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Kieffer C, Primas N, Hutter S, Merckx A, Reininger L, Bach S, Ruchaud S, Gaillard F, Laget M, Amrane D, Hervé L, Castera-Ducros C, Renault J, Dumètre A, Rault S, Doerig C, Rathelot P, Vanelle P, Azas N, Verhaeghe P. Target fishing reveals PfPYK-1 and PfRab6 as potential targets of an antiplasmodial 4-anilino-2-trichloromethylquinazoline hit compound. Bioorg Med Chem 2024; 102:117654. [PMID: 38452406 DOI: 10.1016/j.bmc.2024.117654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
We present investigations about the mechanism of action of a previously reported 4-anilino-2-trichloromethylquinazoline antiplasmodial hit-compound (Hit A), which did not share a common mechanism of action with established commercial antimalarials and presented a stage-specific effect on the erythrocytic cycle of P. falciparum at 8 < t < 16 h. The target of Hit A was searched by immobilising the molecule on a solid support via a linker and performing affinity chromatography on a plasmodial lysate. Several anchoring positions of the linker (6,7 and 3') and PEG-type linkers were assessed, to obtain a linked-hit molecule displaying in vitro antiplasmodial activity similar to that of unmodified Hit A. This allowed us to identify the PfPYK-1 kinase and the PfRab6 GTP-ase as potential targets of Hit A.
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Affiliation(s)
- C Kieffer
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France
| | - N Primas
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, Hôpital Conception, Marseille 13005, France
| | - S Hutter
- Aix Marseille Univ, IHU Méditerranée Infection, UMR VITROME, IRD, SSA, Mycology & Tropical Eucaryotic Pathogens, Marseille, France
| | - A Merckx
- Université Paris Cité, MERIT, IRD, Paris, France
| | - L Reininger
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Sorbonne Université, CNRS, FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680 Roscoff, France
| | - S Bach
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Sorbonne Université, CNRS, FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680 Roscoff, France
| | - S Ruchaud
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Sorbonne Université, CNRS, FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680 Roscoff, France
| | - F Gaillard
- Sorbonne Université, CNRS, UMR8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Sorbonne Université, CNRS, FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680 Roscoff, France
| | - M Laget
- Aix Marseille Univ, INSERMN, SSA, MCT, Marseille, France
| | - D Amrane
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, Marseille, France
| | - L Hervé
- Université Paris Cité, MERIT, IRD, Paris, France
| | - C Castera-Ducros
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, Hôpital Conception, Marseille 13005, France
| | - J Renault
- Université de Rennes - Faculté de Pharmacie, ISCR UMR CNRS 6226, Equipe CORINT, Rennes, France
| | - A Dumètre
- Aix Marseille Univ, IHU Méditerranée Infection, UMR VITROME, IRD, SSA, Mycology & Tropical Eucaryotic Pathogens, Marseille, France
| | - S Rault
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France
| | - C Doerig
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - P Rathelot
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, Hôpital Conception, Marseille 13005, France
| | - P Vanelle
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, Hôpital Conception, Marseille 13005, France
| | - N Azas
- Aix Marseille Univ, IHU Méditerranée Infection, UMR VITROME, IRD, SSA, Mycology & Tropical Eucaryotic Pathogens, Marseille, France.
| | - P Verhaeghe
- Univ. Grenoble Alpes, CNRS, DPM UMR 5063, F-38041 Grenoble, France; LCC-CNRS Université de Toulouse, CNRS, UPS, Toulouse, France; Service de Pharmacie, CHU de Nîmes, Place R. Debré, Nîmes, France.
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2
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Ramli AH, Mohd Faudzi SM. Diarylpentanoids, the privileged scaffolds in antimalarial and anti-infectives drug discovery: A review. Arch Pharm (Weinheim) 2023; 356:e2300391. [PMID: 37806761 DOI: 10.1002/ardp.202300391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Asia is a hotspot for infectious diseases, including malaria, dengue fever, tuberculosis, and the pandemic COVID-19. Emerging infectious diseases have taken a heavy toll on public health and the economy and have been recognized as a major cause of morbidity and mortality, particularly in Southeast Asia. Infectious disease control is a major challenge, but many surveillance systems and control strategies have been developed and implemented. These include vector control, combination therapies, vaccine development, and the development of new anti-infectives. Numerous newly discovered agents with pharmacological anti-infective potential are being actively and extensively studied for their bioactivity, toxicity, selectivity, and mode of action, but many molecules lose their efficacy over time due to resistance developments. These facts justify the great importance of the search for new, effective, and safe anti-infectives. Diarylpentanoids, a curcumin derivative, have been developed as an alternative with better bioavailability and metabolism as a therapeutic agent. In this review, the mechanisms of action and potential targets of antimalarial drugs as well as the classes of antimalarial drugs are presented. The bioactivity of diarylpentanoids as a potential scaffold for a new class of anti-infectives and their structure-activity relationships are also discussed in detail.
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Affiliation(s)
- Amirah H Ramli
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti M Mohd Faudzi
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
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3
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Dillenberger M, Rahlfs S, Becker K, Fritz-Wolf K. Prominent role of cysteine residues C49 and C343 in regulating Plasmodiumfalciparum pyruvate kinase activity. Structure 2022; 30:1452-1461.e3. [PMID: 35998635 DOI: 10.1016/j.str.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 11/27/2022]
Abstract
The protozoan parasite Plasmodium falciparum causes the most severe form of malaria and is highly dependent on glycolysis. Glycolytic enzymes were shown to be massively redox regulated, inter alia via oxidative post-translational modifications (oxPTMs) of their cysteine residues. In this study, we identified P. falciparum pyruvate kinase (PfPK) C49 and C343 as amino acid residues essentially involved in maintaining structural and functional integrity of the enzyme. The mutation of these cysteines resulted in an altered substrate affinity, lower enzymatic activities, and, as studied by X-ray crystallography, conformational changes within the A-domain where the substrate binding site is located. Although the loss of a cysteine evoked an impaired catalysis in both mutants, the effects observed for mutant C49A were more severe: multiple conformational changes, caused by the loss of two hydrogen bonds, impeded proper substrate binding and thus the transfer of phosphate upon catalysis.
