processes that differ radically to those of the host thereby presenting ideal strategies for drug therapy.  ...  The recent identification of a relict chloroplast (apicoplast) in malaria and related parasites offers numerous new targets for drug therapy using well-characterized compounds.  ...  Various derivatives of quinolones and fluoroquinolones have been tested for their ability to inhibit apicoplast DNA replication and models for their mode of action proposed. 6 These findings validate  ... 
doi:10.1054/drup.2001.0205 pmid:11768328 fatcat:6uudlwirazgzthonmrv435mao4

Targeting apicoplasts in malaria parasites

Christopher D Goodman, Geoffrey I McFadden
2012 Expert opinion on therapeutic targets  
the study of anti-malarials targeting the apicoplast.  ...  anti-malarials.  ... 
doi:10.1517/14728222.2013.739158 pmid:23231425 fatcat:y6jgr2thubc2voeq5h5rujglxi

A supervised classifier based chemoinformatics model to predict inhibitors essential for sexual reproduction and transmission of the P. falciparum parasite into mosquitoes

Asif Hassan Syed, Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah, Saudi Arabia, Tabrej Khan, Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah, Saudi Arabia
2019 International Journal of Advanced and Applied Sciences  
The availability of Highthroughput Screening (HTS) anti-malarial bioassay dataset has provided an opportunity to build ML-based chemoinformatics, predictive models, using features extracted from different  ...  The J48 classifier based predictive model was found to accurately predict active anti-PfCDPK4 molecule based on better Accuracy, Recall, Precision, and Area under the Curve (AUC) values.  ...  Compliance with ethical standards Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.21833/ijaas.2019.10.011 fatcat:umv6qbsntfdmlefh2wjsllguc4

Plasmodial sugar transporters as anti-malarial drug targets and comparisons with other protozoa

Ksenija Slavic, Sanjeev Krishna, Elvira T Derbyshire, Henry M Staines
2011 Malaria Journal  
Inhibition of cellular glucose uptake (the first step in its utilization) has, therefore, received attention as a potential therapeutic strategy to treat various unrelated diseases including malaria and  ...  Plasmodium falciparum is the most dangerous human malarial parasite and its hexose transporter has been identified as being the major glucose transporter.  ...  Thus, inhibition of hexose transport may present an attractive approach in the development of other new anti-parasitic drugs, in addition to the discovery of novel anti-malarials.  ... 
doi:10.1186/1475-2875-10-165 pmid:21676209 pmcid:PMC3135577 fatcat:scdlvwexsfbzvcrk4nelwmu3wu

A Systematic In Silico Search for Target Similarity Identifies Several Approved Drugs with Potential Activity against the Plasmodium falciparum Apicoplast

Nadlla Alves Bispo, Richard Culleton, Lourival Almeida Silva, Pedro Cravo, Fabio T. M. Costa
2013 PLoS ONE  
Here, we focus on the apicoplast, a malarial plastid-like organelle of algal source which evolved through secondary endosymbiosis.  ...  We were able to identify several drugs that are expected to interact with forty-seven (47) peptides predicted to be involved in the biology of the P. falciparum apicoplast.  ...  Acknowledgments The authors wish to thank Professor José Clecildo Barreto Bezerra for his encouragements throughout the course of this work. Author Contributions  ... 
doi:10.1371/journal.pone.0059288 pmid:23555651 pmcid:PMC3608639 fatcat:6z3fdtgqrbgnjo5xb2hbfuclie

DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum

E. V. S. R. Ram, R. Naik, M. Ganguli, S. Habib
2008 Nucleic Acids Research  
In contrast to bacterial HUs that bend DNA, PfHU promotes concatenation of linear DNA and inhibits DNA circularization.  ...  Atomic Force Microscopic study of PfHU-DNA complexes shows protein concentration-dependent DNA stiffening, intermolecular bundling and formation of DNA bridges followed by assembly of condensed DNA networks  ...  E.V.S.R.R. and R.N. are recipients of research fellowships from the Council of Scientific and Industrial Research and Department of Biotechnology, respectively. This is CDRI communication no. 7456.  ... 
doi:10.1093/nar/gkn483 pmid:18663012 pmcid:PMC2528193 fatcat:ppq3fscaknf47guypum4xdttui

