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Compton JA, Patrick WM. The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily. Biochem J 2025; 482:467-483. [PMID: 40329473 DOI: 10.1042/bcj20253024] [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: 01/02/2025] [Accepted: 04/14/2025] [Indexed: 05/08/2025]
Abstract
The enzyme 6-phosphofructokinase (PFK) phosphorylates d-fructose 6-phosphate, producing d-fructose 1,6-bisphosphate. The canonical version-discovered almost 90 years ago-is ATP-dependent, allosterically regulated and catalyses the first committed step in glycolysis. However, beyond this textbook enzyme, there is fascinating functional and structural variety among PFKs across the tree of life. While PFKs are found in two non-homologous superfamilies, here, we review the universally distributed enzymes in one, the Phosphofructokinase Superfamily. We focus on summarising the diversity within this superfamily. A key partition regards the identity of the phosphate donor, which can be ATP or inorganic pyrophosphate (PPi). Considerable insights into functional and evolutionary aspects of the ATP- and PPi-dependent PFKs have come through structural biology, with 45 structures now available in the Protein Data Bank. One recent highlight was the use of cryoEM and molecular dynamics simulations to illuminate the structural basis of allosteric regulation in human liver PFK. Others were to explore interactions of drug-like small molecules with the PFKs from Trypanosoma brucei and human liver, revealing new routes to antibiotics and immune modulators, respectively. In contrast with the ATP-dependent enzymes, PPi-dependent PFKs are typically non-allosteric and catalyse a readily reversible reaction. Some also play an additional physiological role by phosphorylating d-sedoheptulose 7-phosphate. We discuss why these properties are plausibly ancestral. Finally, we also emphasise how much remains to be discovered. For example, the 45 experimentally determined structures are from only 14 species. Nine decades in, it is still a great time to be studying PFK.
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Affiliation(s)
- Jordan A Compton
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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2
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Pinto Torres JE, Claes M, Hendrickx R, Yuan M, Smiejkowska N, Van Wielendaele P, Hacisuleyman A, De Winter H, Muyldermans S, Michels PAM, Walkinshaw MD, Versées W, Caljon G, Magez S, Sterckx YGJ. Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody. eLife 2025; 13:RP100066. [PMID: 40163365 PMCID: PMC11957543 DOI: 10.7554/elife.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2025] Open
Abstract
African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.
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Affiliation(s)
- Joar Esteban Pinto Torres
- Laboratory for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB)BrusselBelgium
| | - Mathieu Claes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
| | - Rik Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
| | - Meng Yuan
- School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Natalia Smiejkowska
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
| | - Aysima Hacisuleyman
- Department of Computational Biology, University of LausanneLausanneSwitzerland
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of AntwerpWilrijkBelgium
| | - Serge Muyldermans
- Laboratory for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB)BrusselBelgium
| | - Paul AM Michels
- School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Malcolm D Walkinshaw
- School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Wim Versées
- VIB-VUB Center for Structural Biology, VIBBrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit BrusselBrusselsBelgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
| | - Stefan Magez
- Laboratory for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel (VUB)BrusselBelgium
- Center for Biomedical Research, Ghent University Global CampusIncheonRepublic of Korea
- Department for Biochemistry and Microbiology, Ghent UniversityGhentBelgium
| | - Yann G-J Sterckx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of AntwerpWilrijkBelgium
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Adomako AK, Gasu EN, Mensah JO, Borquaye LS. Antileishmanial natural products as potential inhibitors of the Leishmania pteridine reductase: insights from molecular docking and molecular dynamics simulations. In Silico Pharmacol 2024; 12:70. [PMID: 39091898 PMCID: PMC11289227 DOI: 10.1007/s40203-024-00247-8] [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: 08/14/2023] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Although many natural product-derived compounds possess anti-leishmanial activities in vitro and in vivo, their molecular targets in the Leishmania parasite remain elusive. This is a major challenge in optimizing these compounds into leads. The Leishmania pteridine reductase (PTR1) is peculiar for folate and pterin metabolism and has been validated as a drug target. In this study, 17 compounds with anti-leishmanial activities were screened against Leishmania major PTR1 (LmPTR1) using molecular docking and molecular dynamics (MD) simulations. All ligands were bound in the active site pocket of LmPTR1 with binding affinities ranging from -11.2 to -5.2 kcal/mol. Agnuside, betulin, betulinic acid, gerberinol, ismailin, oleanolic acid, pristimerin, and ursolic acid demonstrated binding affinities similar to a known inhibitor, methyl 1-(4-{[2,4-diaminopteridin-6-yl) methyl] amino} benzoyl) piperidine-4-carboxylate (DVP). MD simulations revealed that betulin, betulinic acid, ismailin, oleanolic acid, pristimerin, and ursolic acid formed stable complexes with LmPTR1. The binding free energies of the complexes were very good (-87 to -148 kJ/mol), and much higher than the complex of the standard DVP inhibitor and LmPTR1 (-27 kJ/mol). Betulin, betulinic acid, ismailin, oleanolic acid, pristimerin, and ursolic acid likely exert their antileishmanial action by inhibiting PTR1 and could thus be used as a basis for the development of potential antileishmanial chemotherapeutic agents. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00247-8.
