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Borba JVVB, Silva ADCE, do Nascimento MN, Ferreira LT, Rimoldi A, Starling L, Ramos PIP, Costa FTM, Andrade CH. Update and elucidation of Plasmodium kinomes: Prioritization of kinases as potential drug targets for malaria. Comput Struct Biotechnol J 2022; 20:3708-3717. [PMID: 35891792 PMCID: PMC9293725 DOI: 10.1016/j.csbj.2022.07.003] [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: 04/23/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 12/05/2022] Open
Abstract
Malaria is a tropical disease caused by Plasmodium spp. and transmitted by the bite of infected Anopheles mosquitoes. Protein kinases (PKs) play key roles in the life cycle of the etiological agent of malaria, turning these proteins attractive targets for antimalarial drug discovery campaigns. As part of an effort to understand parasite signaling functions, we report the results of a bioinformatics pipeline analysis of PKs of eight Plasmodium species. To date, no P. malariae and P. ovale kinome assemble has been conducted. We classified, curated and annotated predicted kinases to update P. falciparum, P. vivax, P. yoelii, P. berghei, P. chabaudi, and P. knowlesi kinomes published to date, as well as report for the first time the kinomes of P. malariae and P. ovale. Overall, from 76 to 97 PKs were identified among all Plasmodium spp. kinomes. Most of the kinases were assigned to seven of nine major kinase groups: AGC, CAMK, CMGC, CK1, STE, TKL, OTHER; and the Plasmodium-specific group FIKK. About 30% of kinases have been deeply classified into group, family and subfamily levels and only about 10% remained unclassified. Furthermore, updating and comparing the kinomes of P. vivax and P. falciparum allowed for the prioritization and selection of kinases as potential drug targets that could be explored for discovering new drugs against malaria. This integrated approach resulted in the selection of 37 protein kinases as potential targets and the identification of investigational compounds with moderate in vitro activity against asexual P. falciparum (3D7 and Dd2 strains) stages that could serve as starting points for the search of potent antimalarial leads in the future.
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Affiliation(s)
- Joyce Villa Verde Bastos Borba
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Arthur de Carvalho E Silva
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Marília Nunes do Nascimento
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Letícia Tiburcio Ferreira
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Aline Rimoldi
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Luísa Starling
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | | | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Lima MNN, Cassiano GC, Tomaz KCP, Silva AC, Sousa BKP, Ferreira LT, Tavella TA, Calit J, Bargieri DY, Neves BJ, Costa FTM, Andrade CH. Integrative Multi-Kinase Approach for the Identification of Potent Antiplasmodial Hits. Front Chem 2019; 7:773. [PMID: 31824917 PMCID: PMC6881481 DOI: 10.3389/fchem.2019.00773] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/25/2019] [Indexed: 11/22/2022] Open
Abstract
Malaria is a tropical infectious disease that affects over 219 million people worldwide. Due to the constant emergence of parasitic resistance to the current antimalarial drugs, the discovery of new antimalarial drugs is a global health priority. Multi-target drug discovery is a promising and innovative strategy for drug discovery and it is currently regarded as one of the best strategies to face drug resistance. Aiming to identify new multi-target antimalarial drug candidates, we developed an integrative computational approach to select multi-kinase inhibitors for Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1 and CDPK4) and protein kinase 6 (PK6). For this purpose, we developed and validated shape-based and machine learning models to prioritize compounds for experimental evaluation. Then, we applied the best models for virtual screening of a large commercial database of drug-like molecules. Ten computational hits were experimentally evaluated against asexual blood stages of both sensitive and multi-drug resistant P. falciparum strains. Among them, LabMol-171, LabMol-172, and LabMol-181 showed potent antiplasmodial activity at nanomolar concentrations (EC50 ≤ 700 nM) and selectivity indices >15 folds. In addition, LabMol-171 and LabMol-181 showed good in vitro inhibition of P. berghei ookinete formation and therefore represent promising transmission-blocking scaffolds. Finally, docking studies with protein kinases CDPK1, CDPK4, and PK6 showed structural insights for further hit-to-lead optimization studies.