Plasmodium falciparum: multifaceted resistance to artemisinins

Lucie Paloque, Arba P. Ramadani, Odile Mercereau-Puijalon, Jean-Michel Augereau, Françoise Benoit-Vical
2016 Malaria Journal  
Plasmodium falciparum resistance to artemisinins, the most potent and fastest acting anti-malarials, threatens malaria elimination strategies.  ...  response, the PI3K/PI3P/AKT pathway, the PfPK4/eIF2α cascade and yet unidentified transcription factor(s), with minimal energetic requirements and fatty acid metabolism maintained in the mitochondrion and apicoplast  ...  supported in part by the French Agence Nationale de la Recherche (Grant ANR-13-BSV3-0018-01) and by the French Government programme Investissement d' Avenir, Laboratoire d'Excellence "Integrative Biology of  ... 
doi:10.1186/s12936-016-1206-9 pmid:26955948 pmcid:PMC4784301 fatcat:jlnqc2eqx5fpdpotftlhbegmmu

The Clp Chaperones and Proteases of the Human Malaria Parasite Plasmodium falciparum

Majida El Bakkouri, Andre Pow, Anne Mulichak, Kevin L.Y. Cheung, Jennifer D. Artz, Mehrnaz Amani, Stuart Fell, Tania F. de Koning-Ward, C. Dean Goodman, Geoffrey I. McFadden, Joaquin Ortega, Raymond Hui (+1 others)
2010 Journal of Molecular Biology  
Our data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.  ...  The proteins were localized to the apicoplast, a non-photosynthetic organelle that accommodates several important metabolic pathways in P. falciparum, with the exception of PfClpB2 (also known as Hsp101  ...  Hence, targeting the activity of this complex might be a promising approach for the development of anti-malarial drugs as was recently suggested. 3 3 Dysregulation 3 4 or selective inhibition 35 of  ... 
doi:10.1016/j.jmb.2010.09.051 pmid:20887733 fatcat:p2yxxunzgvctpkxujey4dqg5i4

Selected Derivatives of Erythromycin B-In Silico and Anti-Malarial Studies

Pranab K. Bhadra, Rachael N. Magwaza, Niroshini Nirmalan, Sally Freeman, Jill Barber, Biljana Arsic
2021 Materials  
segment from the exit tunnel from the apicoplast of P. falciparum is the reason for their weak in vitro anti-malarial activities.  ...  These compounds were investigated for their anti-malarial activities, by their in silico molecular docking into segments of the exit tunnel of the apicoplast ribosome from Plasmodium falciparum.  ...  Molecular docking can also be a good tool for the prediction of anti-malarial activity of derivatives with previously undetermined anti-malarial activity.  ... 
doi:10.3390/ma14226980 pmid:34832380 pmcid:PMC8618316 fatcat:j4qbeahuqbhv3manejfhmyf5pi

The primase domain of PfPrex is a proteolytically matured, essential enzyme of the apicoplast

Scott E. Lindner, Manuel Llinás, James L. Keck, Stefan H.I. Kappe
2011 Molecular and biochemical parasitology (Print)  
Taken together, these observations strongly suggest an essential role of PfPrex primase in the production of RNA primers for lagging strand DNA synthesis of the apicoplast genome.  ...  Finally, overexpression in P. falciparum of PfPrex's trafficking and primase sequences yielded specific and dynamic localization to foci within the apicoplast.  ...  McFadden for providing the anti-PfACP antibody, and J. Berger for purified recombinant EcDnaG. We also thank the Keck and Kappe labs for critical discussion of this work.  ... 
doi:10.1016/j.molbiopara.2011.08.002 pmid:21856338 pmcid:PMC3196721 fatcat:xpy35kcjmjeshhmey22ctumc7e

Homology Modeling And Docking Study Of Shewanella Like Protein Phosphatase Involved In Development Of Ookinetes In Plasmodium [article]

Sandhini Singh, Ruchi Yadav
2018 bioRxiv   pre-print
SHLP deletion results in a reduction in microneme formation, ookinetes (zygote) development and complete ablation of oocyst formation, thereby blocking transmission of parasite.  ...  Structure Modeling of SHLP protein can be helpful in understanding the active site and binding site information and hence can be used for drug designing for therapeutics against malaria.  ...  An antioxidant is a molecule that inhibits the oxidation of other molecules [19] .  ... 
doi:10.1101/297770 fatcat:srw2gdyivjgqnbiryxyj3wmqwa
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