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Affiliation(s)
| | - Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Olanlokun JO, Abiodun OW, Adegbuyi AT, Koorbanally NA, Olorunsogo OO. Mefloquine-curcumin combinations improve host mitochondrial respiration and decrease mitotoxic effects of mefloquine in Plasmodium berghei-infected mice. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2024; 6:100180. [PMID: 38725654 PMCID: PMC11081784 DOI: 10.1016/j.crphar.2024.100180] [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: 11/22/2023] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
Plasmodium infection is a health challenge. Although, antiplasmodial drugs kill the parasites, information on the effects of infection and drugs on the expression of some genes is limited. Malaria was induced in two different studies using NK65 (chloroquine-susceptible, study 1), and ANKA (chloroquine-resistant, study 2) strains of Plasmodium berghei in 30 male Swiss mice (n = 5) in each study. Mice orally received 10 mL/kg distilled water, (infected control), Mefloquine (MF) (10 mg/kg), MF and Curcumin (CM) (25 mg/kg), MF and CM (50 mg/kg), CM (25 mg/kg) and CM (50 mg/kg). Five mice (un-infected) were used as the control. After treatment, total Ribonucleic acid (RNA) was isolated from liver and erythrocytes while Deoxyribonucleic acid (DNA)-free RNA were converted to cDNA. Polymerase Chain Reaction (PCR) amplification was performed and relative expressions of FIKK12, AQP3, P38 MAPK, NADH oxidoreductase, and cytochrome oxidase expressions were determined. Markers of glycolysis, toxicity and antioxidants were determined using ELISA assays. While the expression of FIKK12 was blunted by MF in the susceptible study, co-treatment with curcumin (25 mg/kg) yielded the same results in the chloroquine-resistant study. Similar results were obtained on AQP3 in both studies. Curcumin decreased P38 MAPK in both studies. Plasmodium infection decreased NADH oxidoreductase and cytochrome oxidase but mefloquine-curcumin restored the expression of these genes. While glycolysis and toxicity were inhibited, antioxidant systems improved in the treated groups. Curcumin is needed for effective therapeutic efficacy and prevention of toxicity. Plasmodium infection and treatment modulate the expressions of some genes in the host. Curcumin combination with mefloquine modulates the expression of some genes in the host.