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Affiliation(s)
- Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany
| | - Karin Fritz-Wolf
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, 35392 Giessen, Germany; Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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4
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Akunuri R, Unnissa T, Vadakattu M, Bujji S, Mahammad Ghouse S, Madhavi Yaddanapudi V, Chopra S, Nanduri S. Bacterial Pyruvate Kinase: A New Potential Target to Combat Drug‐Resistant
Staphylococcus aureus
Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202201403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ravikumar Akunuri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Tanveer Unnissa
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Manasa Vadakattu
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sushmitha Bujji
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Shaik Mahammad Ghouse
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology CSIR-Central Drug Research Institute (CDRI) Sitapur Road, Sector 10, Janakipuram Extension Lucknow 226 031, Uttar Pradesh India
| | - Srinivas Nanduri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
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5
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Gao P, Liu YQ, Xiao W, Xia F, Chen JY, Gu LW, Yang F, Zheng LH, Zhang JZ, Zhang Q, Li ZJ, Meng YQ, Zhu YP, Tang H, Shi QL, Guo QY, Zhang Y, Xu CC, Dai LY, Wang JG. Identification of antimalarial targets of chloroquine by a combined deconvolution strategy of ABPP and MS-CETSA. Mil Med Res 2022; 9:30. [PMID: 35698214 PMCID: PMC9195458 DOI: 10.1186/s40779-022-00390-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria is a devastating infectious disease that disproportionally threatens hundreds of millions of people in developing countries. In the history of anti-malaria campaign, chloroquine (CQ) has played an indispensable role, however, its mechanism of action (MoA) is not fully understood. METHODS We used the principle of photo-affinity labeling and click chemistry-based functionalization in the design of a CQ probe and developed a combined deconvolution strategy of activity-based protein profiling (ABPP) and mass spectrometry-coupled cellular thermal shift assay (MS-CETSA) that identified the protein targets of CQ in an unbiased manner in this study. The interactions between CQ and these identified potential protein hits were confirmed by biophysical and enzymatic assays. RESULTS We developed a novel clickable, photo-affinity chloroquine analog probe (CQP) which retains the antimalarial activity in the nanomole range, and identified a total of 40 proteins that specifically interacted and photo-crosslinked with CQP which was inhibited in the presence of excess CQ. Using MS-CETSA, we identified 83 candidate interacting proteins out of a total of 3375 measured parasite proteins. At the same time, we identified 8 proteins as the most potential hits which were commonly identified by both methods. CONCLUSIONS We found that CQ could disrupt glycolysis and energy metabolism of malarial parasites through direct binding with some of the key enzymes, a new mechanism that is different from its well-known inhibitory effect of hemozoin formation. This is the first report of identifying CQ antimalarial targets by a parallel usage of labeled (ABPP) and label-free (MS-CETSA) methods.
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Affiliation(s)
- Peng Gao
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yan-Qing Liu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wei Xiao
- Department of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Fei Xia
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jia-Yun Chen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Li-Wei Gu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fan Yang
- Department of Geriatrics, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Liu-Hai Zheng
- Department of Geriatrics, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Jun-Zhe Zhang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qian Zhang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhi-Jie Li
- Department of Geriatrics, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Yu-Qing Meng
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yong-Ping Zhu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huan Tang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiao-Li Shi
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiu-Yan Guo
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ying Zhang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Cheng-Chao Xu
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Ling-Yun Dai
- Department of Geriatrics, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China. .,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore.
| | - Ji-Gang Wang
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. .,Department of Geriatrics, the Second Clinical Medical College of Jinan University, the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, 518020, Guangdong, China. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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6
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Pyruvate kinase from Plasmodium falciparum: Structural and kinetic insights into the allosteric mechanism. Biochem Biophys Res Commun 2020; 532:370-376. [DOI: 10.1016/j.bbrc.2020.08.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/23/2022]
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7
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Swift RP, Rajaram K, Keutcha C, Liu HB, Kwan B, Dziedzic A, Jedlicka AE, Prigge ST. The NTP generating activity of pyruvate kinase II is critical for apicoplast maintenance in Plasmodium falciparum. eLife 2020; 9:e50807. [PMID: 32815516 PMCID: PMC7556864 DOI: 10.7554/elife.50807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
The apicoplast of Plasmodium falciparum parasites is believed to rely on the import of three-carbon phosphate compounds for use in organelle anabolic pathways, in addition to the generation of energy and reducing power within the organelle. We generated a series of genetic deletions in an apicoplast metabolic bypass line to determine which genes involved in apicoplast carbon metabolism are required for blood-stage parasite survival and organelle maintenance. We found that pyruvate kinase II (PyrKII) is essential for organelle maintenance, but that production of pyruvate by PyrKII is not responsible for this phenomenon. Enzymatic characterization of PyrKII revealed activity against all NDPs and dNDPs tested, suggesting that it may be capable of generating a broad range of nucleotide triphosphates. Conditional mislocalization of PyrKII resulted in decreased transcript levels within the apicoplast that preceded organelle disruption, suggesting that PyrKII is required for organelle maintenance due to its role in nucleotide triphosphate generation.