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Affiliation(s)
- Marilia N N Lima
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Gustavo C Cassiano
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Kaira C P Tomaz
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Arthur C Silva
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Bruna K P Sousa
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Leticia T Ferreira
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Tatyana A Tavella
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Y Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bruno J Neves
- Laboratory of Cheminformatics, University Center of Anápolis/UniEVANGELICA, Anápolis, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Carolina Horta Andrade
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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Pedro L, Cross M, Hofmann A, Mak T, Quinn RJ. Development of an HPLC-based guanosine monophosphate kinase assay and application to Plasmodium vivax guanylate kinase. Anal Biochem 2019; 575:63-69. [PMID: 30943378 PMCID: PMC6494078 DOI: 10.1016/j.ab.2019.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/18/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
The development of a high-performance liquid chromatography (HPLC)-based method, for guanosine monophosphate kinase activity assays, is presented. The method uses the intrinsic UV absorption (at 260 nm) of substrates and products of the enzymatic reaction (GMP, ATP, ADP and GDP) to unambiguously determine percent conversion of substrate into product. It uses a commercially available C18 column which can separate reaction samples by elution under isocratic conditions in 12 min per run. The kinetics of the forward reaction catalyzed by Plasmodium vivax guanylate kinase (PvGK), a potential drug target against malaria, was determined. The relative concentrations of the two substrates (GMP and ATP) have a distinct effect on reaction velocity. Kinetic analyses showed the PvGK-catalyzed reaction to be associated with atypical kinetics, where substrate inhibition kinetics and non-Michaelis-Menten (sigmoidal) kinetics were found with respect to GMP and ATP, respectively. Additionally, the method was used in inhibition assays to screen twenty fragment-like compounds. The assays were robust and reproducible, with a signal window of 3.8 and a Z’ factor of 0.6. For the best inhibitor, an IC50 curve was generated. Simple HPLC separation of nucleotides involved in the guanylate kinase reaction. Direct and unambiguous determination of percent conversion of substrate into product. Successful application to Plasmodium vivax guanylate kinase (PvGK) activity studies. Reaction catalyzed by PvGK found to be associated with atypical kinetics. Robust and reproducible inhibition assay for compound screening.
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Affiliation(s)
- Liliana Pedro
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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Ahmad M, Tarique M, Afrin F, Tuteja N, Tuteja R. Identification of inhibitors of Plasmodium falciparum RuvB1 helicase using biochemical assays. PROTOPLASMA 2015; 252:117-125. [PMID: 24934654 DOI: 10.1007/s00709-014-0664-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/06/2014] [Indexed: 06/03/2023]
Abstract
Human malaria is a major parasitic infection, and the situation has worsened mainly due to the emergence of resistant malaria parasites to several anti-malarial drugs. Thus, an urgent need to find suitable drug targets has led to the development of newer classes of anti-malarial drugs. Helicases have been targeted to develop therapeutics for viral, bacterial, and other microorganism infections. Recently, Plasmodium falciparum RuvB ATPases/helicases have been characterized and proposed as a suitable antimalarial drug target. In the present study, the screening of various compounds was done and the results suggest that PfRuvB1 ATPase activity is inhibited considerably by the novobiocin and partially by cisplatin and ciprofloxacin. Helicase assay of PfRuvB1 in the presence of various compounds suggest novobiocin, actinomycin, and ethidium bromide as potent inhibitors. Novobiocin inhibits the helicase activity of PfRuvB1 possibly by blocking the ATPase activity of PfRuvB1. This study is unique in respect to the identification of novobiocin as inhibitor of PfRuvB1, partially by competing with ATP binding at its active site and provides evidence for PfRuvB1 as target of novobiocin after DNA gyrase-B and HSP90. These studies will certainly help the pharmacologist to design and develop some novel inhibitor specific to PfRuvB1, which may serve as suitable chemotherapeutics to target malaria.
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Affiliation(s)
- Moaz Ahmad
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, P.O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth. BMC BIOCHEMISTRY 2014; 15:9. [PMID: 24707807 PMCID: PMC4234510 DOI: 10.1186/1471-2091-15-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/31/2014] [Indexed: 12/11/2022]
Abstract
Background Human malaria parasite infection and its control is a global challenge which is responsible for ~0.65 million deaths every year globally. The emergence of drug resistant malaria parasite is another challenge to fight with malaria. Enormous efforts are being made to identify suitable drug targets in order to develop newer classes of drug. Helicases play crucial roles in DNA metabolism and have been proposed as therapeutic targets for cancer therapy as well as viral and parasitic infections. Genome wide analysis revealed that Plasmodium falciparum possesses UvrD helicase, which is absent in the human host. Results Recently the biochemical characterization of P. falciparum UvrD helicase revealed that N-terminal UvrD (PfUDN) hydrolyses ATP, translocates in 3’ to 5’ direction and interacts with MLH to modulate each other’s activity. In this follow up study, further characterization of P. falciparum UvrD helicase is presented. Here, we screened the effect of various DNA interacting compounds on the ATPase and helicase activity of PfUDN. This study resulted into the identification of daunorubicin (daunomycin), netropsin, nogalamycin, and ethidium bromide as the potential inhibitor molecules for the biochemical activities of PfUDN with IC50 values ranging from ~3.0 to ~5.0 μM. Interestingly etoposide did not inhibit the ATPase activity but considerable inhibition of unwinding activity was observed at 20 μM. Further study for analyzing the importance of PfUvrD enzyme in parasite growth revealed that PfUvrD is crucial/important for its growth ex-vivo. Conclusions As PfUvrD is absent in human hence on the basis of this study we propose PfUvrD as suitable drug target to control malaria. Some of the PfUvrD inhibitors identified in the present study can be utilized to further design novel and specific inhibitor molecules.
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“Omics” in the study of the major parasitic diseases malaria and schistosomiasis. INFECTION GENETICS AND EVOLUTION 2013; 19:258-73. [DOI: 10.1016/j.meegid.2013.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 07/04/2013] [Accepted: 07/07/2013] [Indexed: 01/21/2023]
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