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Affiliation(s)
- John Oludele Olanlokun
- Laboratories for Biomemebrane Research and Biotechnology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oshireku Wisdom Abiodun
- Laboratories for Biomemebrane Research and Biotechnology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Neil Anthony Koorbanally
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Olufunso Olabode Olorunsogo
- Laboratories for Biomemebrane Research and Biotechnology, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Adessi TG, Cantero J, Ballesteros-Casallas A, García ME, Nicotra VE, Paulino M. Identification of potential biological target for trypanocidal sesquiterpene lactones derivatives. J Biomol Struct Dyn 2023; 41:14510-14523. [PMID: 36856082 DOI: 10.1080/07391102.2023.2183031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
Sesquiterpene lactones are natural products of the Asteraceae family that have shown trypanocidal activity against Trypanosoma cruzi, even exceeding the effectiveness of drugs used in the treatment of American trypanosomiasis. However, there is no agreement on their mechanism of action and their specificity to interact with parasite proteins. For this reason, we aimed to find biological targets that can interact with these compounds by reverse virtual screening with ligand pharmacophores and putative binding sites and the use of bioinformatic databases. Therefore, 41 possible biological targets were found, and four of them (with crystallized proteins), interfering directly or indirectly in the trypanosomatid redox system, were studied in detail. As a first approach, we focused on the study of trypanothione reductase, and protein-ligand interaction fingerprint analyses were performed to find binding site determinants that promote a possible inhibition of the enzyme. This study contributes to the understanding of one of the putative mechanisms of action of sesquiterpene lactones on one of the numerous suggested targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tonino G Adessi
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Jorge Cantero
- Centro de Investigaciones Médicas, Facultad de Ciencias de la Salud, Universidad Nacional del Este, Minga Guazu, Paraguay
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
| | | | - Manuela E García
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Viviana E Nicotra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Margot Paulino
- Área Bioinformática, Departamento DETEMA, Facultad de Química, Universidad de la República, Uruguay
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Moreira RS, Calomeno NA, das Neves GB, do Nascimento LFN, Filho VB, Wagner G, Miletti LC. Trypanosoma evansi secretome carries potential biomarkers for Surra diagnosis. J Proteomics 2023; 272:104789. [PMID: 36464092 DOI: 10.1016/j.jprot.2022.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Trypanosoma evansi is a parasite that is phylogenetically close to Trypanosoma brucei and is the causative agent of a disease known as surra. Surra is responsible for a high mortality rate in livestock and large economic losses in the Americas, Africa, and Asia. This work aimed to analyze in vitro secreted proteins from T. evansi and identify potential treatment and diagnostic biomarkers for surra diagnosis. Two groups were used. In one group the parasites were purified using a DEAE-Cellulose column and maintained in a secretion medium while in the other group the parasites were not purified. Each group was further divided to be maintained at either 37 °C or 27 °C. We identified 246 proteins through mass spectrometry and found that the temperature appears to modulate protein secretion. We found minimal variations in the protein pools from pure and non-purified sets. We observed an emphasis on proteins associated to vesicles, glycolysis, and cellular homeostasis through the enrichment of GO. Also, we found that most secretome proteins share homologous proteins with T. b. brucei, T. b. gambiense, T. vivax, T. equiperdum, and T. b. rhodesiense secretome but unique T. evansi epitopes with potential biomarkers for surra diagnosis were detected. SIGNIFICANCE: Trypanosoma evansi is a parasite of African origin that is phylogenetically close to Trypanosoma brucei. As with other trypanosomatids and blood parasites, its infection causes non-pathognomonic symptoms, which makes its diagnosis difficult. One great problem is the fact that no diagnostic test differentiates between Trypanosoma equiperdum and T. evansi, which is a problem in South America and Asia, and Africa. Thus, it is urgent to study the biochemistry of the parasite to discover proteins that can be used for differential diagnosis or be possible therapeutic targets. In addition, the study of the secretome can point out proteins that are used by the parasite in its interactions with the host, helping to understand the progression of the disease.
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Affiliation(s)
- Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil; Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510 - Bela Vista, Gaspar, SC 89111-009, Brazil
| | - Nathália Anderson Calomeno
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Gabriella Bassi das Neves
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Luiz Flávio Nepomuceno do Nascimento
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil.
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Gupta D, Singh PK, Yadav PK, Narender T, Patil UK, Jain SK, Chourasia MK. Emerging strategies and challenges of molecular therapeutics in antileishmanial drug development. Int Immunopharmacol 2023; 115:109649. [PMID: 36603357 DOI: 10.1016/j.intimp.2022.109649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/16/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023]
Abstract
Molecular therapy refers to targeted therapies based on molecules which have been intelligently directed towards specific biomolecular structures and include small molecule drugs, monoclonal antibodies, proteins and peptides, DNA or RNA-based strategies, targeted chemotherapy and nanomedicines. Molecular therapy is emerging as the most effective strategy to combat the present challenges of life-threatening visceral leishmaniasis, where the successful human vaccine is currently unavailable. Moreover, current chemotherapy-based strategies are associated with the issues of ineffective targeting, unavoidable toxicities, invasive therapies, prolonged treatment, high treatment costs and the development of drug-resistant strains. Thus, the rational approach to antileishmanial drug development primarily demands critical exploration and exploitation of biochemical differences between host and parasite biology, immunocharacteristics of parasite homing, and host-parasite interactions at the molecular/cellular level. Following this, the novel technology-based designing and development of host and/or parasite-targeted therapeutics having leishmanicidal and immunomodulatory activity is utmost essential to improve treatment efficacy. Thus, the present review is focused on immunological and molecular checkpoint targets in host-pathogen interaction, and molecular therapeutic prospects for Leishmania intervention, and the challenges ahead.
