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Chheda PR, Nieto N, Kaur S, Beck JM, Beck JR, Honzatko R, Kerns RJ, Nelson SW. Promising antimalarials targeting apicoplast DNA polymerase from Plasmodium falciparum. Eur J Med Chem 2022; 243:114751. [DOI: 10.1016/j.ejmech.2022.114751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/22/2022] [Accepted: 09/04/2022] [Indexed: 11/25/2022]
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Kumari A, Yadav A, Lahiri I. Transient State Kinetics of Plasmodium falciparum Apicoplast DNA Polymerase Suggests the Involvement of Accessory Factors for Efficient and Accurate DNA Synthesis. Biochemistry 2022; 61:2319-2333. [PMID: 36251801 DOI: 10.1021/acs.biochem.2c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium, the causative agent of malaria, belongs to the phylum Apicomplexa. Most apicomplexans, including Plasmodium, contain an essential nonphotosynthetic plastid called the apicoplast that harbors its own genome that is replicated by a dedicated organellar replisome. This replisome employs a single DNA polymerase (apPol), which is expected to perform both replicative and translesion synthesis. Unlike other replicative polymerases, no processivity factor for apPol has been identified. While preliminary structural and biochemical studies have provided an overall characterization of apPol, the kinetic mechanism of apPol's activity remains unknown. We have used transient state methods to determine the kinetics of replicative and translesion synthesis by apPol and show that apPol has low processivity and efficiency while copying undamaged DNA. Moreover, while apPol can bypass oxidatively damaged lesions, the bypass is error-prone. Taken together, our results raise the following question─how does a polymerase with low processivity, efficiency, and fidelity (for translesion synthesis) faithfully replicate the apicoplast organellar DNA within the hostile environment of the human host? We hypothesize that interactions with putative components of the apicoplast replisome and/or an as-yet-undiscovered processivity factor transform apPol into an efficient and accurate enzyme.
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Affiliation(s)
- Anamika Kumari
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Anjali Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India.,Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
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Sharma M, Nair DT. Pfprex from
Plasmodium falciparum
can bypass oxidative stress‐induced DNA lesions. FEBS J 2022; 289:5218-5240. [DOI: 10.1111/febs.16414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/13/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Minakshi Sharma
- Regional Centre for Biotechnology Faridabad India
- Kalinga Institute of Industrial Technology Bhubaneshwar India
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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.
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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
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Kaur S, Nieto NS, McDonald P, Beck JR, Honzatko RB, Roy A, Nelson SW. Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase. J Enzyme Inhib Med Chem 2022; 37:1320-1326. [PMID: 35514163 PMCID: PMC9090415 DOI: 10.1080/14756366.2022.2070909] [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] [Indexed: 11/01/2022] Open
Abstract
Malaria is caused by infection with protozoan parasites of the Plasmodium genus, which is part of the phylum Apicomplexa. Most organisms in this phylum contain a relic plastid called the apicoplast. 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. Dose/response analysis and counter-screening identified 186 specific apPOL inhibitors. Toxicity screening against human HepaRG human cells removed 84 compounds and the remaining were subjected to parasite killing assays using chloroquine resistant P. falciparum parasites. Nine compounds were potent inhibitors of parasite growth and may serve as lead compounds in efforts to discover novel malaria drugs.
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Affiliation(s)
- Supreet Kaur
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Nicholas S Nieto
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Peter McDonald
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, USA
| | - Josh R Beck
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Richard B Honzatko
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, USA
| | - Scott W Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
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Nasiri AH, Nasiri HR. Polymerase assays for lead discovery: An overall review of methodologies and approaches. Anal Biochem 2018; 563:40-50. [PMID: 30291837 DOI: 10.1016/j.ab.2018.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/26/2018] [Accepted: 09/30/2018] [Indexed: 12/18/2022]
Abstract
Polymerases represent an attractive molecular target for antibacterial drug development, antiviral intervention and cancer therapy. Over the past decade, academic groups and scientists from pharmaceutical industry have developed a large plethora of different functional assays to monitor the enzymatic reaction catalyzed by polymerases. These assays were used to enable high-throughput screening (HTS) for lead discovery purposes, as well as hit-to-lead (H2L) drug profiling activities. In both cases the choice of the assay technology is critical and to the best of our knowledge, there is no review available to help scientists to choose the most suitable assay. This review summarizes the most common functional assays developed to monitor the enzymatic activity of polymerases and discusses the advantages and disadvantages of each assay. Assays are presented and evaluated in term of cost, ease of use, high-throughput screening compatibility and liability towards delivering false positives and false negatives.
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Affiliation(s)
- Amir H Nasiri
- Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, D-60438, Frankfurt am Main, Germany; CARD Center of Aptamer Research and Development, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Hamid R Nasiri
- Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, D-60438, Frankfurt am Main, Germany; Sysmex-inostics GmbH, Falkenried 88, CiM centrum für innovative medizin Haus A, 20251, Hamburg, Germany.