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Affiliation(s)
- Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Cyrianne Keutcha
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Hans B Liu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Bobby Kwan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Anne E Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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8
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Sissoko A, Vásquez-Ocmín P, Maciuk A, Barbieri D, Neveu G, Rondepierre L, Grougnet R, Leproux P, Blaud M, Hammad K, Michel S, Lavazec C, Clain J, Houzé S, Duval R. A Chemically Stable Fluorescent Mimic of Dihydroartemisinin, Artemether, and Arteether with Conserved Bioactivity and Specificity Shows High Pharmacological Relevance to the Antimalarial Drugs. ACS Infect Dis 2020; 6:1532-1547. [PMID: 32267151 DOI: 10.1021/acsinfecdis.9b00430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Three novel tracers designed as fluorescent surrogates of artemisinin-derived antimalarial drugs (i.e., dihydroartemisinin, artemether, arteether, and artemisone) were synthesized from dihydroartemisinin. One of these tracers, corresponding to a dihydroartemisinin/artemether/arteether mimic, showed a combination of excellent physicochemical and biological properties such as hydrolytic stability, high inhibitory potency against blood-stage parasites, similar ring-stage survival assay values than the clinical antimalarials, high cytopermeability and specific labeling of live P. falciparum cells, alkylation of heme, as well as specific covalent labeling of drug-sensitive and drug-resistant P. falciparum proteomes at physiological concentrations, consistent with a multitarget action of the drugs. Our study demonstrates that probes containing the complete structural core of clinical artemisinin derivatives can be stable in biochemical and cellular settings, and recapitulate the complex mechanisms of these frontline, yet threatened, antimalarial drugs.
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Affiliation(s)
- Abdoulaye Sissoko
- Université de Paris, MERIT, IRD, F-75006 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
| | | | - Alexandre Maciuk
- Université Paris-Saclay, CNRS, BioCIS, F-92290 Châtenay-Malabry, France
| | - Daniela Barbieri
- Laboratoire d’Excellence GR-Ex, Paris, France
- Université de Paris, U1016, INSERM, and UMR 8104,
CNRS, F-75014 Paris, France
| | - Gaëlle Neveu
- Laboratoire d’Excellence GR-Ex, Paris, France
- Université de Paris, U1016, INSERM, and UMR 8104,
CNRS, F-75014 Paris, France
| | - Laurine Rondepierre
- Université de Paris, MERIT, IRD, F-75006 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
| | | | | | - Magali Blaud
- Université de Paris, CiTCoM, CNRS, F-75006 Paris, France
| | - Karim Hammad
- Université de Paris, CiTCoM, CNRS, F-75006 Paris, France
| | - Sylvie Michel
- Université de Paris, CiTCoM, CNRS, F-75006 Paris, France
| | - Catherine Lavazec
- Laboratoire d’Excellence GR-Ex, Paris, France
- Université de Paris, U1016, INSERM, and UMR 8104,
CNRS, F-75014 Paris, France
| | - Jérôme Clain
- Université de Paris, MERIT, IRD, F-75006 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
| | - Sandrine Houzé
- Université de Paris, MERIT, IRD, F-75006 Paris, France
- CNR du Paludisme, AP-HP, Hôpital Bichat − Claude-Bernard, F-75018 Paris, France
| | - Romain Duval
- Université de Paris, MERIT, IRD, F-75006 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
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9
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Tewari SG, Swift RP, Reifman J, Prigge ST, Wallqvist A. Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite. Malar J 2020; 19:94. [PMID: 32103749 PMCID: PMC7045481 DOI: 10.1186/s12936-020-03174-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Background Human blood cells (erythrocytes) serve as hosts for the malaria parasite Plasmodium falciparum during its 48-h intraerythrocytic developmental cycle (IDC). Established in vitro protocols allow for the study of host–parasite interactions during this phase and, in particular, high-resolution metabolomics can provide a window into host–parasite interactions that support parasite development. Methods Uninfected and parasite-infected erythrocyte cultures were maintained at 2% haematocrit for the duration of the IDC, while parasitaemia was maintained at 7% in the infected cultures. The parasite-infected cultures were synchronized to obtain stage-dependent information of parasite development during the IDC. Samples were collected in quadruplicate at six time points from the uninfected and parasite-infected cultures and global metabolomics was used to analyse cell fractions of these cultures. Results In uninfected and parasite-infected cultures during the IDC, 501 intracellular metabolites, including 223 lipid metabolites, were successfully quantified. Of these, 19 distinct metabolites were present only in the parasite-infected culture, 10 of which increased to twofold in abundance during the IDC. This work quantified approximately five times the metabolites measured in previous studies of similar research scope, which allowed for more detailed analyses. Enrichment in lipid metabolism pathways exhibited a time-dependent association with different classes of lipids during the IDC. Specifically, enrichment occurred in sphingolipids at the earlier stages, and subsequently in lysophospholipid and phospholipid metabolites at the intermediate and end stages of the IDC, respectively. In addition, there was an accumulation of 18-, 20-, and 22-carbon polyunsaturated fatty acids, which produce eicosanoids and promote gametocytogenesis in infected erythrocyte cultures. Conclusions The current study revealed a number of heretofore unidentified metabolic components of the host–parasite system, which the parasite may exploit in a time-dependent manner to grow over the course of its development in the blood stage. Notably, the analyses identified components, such as precursors of immunomodulatory molecules, stage-dependent lipid dynamics, and metabolites, unique to parasite-infected cultures. These conclusions are reinforced by the metabolic alterations that were characterized during the IDC, which were in close agreement with those known from previous studies of blood-stage infection.