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Affiliation(s)
- Deepak Gupta
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India; Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Pankaj K Singh
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India; Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, Telangana, India
| | - Pavan K Yadav
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Tadigoppula Narender
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Umesh K Patil
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India
| | - Sanjay K Jain
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India
| | - Manish K Chourasia
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India.
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Guhe V, Ingale P, Tambekar A, Singh S. Systems biology of autophagy in leishmanial infection and its diverse role in precision medicine. Front Mol Biosci 2023; 10:1113249. [PMID: 37152895 PMCID: PMC10160387 DOI: 10.3389/fmolb.2023.1113249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Autophagy is a contentious issue in leishmaniasis and is emerging as a promising therapeutic regimen. Published research on the impact of autophagic regulation on Leishmania survival is inconclusive, despite numerous pieces of evidence that Leishmania spp. triggers autophagy in a variety of cell types. The mechanistic approach is poorly understood in the Leishmania parasite as autophagy is significant in both Leishmania and the host. Herein, this review discusses the autophagy proteins that are being investigated as potential therapeutic targets, the connection between autophagy and lipid metabolism, and microRNAs that regulate autophagy and lipid metabolism. It also highlights the use of systems biology to develop novel autophagy-dependent therapeutics for leishmaniasis by utilizing artificial intelligence (AI), machine learning (ML), mathematical modeling, network analysis, and other computational methods. Additionally, we have shown many databases for autophagy and metabolism in Leishmania parasites that suggest potential therapeutic targets for intricate signaling in the autophagy system. In a nutshell, the detailed understanding of the dynamics of autophagy in conjunction with lipids and miRNAs unfolds larger dimensions for future research.
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Patil N, Howe O, Cahill P, Byrne HJ. Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives. Mol Metab 2022; 66:101635. [PMID: 36379354 PMCID: PMC9703637 DOI: 10.1016/j.molmet.2022.101635] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical. SCOPE OF REVIEW This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered. MAJOR CONCLUSIONS Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other omics technologies for non-destructive, real-time, in vivo label-free monitoring of glycolysis dynamics at a cellular and subcellular level.
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Affiliation(s)
- Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland; School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological and Health Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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Schachner LF, Soye BD, Ro S, Kenney GE, Ives AN, Su T, Goo YA, Jewett MC, Rosenzweig AC, Kelleher NL. Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. ACS Chem Biol 2022; 17:2769-2780. [PMID: 35951581 PMCID: PMC9588721 DOI: 10.1021/acschembio.2c00324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Triosephosphate isomerase (TPI) performs the 5th step in glycolysis, operates near the limit of diffusion, and is involved in "moonlighting" functions. Its dimer was found singly phosphorylated at Ser20 (pSer20) in human cells, with this post-translational modification (PTM) showing context-dependent stoichiometry and loss under oxidative stress. We generated synthetic pSer20 proteoforms using cell-free protein synthesis that showed enhanced TPI activity by 4-fold relative to unmodified TPI. Molecular dynamics simulations show that the phosphorylation enables a channel to form that shuttles substrate into the active site. Refolding, kinetic, and crystallographic analyses of point mutants including S20E/G/Q indicate that hetero-dimerization and subunit asymmetry are key features of TPI. Moreover, characterization of an endogenous human TPI tetramer also implicates tetramerization in enzymatic regulation. S20 is highly conserved across eukaryotic TPI, yet most prokaryotes contain E/D at this site, suggesting that phosphorylation of human TPI evolved a new switch to optionally boost an already fast enzyme. Overall, complete characterization of TPI shows how endogenous proteoform discovery can prioritize functional versus bystander PTMs.