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Validation of Putative Apicoplast-Targeting Drugs Using a Chemical Supplementation Assay in Cultured Human Malaria Parasites. Antimicrob Agents Chemother 2017; 62:AAC.01161-17. [PMID: 29109165 DOI: 10.1128/aac.01161-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/18/2017] [Indexed: 11/20/2022] Open
Abstract
Malaria parasites contain a relict plastid, the apicoplast, which is considered an excellent drug target due to its bacterial-like ancestry. Numerous parasiticidals have been proposed to target the apicoplast, but few have had their actual targets substantiated. Isopentenyl pyrophosphate (IPP) production is the sole required function of the apicoplast in the blood stage of the parasite life cycle, and IPP supplementation rescues parasites from apicoplast-perturbing drugs. Hence, any drug that kills parasites when IPP is supplied in culture must have a nonapicoplast target. Here, we use IPP supplementation to discriminate whether 23 purported apicoplast-targeting drugs are on- or off-target. We demonstrate that a prokaryotic DNA replication inhibitor (ciprofloxacin), several prokaryotic translation inhibitors (chloramphenicol, doxycycline, tetracycline, clindamycin, azithromycin, erythromycin, and clarithromycin), a tRNA synthase inhibitor (mupirocin), and two IPP synthesis pathway inhibitors (fosmidomycin and FR900098) have apicoplast targets. Intriguingly, fosmidomycin and FR900098 leave the apicoplast intact, whereas the others eventually result in apicoplast loss. Actinonin, an inhibitor of bacterial posttranslational modification, does not produce a typical delayed-death response but is rescued with IPP, thereby confirming its apicoplast target. Parasites treated with putative apicoplast fatty acid pathway inhibitors could not be rescued, demonstrating that these drugs have their primary targets outside the apicoplast, which agrees with the dispensability of the apicoplast fatty acid synthesis pathways in the blood stage of malaria parasites. IPP supplementation provides a simple test of whether a compound has a target in the apicoplast and can be used to screen novel compounds for mode of action.
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Milton ME, Choe JY, Honzatko RB, Nelson SW. Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase. J Mol Biol 2016; 428:3920-3934. [PMID: 27487482 DOI: 10.1016/j.jmb.2016.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/18/2022]
Abstract
Plasmodium falciparum, the primary cause of malaria, contains a non-photosynthetic plastid called the apicoplast. The apicoplast exists in most members of the phylum Apicomplexa and has its own genome along with organelle-specific enzymes for its replication. The only DNA polymerase found in the apicoplast (apPOL) was putatively acquired through horizontal gene transfer from a bacteriophage and is classified as an atypical A-family polymerase. Here, we present its crystal structure at a resolution of 2.9Å. P. falciparum apPOL, the first structural representative of a plastidic A-family polymerase, diverges from typical A-family members in two of three previously identified signature motifs and in a region not implicated by sequence. Moreover, apPOL has an additional N-terminal subdomain, the absence of which severely diminishes its 3' to 5' exonuclease activity. A compound known to be toxic to Plasmodium is a potent inhibitor of apPOL, suggesting that apPOL is a viable drug target. The structure provides new insights into the structural diversity of A-family polymerases and may facilitate structurally guided antimalarial drug design.
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Affiliation(s)
- Morgan E Milton
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jun-Yong Choe
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Richard B Honzatko
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Scott W Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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Milton ME, Nelson SW. Replication and maintenance of the Plasmodium falciparum apicoplast genome. Mol Biochem Parasitol 2016; 208:56-64. [PMID: 27338018 DOI: 10.1016/j.molbiopara.2016.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/14/2016] [Accepted: 06/19/2016] [Indexed: 12/18/2022]
Abstract
Members of the phylum Apicomplexa are responsible for many devastating diseases including malaria (Plasmodium spp.), toxoplasmosis (Toxoplasma gondii), babesiosis (Babesia bovis), and cyclosporiasis (Cyclospora cayetanensis). Most Apicomplexans contain a unique and essential organelle called the apicoplast. Derived from an ancient chloroplast, the apicoplast replicates and maintains a 35 kilobase (kb) circular genome. Due to its essential nature within the parasite, drugs targeted to proteins involved in DNA replication and repair of the apicoplast should be potent and specific. This review summarizes the current knowledge surrounding the replication and repair of the Plasmodium falciparum apicoplast genome and identifies several putative proteins involved in replication and repair pathways.
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Affiliation(s)
- Morgan E Milton
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames IA 50011, USA
| | - Scott W Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames IA 50011, USA.
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Milton ME, Choe JY, Honzatko RB, Nelson SW. Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase. Acta Crystallogr F Struct Biol Commun 2015; 71:333-7. [PMID: 25760711 PMCID: PMC4356312 DOI: 10.1107/s2053230x15002423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/04/2015] [Indexed: 11/11/2022] Open
Abstract
Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals of P. falciparum apPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space group P6522 (unit-cell parameters a = b = 141.8, c = 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress.
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Affiliation(s)
- Morgan E. Milton
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, IA 50011, USA
| | - Jun-yong Choe
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, IL 60064, USA
| | - Richard B. Honzatko
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, IA 50011, USA
| | - Scott W. Nelson
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, IA 50011, USA
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