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Affiliation(s)
- Shivendra G Tewari
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA. .,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, MD, USA.
| | - Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA.
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10
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Schormann N, Hayden KL, Lee P, Banerjee S, Chattopadhyay D. An overview of structure, function, and regulation of pyruvate kinases. Protein Sci 2019; 28:1771-1784. [PMID: 31342570 DOI: 10.1002/pro.3691] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/24/2022]
Abstract
In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available.
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Affiliation(s)
- Norbert Schormann
- Department of Biochemistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katherine L Hayden
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama
| | - Paul Lee
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois
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11
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Yadav DK, Kumar S, Teli MK, Yadav R, Chaudhary S. Molecular Targets for Malarial Chemotherapy: A Review. Curr Top Med Chem 2019; 19:861-873. [DOI: 10.2174/1568026619666190603080000] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 11/22/2022]
Abstract
The malaria parasite resistance to the existing drugs is a serious problem to the currently used
antimalarials and, thus, highlights the urgent need to develop new and effective anti-malarial molecules.
This could be achieved either by the identification of the new drugs for the validated targets or by further
refining/improving the existing antimalarials; or by combining previously effective agents with
new/existing drugs to have a synergistic effect that counters parasite resistance; or by identifying novel
targets for the malarial chemotherapy. In this review article, a comprehensive collection of some of the
novel molecular targets has been enlisted for the antimalarial drugs. The targets which could be deliberated
for developing new anti-malarial drugs could be: membrane biosynthesis, mitochondrial system,
apicoplasts, parasite transporters, shikimate pathway, hematin crystals, parasite proteases, glycolysis,
isoprenoid synthesis, cell cycle control/cycline dependent kinase, redox system, nucleic acid metabolism,
methionine cycle and the polyamines, folate metabolism, the helicases, erythrocyte G-protein, and
farnesyl transferases. Modern genomic tools approaches such as structural biology and combinatorial
chemistry, novel targets could be identified followed by drug development for drug resistant strains providing
wide ranges of novel targets in the development of new therapy. The new approaches and targets
mentioned in the manuscript provide a basis for the development of new unique strategies for antimalarial
therapy with limited off-target effects in the near future.
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Affiliation(s)
- Dharmendra K. Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, 191, Yeonsu-gu, Incheon 406-799, South Korea
| | - Surendra Kumar
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, 191, Yeonsu-gu, Incheon 406-799, South Korea
| | - Mahesh K. Teli
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, 191, Yeonsu-gu, Incheon 406-799, South Korea
| | - Ravikant Yadav
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Malaviya National Institute of Technology, Jawaharlal Nehru Marg, Jaipur-302017, India
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Malaviya National Institute of Technology, Jawaharlal Nehru Marg, Jaipur-302017, India
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12
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Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. Sci Rep 2019; 9:9085. [PMID: 31235822 PMCID: PMC6591293 DOI: 10.1038/s41598-019-45548-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Targeting chokepoint enzymes in metabolic pathways has led to new drugs for cancers, autoimmune disorders and infectious diseases. This is also a cornerstone approach for discovery and development of anthelmintics against nematode and flatworm parasites. Here, we performed omics-driven knowledge-based identification of chokepoint enzymes as anthelmintic targets. We prioritized 10 of 186 phylogenetically conserved chokepoint enzymes and undertook a target class repurposing approach to test and identify new small molecules with broad spectrum anthelmintic activity. First, we identified and tested 94 commercially available compounds using an in vitro phenotypic assay, and discovered 11 hits that inhibited nematode motility. Based on these findings, we performed chemogenomic screening and tested 32 additional compounds, identifying 6 more active hits. Overall, 6 intestinal (single-species), 5 potential pan-intestinal (whipworm and hookworm) and 6 pan-Phylum Nematoda (intestinal and filarial species) small molecule inhibitors were identified, including multiple azoles, Tadalafil and Torin-1. The active hit compounds targeted three different target classes in humans, which are involved in various pathways, including carbohydrate, amino acid and nucleotide metabolism. Last, using representative inhibitors from each target class, we demonstrated in vivo efficacy characterized by negative effects on parasite fecundity in hamsters infected with hookworms.
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13
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Dziekan JM, Yu H, Chen D, Dai L, Wirjanata G, Larsson A, Prabhu N, Sobota RM, Bozdech Z, Nordlund P. Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay. Sci Transl Med 2019; 11. [DOI: 10.1126/scitranslmed.aau3174] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
A cellular thermal shift assay (CETSA) protocol identifies and resolves antimalarial drug targets in
P. falciparum
.
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Affiliation(s)
- Jerzy M. Dziekan
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Dan Chen
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Andreas Larsson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Radoslaw M. Sobota
- Institute of Molecular and Cell Biology, Functional Proteomics Laboratory, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 138648, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17177, Sweden
- Institute of Molecular and Cell Biology, Functional Proteomics Laboratory, Agency for Science, Technology and Research (A*STAR), 138673, Singapore
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14
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Kumar S, Bhardwaj TR, Prasad DN, Singh RK. Drug targets for resistant malaria: Historic to future perspectives. Biomed Pharmacother 2018; 104:8-27. [PMID: 29758416 DOI: 10.1016/j.biopha.2018.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/22/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
New antimalarial targets are the prime need for the discovery of potent drug candidates. In order to fulfill this objective, antimalarial drug researches are focusing on promising targets in order to develop new drug candidates. Basic metabolism and biochemical process in the malaria parasite, i.e. Plasmodium falciparum can play an indispensable role in the identification of these targets. But, the emergence of resistance to antimalarial drugs is an escalating comprehensive problem with the progress of antimalarial drug development. The development of resistance has highlighted the need for the search of novel antimalarial molecules. The pharmaceutical industries are committed to new drug development due to the global recognition of this life threatening resistance to the currently available antimalarial therapy. The recent developments in the understanding of parasite biology are exhilarating this resistance issue which is further being ignited by malaria genome project. With this background of information, this review was aimed to highlights and provides useful information on various present and promising treatment approaches for resistant malaria, new progresses, pursued by some innovative targets that have been explored till date. This review also discusses modern and futuristic multiple approaches to antimalarial drug discovery and development with pictorial presentations highlighting the various targets, that could be exploited for generating promising new drugs in the future for drug resistant malaria.