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Affiliation(s)
- Luis F Schachner
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin Des Soye
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Soo Ro
- Department Molecular and Biological Sciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Grace E Kenney
- Department Molecular and Biological Sciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02140, United States
| | - Ashley N Ives
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Taojunfeng Su
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Young Ah Goo
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Department Molecular and Biological Sciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Department of Chemistry, the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department Molecular and Biological Sciences, Northwestern University, Evanston, Illinois 60208, United States
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Britten NS, Butler JA. Ruthenium metallotherapeutics: novel approaches to combatting parasitic infections. Curr Med Chem 2022; 29:5159-5178. [PMID: 35366762 DOI: 10.2174/0929867329666220401105444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022]
Abstract
Human parasitic infections cause a combined global mortality rate of over one million people per annum and represent some of the most challenging diseases for medical intervention. Current chemotherapeutic strategies often require prolonged treatment, coupled with subsequent drug-induced cytotoxic morbidity to the host, while resistance generation is also a major concern. Metals have been used extensively throughout the history of medicine, with more recent applications as anticancer and antimicrobial agents. Ruthenium metallotherapeutic antiparasitic agents are highly effective at targeting a range of key parasites, including the causative agents of malaria, trypanosomiasis, leishmaniasis, amoebiasis, toxoplasmosis and other orphan diseases, while demonstrating lower cytotoxicity profiles than current treatment strategies. Generally, such compounds also demonstrate activity against multiple cellular target sites within parasites, including inhibition of enzyme function, cell membrane perturbation, and alterations to metabolic pathways, therefore reducing the opportunity for resistance generation. This review provides a comprehensive and subjective analysis of the rapidly developing area of ruthenium metal-based antiparasitic chemotherapeutics, in the context of rational drug design and potential clinical approaches to combatting human parasitic infections.
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Affiliation(s)
- Nicole S. Britten
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Jonathan A. Butler
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
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12
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Michels PAM, Gualdrón-López M. Biogenesis and metabolic homeostasis of trypanosomatid glycosomes: new insights and new questions. J Eukaryot Microbiol 2022; 69:e12897. [PMID: 35175680 DOI: 10.1111/jeu.12897] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Kinetoplastea and Diplonemea possess peroxisome-related organelles that, uniquely, contain most of the enzymes of the glycolytic pathway and are hence called glycosomes. Enzymes of several other core metabolic pathways have also been located in glycosomes, in addition to some characteristic peroxisomal systems such as pathways of lipid metabolism. A considerable amount of research has been performed on glycosomes of trypanosomes since their discovery four decades ago. Not only the role of the glycosomal enzyme systems in the overall cell metabolism appeared to be unique, but the organelles display also remarkable features regarding their biogenesis and structural properties. These features are similar to those of the well-studied peroxisomes of mammalian and plant cells and yeasts yet exhibit also differences reflecting the large evolutionary distance between these protists and the representatives of other major eukaryotic lineages. Despite all research performed, many questions remain about various properties and the biological roles of glycosomes and peroxisomes. Here we review the current knowledge about glycosomes, often comparing it with information about peroxisomes. Furthermore, we highlight particularly many questions that remain about the biogenesis, and the heterogeneity in structure and content of these enigmatic organelles, and the properties of their boundary membrane.