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Affiliation(s)
- Sahil Kumar
- School of Pharmacy and Emerging Sciences, Baddi University of Emerging Sciences & Technology, Baddi, Dist. Solan, 173205, Himachal Pradesh, India
| | - T R Bhardwaj
- School of Pharmacy and Emerging Sciences, Baddi University of Emerging Sciences & Technology, Baddi, Dist. Solan, 173205, Himachal Pradesh, India
| | - D N Prasad
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, Dist. Rupnagar, 140126, Punjab, India
| | - Rajesh K Singh
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, Dist. Rupnagar, 140126, Punjab, India.
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15
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Oyelade J, Isewon I, Rotimi S, Okunoren I. Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets. Bioinform Biol Insights 2016; 10:49-57. [PMID: 27199550 PMCID: PMC4869600 DOI: 10.4137/bbi.s37296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 01/15/2023] Open
Abstract
Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway.
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Affiliation(s)
- Jelili Oyelade
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Solomon Rotimi
- Department of Biological Sciences, Covenant University, Ota, Ogun State, Nigeria
| | - Ifeoluwa Okunoren
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria
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16
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Penkler G, du Toit F, Adams W, Rautenbach M, Palm DC, van Niekerk DD, Snoep JL. Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J 2015; 282:1481-511. [PMID: 25693925 DOI: 10.1111/febs.13237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 02/07/2015] [Accepted: 02/13/2015] [Indexed: 11/26/2022]
Abstract
UNLABELLED The enzymes in the Embden-Meyerhof-Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation of the model, we compared model predictions for steady-state fluxes and metabolite concentrations of the hexose phosphates with experimental values for intact parasites. The model, which is completely based on kinetic parameters that were measured for the individual enzymes, gives an accurate prediction of the steady-state fluxes and intermediate concentrations. This is the first detailed kinetic model for glucose metabolism in P. falciparum, one of the most prolific malaria-causing protozoa, and the high predictive power of the model makes it a strong tool for future drug target identification studies. The modelling workflow is transparent and reproducible, and completely documented in the SEEK platform, where all experimental data and model files are available for download. DATABASE The mathematical models described in the present study have been submitted to the JWS Online Cellular Systems Modelling Database (http://jjj.bio.vu.nl/database/penkler). The investigation and complete experimental data set is available on SEEK (10.15490/seek.1. INVESTIGATION 56).
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Affiliation(s)
- Gerald Penkler
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa; Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands
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17
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Fatty acid metabolism in the Plasmodium apicoplast: Drugs, doubts and knockouts. Mol Biochem Parasitol 2015; 199:34-50. [DOI: 10.1016/j.molbiopara.2015.03.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/25/2022]
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18
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Taylor CM, Wang Q, Rosa BA, Huang SCC, Powell K, Schedl T, Pearce EJ, Abubucker S, Mitreva M. Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PLoS Pathog 2013; 9:e1003505. [PMID: 23935495 PMCID: PMC3731235 DOI: 10.1371/journal.ppat.1003505] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022] Open
Abstract
Parasitic roundworm infections plague more than 2 billion people (1/3 of humanity) and cause drastic losses in crops and livestock. New anthelmintic drugs are urgently needed as new drug resistance and environmental concerns arise. A “chokepoint reaction” is defined as a reaction that either consumes a unique substrate or produces a unique product. A chokepoint analysis provides a systematic method of identifying novel potential drug targets. Chokepoint enzymes were identified in the genomes of 10 nematode species, and the intersection and union of all chokepoint enzymes were found. By studying and experimentally testing available compounds known to target proteins orthologous to nematode chokepoint proteins in public databases, this study uncovers features of chokepoints that make them successful drug targets. Chemogenomic screening was performed on drug-like compounds from public drug databases to find existing compounds that target homologs of nematode chokepoints. The compounds were prioritized based on chemical properties frequently found in successful drugs and were experimentally tested using Caenorhabditis elegans. Several drugs that are already known anthelmintic drugs and novel candidate targets were identified. Seven of the compounds were tested in Caenorhabditis elegans and three yielded a detrimental phenotype. One of these three drug-like compounds, Perhexiline, also yielded a deleterious effect in Haemonchus contortus and Onchocerca lienalis, two nematodes with divergent forms of parasitism. Perhexiline, known to affect the fatty acid oxidation pathway in mammals, caused a reduction in oxygen consumption rates in C. elegans and genome-wide gene expression profiles provided an additional confirmation of its mode of action. Computational modeling of Perhexiline and its target provided structural insights regarding its binding mode and specificity. Our lists of prioritized drug targets and drug-like compounds have potential to expedite the discovery of new anthelmintic drugs with broad-spectrum efficacy. The World Health Organization estimates that 2.9 million people are infected with parasitic roundworms, causing high-morbidity and mortality rates, developmental delays in children, and low productivity of affected individuals. The agricultural industry experiences drastic losses in crop and livestock due to parasitic worm infections. Therefore, there is an urgent need to identify new targets and drugs to fight parasitic nematode infection. This study identified metabolic chokepoint compounds that were either produced or consumed by a single reaction and elucidated the chokepoint enzyme that drives the reaction. If the enzyme that catalyzes that reaction is blocked, a toxic build-up of a compound or lack of compound necessary for subsequent reaction will occur, potentially causing adverse effects to the parasite organism. Compounds that target some of the chokepoint enzymes were tested in C. elegans and several compounds showed efficacy. One drug-like compound, Perhexiline, showed efficacy in two different parasitic worms and yielded expected physiological effects, indicating that this drug-like compound may have efficacy on a pan-phylum level through the predicted mode of action. The methodology to find and prioritize metabolic chokepoint targets and prioritize compounds could be applied to other parasites.
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Affiliation(s)
- Christina M. Taylor
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Qi Wang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bruce A. Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stanley Ching-Cheng Huang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerrie Powell
- SCYNEXIS, Inc, Research Triangle Park, North Carolina, United States of America
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Edward J. Pearce
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sahar Abubucker
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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19
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Angelopoulos N, Hadjiprocopis A, Walkinshaw MD. Learning Binding Affinity from Augmented High Throughput Screening Data. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In high throughput screening a large number of molecules are tested against a single target protein to determine binding affinity of each molecule to the target. The objective of such tests within the pharmaceutical industry is to identify potential drug-like lead molecules. Current technology allows for thousands of molecules to be tested inexpensively. The analysis of linking such biological data with molecular properties is thus becoming a major goal in both academic and pharmaceutical research. This chapter details how screening data can be augmented with high-dimensional descriptor data and how machine learning techniques can be utilised to build predictive models. The pyruvate kinase protein is used as a model target throughout the chapter. Binding affinity data from a public repository provide binding information on a large set of screened molecules. The authors consider three machine learning paradigms: Bayesian model averaging, Neural Networks, and Support Vector Machines. The authors apply algorithms from the three paradigms to three subsets of the data and comment on the relative merits of each. They also used the learnt models to classify the molecules in a large in-house molecular database that holds commercially available chemical structures from a large number of suppliers. They discuss the degree of agreement in compounds selected and ranked for three algorithms. Details of the technical challenges in such large scale classification and the ability of each paradigm to cope with these are put forward. The application of machine learning techniques to binding data augmented by high-dimensional can provide a powerful tool in compound testing. The emphasis of this work is on making very few assumptions or technical choices with regard to the machine learning techniques. This is to facilitate application of such techniques by non-experts.
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20
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Hofmann J, Heider C, Li W, Krausze J, Roessle M, Wilharm G. Recombinant production of Yersinia enterocolitica pyruvate kinase isoenzymes PykA and PykF. Protein Expr Purif 2013; 88:243-7. [PMID: 23384479 DOI: 10.1016/j.pep.2013.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
The glycolytic enzyme pyruvate kinase (PK) generates ATP from ADP through substrate-level phosphorylation powered by the conversion of phosphoenolpyruvate to pyruvate. In contrast to other bacteria, Enterobacteriaceae, such as pathogenic yersiniae, harbour two pyruvate kinases encoded by pykA and pykF. The individual roles of these isoenzymes are poorly understood. In an attempt to make the Yersinia enterocolitica pyruvate kinases PykA and PykF amenable to structural and functional characterisation, we produced them untagged in Escherichia coli and purified them to near homogeneity through a combination of ion exchange and size exclusion chromatography, yielding more than 180 mg per litre of batch culture. The solution structure of PykA and PykF was analysed through small angle X-ray scattering which revealed the formation of PykA and PykF tetramers and confirmed the binding of the allosteric effector fructose-1,6-bisphosphate (FBP) to PykF but not to PykA.
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Affiliation(s)
- Julia Hofmann
- Robert Koch-Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany
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21
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Abstract
Malaria, the disease caused by infection with protozoan parasites from the genus Plasmodium, claims the lives of nearly 1 million people annually. Developing nations, particularly in the African Region, bear the brunt of this malaria burden. Alarmingly, the most dangerous etiologic agent of malaria, Plasmodium falciparum, is becoming increasingly resistant to current first-line antimalarials. In light of the widespread devastation caused by malaria, the emergence of drug-resistant P. falciparum strains, and the projected decrease in funding for malaria eradication that may occur over the next decade, the identification of promising new targets for antimalarial drug design is imperative. P. falciparum kinases have been proposed as ideal drug targets for antimalarial drug design because they mediate critical cellular processes within the parasite and are, in many cases, structurally and mechanistically divergent when compared with kinases from humans. Identifying a molecule capable of inhibiting the activity of a target enzyme is generally an arduous and expensive process that can be greatly aided by utilizing in silico drug design techniques. Such methods have been extensively applied to human kinases, but as yet have not been fully exploited for the exploration and characterization of antimalarial kinase targets. This review focuses on in silico methods that have been used for the evaluation of potential antimalarials and the Plasmodium kinases that could be explored using these techniques.