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Affiliation(s)
- Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Melisa Gualdrón-López
- Instituto Salud Global, Hospital Clinic-Universitat de Barcelona, and Institute for Health Sciences Trias i Pujol, Barcelona, Spain
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13
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Vázquez-Jiménez LK, Moreno-Herrera A, Juárez-Saldivar A, González-González A, Ortiz-Pérez E, Paz-González AD, Palos-Pizarro I, Ramírez-Moreno E, Rivera G. Recent Advances in the Development of Triose Phosphate Isomerase Inhibitors as Antiprotozoal Agents. Curr Med Chem 2021; 29:2504-2529. [PMID: 34517794 DOI: 10.2174/0929867328666210913090928] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/10/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Parasitic diseases caused by protozoa such as Chagas disease, leishmaniasis, malaria, African trypanosomiasis, amebiasis, trichomoniasis, and giardiasis are considered serious public health problems in developing countries. Drug-resistance among parasites justifies the search for new therapeutic drugs and the identification of new targets becomes a valuable approach. In this scenario, glycolysis pathway which consists of the conversion of glucose into pyruvate plays an important role in the protozoa energy supply and it is therefore considered as a promising target. In this pathway, triose phosphate isomerase (TIM) plays an essential role in efficient energy production. Furthermore, protozoa TIM show structural differences with human enzyme counterparts suggesting the possibility of obtaining selective inhibitors. Therefore, TIM is considered a valid approach to develop new antiprotozoal agents, inhibiting the glycolysis in the parasite. OBJECTIVE In this review, we discuss the drug design strategies, structure-activity relationship, and binding modes of outstanding TIM inhibitors against Trypanosoma cruzi, Trypanosoma brucei, Plasmodium falciparum, Giardia lamblia, Leishmania mexicana, Trichomonas vaginalis, and Entamoeba histolytica. RESULTS TIM inhibitors showed mainly aromatic systems and symmetrical structure, where the size and type of heteroatom are important for enzyme inhibition. This inhibition is mainly based on the interaction with i) the interfacial region of TIM inducing changes on the quaternary and tertiary structure or ii) with the TIM catalytic region were the main pathways that disabled the catalytic activity of the enzyme. CONCLUSION Benzothiazole, benzoxazole, benzimidazole, and sulfhydryl derivatives stand out as TIM inhibitors. In silico and in vitro studies demonstrate that the inhibitors bind mainly at the TIM dimer interface. In this review, the development of new TIM inhibitors as antiprotozoal drugs is demonstrated as an important pharmaceutical strategy that may lead to new therapies for these ancient parasitic diseases.
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Affiliation(s)
- Lenci K Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Antonio Moreno-Herrera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alfredo Juárez-Saldivar
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alonzo González-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Eyra Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
| | - Isidro Palos-Pizarro
- Unidad Académica Multidisciplinaria Reynosa-Rodhe, Universidad Autónoma de Tamaulipas, 88779 Reynosa. Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, 07320 Ciudad de México. Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710 Reynosa. Mexico
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14
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Gomes MT, Paes-Vieira L, Gomes-Vieira AL, Cosentino-Gomes D, da Silva APP, Giarola NLL, Da Silva D, Sola-Penna M, Galina A, Meyer-Fernandes JR. 3-Bromopyruvate: A new strategy for inhibition of glycolytic enzymes in Leishmania amazonensis. Exp Parasitol 2021; 229:108154. [PMID: 34481863 DOI: 10.1016/j.exppara.2021.108154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 05/14/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022]
Abstract
The compound 3-bromopyruvate (3-BrPA) is well-known and studies from several researchers have demonstrated its involvement in tumorigenesis. It is an analogue of pyruvic acid that inhibits ATP synthesis by inhibiting enzymes from the glycolytic pathway and oxidative phosphorylation. In this work, we investigated the effect of 3-BrPA on energy metabolism of L. amazonensis. In order to verify the effect of 3-BrPA on L. amazonensis glycolysis, we measured the activity level of three glycolytic enzymes located at different points of the pathway: (i) glucose kinases, step 1, (ii) glyceraldehyde 3-phosphate dehydrogenase (GAPDH), step 6, and (iii) enolase, step 9. 3-BrPA, in a dose-dependent manner, significantly reduced the activity levels of all the enzymes. In addition, 3-BrPA treatment led to a reduction in the levels of phosphofruto-1-kinase (PFK) protein, suggesting that the mode of action of 3-BrPA involves the downregulation of some glycolytic enzymes. Measurement of ATP levels in promastigotes of L. amazonensis showed a significant reduction in ATP generation. The O2 consumption was also significantly inhibited in promastigotes, confirming the energy depletion effect of 3-BrPA. When 3-BrPA was added to the cells at the beginning of growth cycle, it significantly inhibited L. amazonensis proliferation in a dose-dependent manner. Furthermore, the ability to infect macrophages was reduced by approximately 50% when promastigotes were treated with 3-BrPA. Taken together, these studies corroborate with previous reports which suggest 3-BrPA as a potential drug against pathogenic microorganisms that are reliant on glucose catabolism for ATP supply.