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Zoraghi R, Worrall L, See RH, Strangman W, Popplewell WL, Gong H, Samaai T, Swayze RD, Kaur S, Vuckovic M, Finlay BB, Brunham RC, McMaster WR, Davies-Coleman MT, Strynadka NC, Andersen RJ, Reiner NE. Methicillin-resistant Staphylococcus aureus (MRSA) pyruvate kinase as a target for bis-indole alkaloids with antibacterial activities. J Biol Chem 2011; 286:44716-25. [PMID: 22030393 PMCID: PMC3248012 DOI: 10.1074/jbc.m111.289033] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/29/2011] [Indexed: 11/06/2022] Open
Abstract
Novel classes of antimicrobials are needed to address the emergence of multidrug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). We have recently identified pyruvate kinase (PK) as a potential novel drug target based upon it being an essential hub in the MRSA interactome (Cherkasov, A., Hsing, M., Zoraghi, R., Foster, L. J., See, R. H., Stoynov, N., Jiang, J., Kaur, S., Lian, T., Jackson, L., Gong, H., Swayze, R., Amandoron, E., Hormozdiari, F., Dao, P., Sahinalp, C., Santos-Filho, O., Axerio-Cilies, P., Byler, K., McMaster, W. R., Brunham, R. C., Finlay, B. B., and Reiner, N. E. (2011) J. Proteome Res. 10, 1139-1150; Zoraghi, R., See, R. H., Axerio-Cilies, P., Kumar, N. S., Gong, H., Moreau, A., Hsing, M., Kaur, S., Swayze, R. D., Worrall, L., Amandoron, E., Lian, T., Jackson, L., Jiang, J., Thorson, L., Labriere, C., Foster, L., Brunham, R. C., McMaster, W. R., Finlay, B. B., Strynadka, N. C., Cherkasov, A., Young, R. N., and Reiner, N. E. (2011) Antimicrob. Agents Chemother. 55, 2042-2053). Screening of an extract library of marine invertebrates against MRSA PK resulted in the identification of bis-indole alkaloids of the spongotine (A), topsentin (B, D), and hamacanthin (C) classes isolated from the Topsentia pachastrelloides as novel bacterial PK inhibitors. These compounds potently and selectively inhibited both MRSA PK enzymatic activity and S. aureus growth in vitro. The most active compounds, cis-3,4-dihyrohyrohamacanthin B (C) and bromodeoxytopsentin (D), were identified as highly potent MRSA PK inhibitors (IC(50) values of 16-60 nM) with at least 166-fold selectivity over human PK isoforms. These novel anti-PK natural compounds exhibited significant antibacterial activities against S. aureus, including MRSA (minimal inhibitory concentrations (MIC) of 12.5 and 6.25 μg/ml, respectively) with selectivity indices (CC(50)/MIC) >4. We also report the discrete structural features of the MRSA PK tetramer as determined by x-ray crystallography, which is suitable for selective targeting of the bacterial enzyme. The co-crystal structure of compound C with MRSA PK confirms that the latter is a target for bis-indole alkaloids. It elucidates the essential structural requirements for PK inhibitors in "small" interfaces that provide for tetramer rigidity and efficient catalytic activity. Our results identified a series of natural products as novel MRSA PK inhibitors, providing the basis for further development of potential novel antimicrobials.
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Affiliation(s)
- Roya Zoraghi
- From the Division of Infectious Diseases, Department of Medicine
| | - Liam Worrall
- the Department of Biochemistry and Molecular Biology
| | - Raymond H. See
- From the Division of Infectious Diseases, Department of Medicine
- the Center for Disease Control, and
| | | | - Wendy L. Popplewell
- the Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa, and
| | - Huansheng Gong
- From the Division of Infectious Diseases, Department of Medicine
| | - Toufiek Samaai
- the Department of Environmental Affairs, Ocean & Coast, Biodiversity and Ecosystem Research, Cape Town, Private Bag X447, South Africa
| | | | - Sukhbir Kaur
- From the Division of Infectious Diseases, Department of Medicine
| | | | - B. Brett Finlay
- the Department of Biochemistry and Molecular Biology
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
| | - Robert C. Brunham
- From the Division of Infectious Diseases, Department of Medicine
- the Center for Disease Control, and
| | - William R. McMaster
- From the Division of Infectious Diseases, Department of Medicine
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
| | | | | | | | - Neil E. Reiner
- From the Division of Infectious Diseases, Department of Medicine
- Microbiology and Immunology, University of British Columbia, British Columbia, Vancouver V5Z 3J5, Canada
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Identification of pyruvate kinase in methicillin-resistant Staphylococcus aureus as a novel antimicrobial drug target. Antimicrob Agents Chemother 2011; 55:2042-53. [PMID: 21357306 DOI: 10.1128/aac.01250-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel classes of antimicrobials are needed to address the challenge of multidrug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). Using the architecture of the MRSA interactome, we identified pyruvate kinase (PK) as a potential novel drug target based upon it being a highly connected, essential hub in the MRSA interactome. Structural modeling, including X-ray crystallography, revealed discrete features of PK in MRSA, which appeared suitable for the selective targeting of the bacterial enzyme. In silico library screening combined with functional enzymatic assays identified an acyl hydrazone-based compound (IS-130) as a potent MRSA PK inhibitor (50% inhibitory concentration [IC50] of 0.1 μM) with >1,000-fold selectivity over human PK isoforms. Medicinal chemistry around the IS-130 scaffold identified analogs that more potently and selectively inhibited MRSA PK enzymatic activity and S. aureus growth in vitro (MIC of 1 to 5 μg/ml). These novel anti-PK compounds were found to possess antistaphylococcal activity, including both MRSA and multidrug-resistant S. aureus (MDRSA) strains. These compounds also exhibited exceptional antibacterial activities against other Gram-positive genera, including enterococci and streptococci. PK lead compounds were found to be noncompetitive inhibitors and were bactericidal. In addition, mutants with significant increases in MICs were not isolated after 25 bacterial passages in culture, indicating that resistance may be slow to emerge. These findings validate the principles of network science as a powerful approach to identify novel antibacterial drug targets. They also provide a proof of principle, based upon PK in MRSA, for a research platform aimed at discovering and optimizing selective inhibitors of novel bacterial targets where human orthologs exist, as leads for anti-infective drug development.
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Zoraghi R, See RH, Gong H, Lian T, Swayze R, Finlay BB, Brunham RC, McMaster WR, Reiner NE. Functional analysis, overexpression, and kinetic characterization of pyruvate kinase from methicillin-resistant Staphylococcus aureus. Biochemistry 2010; 49:7733-47. [PMID: 20707314 DOI: 10.1021/bi100780t] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Novel antimicrobial targets are urgently needed to overcome rising antibiotic resistance of important human pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Here we report the essentiality and kinetic properties of MRSA pyruvate kinase (PK). Targetron-mediated gene disruption demonstrated PK is essential for S. aureus growth and survival, suggesting that this protein may be a potential drug target. The presence of the pfk (6-phosphofructokinase)-pyk operon in MRSA252, and the nonessential nature of PFK shown by targetron, further emphasized the essential role of PK in cell viability. The importance of PK in bacterial growth was confirmed by showing that its enzymatic activity peaked during the logarithmic phase of S. aureus growth. PK from Staphylococcus and several other species of bacteria have an extra C-terminal domain (CT) containing a phosphoenolpyruvate (PEP) binding motif. To elucidate the possible structure and function of this sequence, the quaternary structures and kinetic properties of the full-length MRSA PK and truncated MRSA PK lacking the CT domain were characterized. Our results showed that (1) MRSA PK is an allosteric enzyme with homotetramer architecture activated by AMP or ribose 5-phosphate (R5P), but not by fructose 1,6-bisphosphate (FBP), which suggests a different mode of allosteric regulation when compared with human isozymes, (2) the CT domain is not required for the tetramerization of the enzyme; homotetramerization occurred in a truncated PK lacking the domain, (3) truncated enzyme exhibited high affinity toward both PEP and ADP and exhibited hyperbolic kinetics toward PEP in the presence of activators (AMP and R5P) consistent with kinetic properties of full-length enzyme, indicating that the CT domain is not required for substrate binding or allosteric regulation observed in the holoenzyme, (4) the kinetic efficiency (k(cat)/S(0.5)) of truncated enzyme was decreased by 24- and 16-fold, in ligand-free state, toward PEP and ADP, respectively, but was restored by 3-fold in AMP-bound state, suggesting that the sequence containing the CT domain (Gly(473)-Leu(585)) plays a substantial role in enzyme activity and comformational stability, and (5) full-length MRSA PK activity was stimulated at low concentrations of ATP (e.g., 1 mM) and inhibited by inorganic phosphate and high concentrations of FBP (10 mM) and ATP (e.g., >2.5 mM), whereas for truncated enzyme, stimulation at low concentrations of ATP was lost. These findings suggest that the CT domain is involved in maintaining the specificity of allosteric regulation of MRSA PK by AMP, R5P, and ATP. The CT extension also encodes a protein domain with homology to enzyme I of the Escherichia coli sugar-PTS system, suggesting that MRSA PK may also exert an important regulatory role in sugar transport metabolism. These findings yield new insights into MRSA PK function and mode of allosteric regulation which may aid in the development of clinically important drugs targeting this enzyme and further define the role of the extra C-terminal domain in modulating the enzyme's activity.
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Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of BritishColumbia, Vancouver,Britsih Columbia,CanadaV5Z3J5
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Angelopoulos N, Hadjiprocopis A, Walkinshaw MD. Bayesian Model Averaging for Ligand Discovery. J Chem Inf Model 2009; 49:1547-57. [DOI: 10.1021/ci900046u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicos Angelopoulos
- Department of Biological Sciences, Edinburgh University, Scotland, U.K., and Department of Computing, Higher Technical Institute, Nicosia, Cyprus
| | - Andreas Hadjiprocopis
- Department of Biological Sciences, Edinburgh University, Scotland, U.K., and Department of Computing, Higher Technical Institute, Nicosia, Cyprus
| | - Malcolm D. Walkinshaw
- Department of Biological Sciences, Edinburgh University, Scotland, U.K., and Department of Computing, Higher Technical Institute, Nicosia, Cyprus
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Leroy D, Doerig C. Drugging the Plasmodium kinome: the benefits of academia-industry synergy. Trends Pharmacol Sci 2008; 29:241-9. [PMID: 18394721 DOI: 10.1016/j.tips.2008.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 01/21/2023]
Abstract
Malaria remains a major killer in many parts of the world. Recently, the development of nonprofit organisations aimed at fighting this deadly scourge incited academic and industrial scientists to merge their expertise in drug-target validation and lead discovery. Expectations are clear: identification and characterisation of new molecules showing high efficacy, low toxicity and little propensity to induce resistance in the parasite. In this context, protein kinase inhibitors represent an attractive possibility. Here, we compare traditional target-based drug-discovery approaches with innovative exploratory paths (parallel screening, cell-based assays, integrated systems biology and allosteric inhibition) and discuss the benefits of acadaemia-industry cooperation. Early characterisation of distribution, metabolism, pharmacokinetic (DMPK) and toxicology parameters are considered as well.
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Affiliation(s)
- Didier Leroy
- Merck-Serono International S.A., Geneva Research Center, 9, Chemin des Mines, Case postale 54, CH-1211 Genève 20, Switzerland.
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Sahu NK, Sahu S, Kohli DV. Novel Molecular Targets for Antimalarial Drug Development. Chem Biol Drug Des 2008; 71:287-97. [DOI: 10.1111/j.1747-0285.2008.00640.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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