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Affiliation(s)
- Marta Teixeira Gomes
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN, USA; Laboratório de Bioquímica Celular, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Lisvane Paes-Vieira
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André Luiz Gomes-Vieira
- Instituto de Química, Departamento de Bioquímica, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Daniela Cosentino-Gomes
- Instituto de Química, Departamento de Bioquímica, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Ana Paula Pereira da Silva
- Instituto de Química, Departamento de Bioquímica, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Naira Ligia Lima Giarola
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Daniel Da Silva
- Laboratório de Enzimologia e Controle do Metabolismo, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mauro Sola-Penna
- Laboratório de Enzimologia e Controle do Metabolismo, Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Antonio Galina
- Laboratorio de Bioenergética e Fisiologia Mitocondrial, Programa de Bioquímica e Biofísica Celular, Instituto de Bioquímica Medica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - José Roberto Meyer-Fernandes
- Laboratório de Bioquímica Celular, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil.
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15
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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16
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Peixoto JF, Oliveira ADS, Monteiro PQ, Gonçalves-Oliveira LF, Andrade-Neto VV, Ferreira VF, Souza-Silva F, Alves CR. In Silico Insights into the Mechanism of Action of Epoxy-α-Lapachone and Epoxymethyl-Lawsone in Leishmania spp. Molecules 2021; 26:molecules26123537. [PMID: 34200517 PMCID: PMC8229338 DOI: 10.3390/molecules26123537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/04/2022] Open
Abstract
Epoxy-α-lapachone (Lap) and Epoxymethyl-lawsone (Law) are oxiranes derived from Lapachol and have been shown to be promising drugs for Leishmaniases treatment. Although, it is known the action spectrum of both compounds affect the Leishmania spp. multiplication, there are gaps in the molecular binding details of target enzymes related to the parasite’s physiology. Molecular docking assays simulations were performed using DockThor server to predict the preferred orientation of both compounds to form stable complexes with key enzymes of metabolic pathway, electron transport chain, and lipids metabolism of Leishmania spp. This study showed the hit rates of both compounds interacting with lanosterol C-14 demethylase (−8.4 kcal/mol to −7.4 kcal/mol), cytochrome c (−10.2 kcal/mol to −8.8 kcal/mol), and glyceraldehyde-3-phosphate dehydrogenase (−8.5 kcal/mol to −7.5 kcal/mol) according to Leishmania spp. and assessed compounds. The set of molecular evidence reinforces the potential of both compounds as multi-target drugs for interrupt the network interactions between parasite enzymes, which can lead to a better efficacy of drugs for the treatment of leishmaniases.
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Affiliation(s)
- Juliana Figueiredo Peixoto
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (J.F.P.); (A.d.S.O.); or (P.Q.M.); (L.F.G.-O.)
| | - Adriane da Silva Oliveira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (J.F.P.); (A.d.S.O.); or (P.Q.M.); (L.F.G.-O.)
| | - Patrícia Queiroz Monteiro
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (J.F.P.); (A.d.S.O.); or (P.Q.M.); (L.F.G.-O.)
| | - Luiz Filipe Gonçalves-Oliveira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (J.F.P.); (A.d.S.O.); or (P.Q.M.); (L.F.G.-O.)
| | - Valter Viana Andrade-Neto
- Laboratório de Bioquímica de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Vitor Francisco Ferreira
- Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói 24241-002, Brazil;
| | - Franklin Souza-Silva
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
- Faculdade de Ciências Biológicas e da Saúde, Universidade Iguaçu, Avenida Abílio Augusto Távora, 2134, Dom Rodrigo, Nova Iguaçu CEP 26260-045, Brazil
- Correspondence: (F.S.-S.); (C.R.A.)
| | - Carlos Roberto Alves
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (J.F.P.); (A.d.S.O.); or (P.Q.M.); (L.F.G.-O.)
- Correspondence: (F.S.-S.); (C.R.A.)
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17
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Wiedmann M, Dranchak PK, Aitha M, Queme B, Collmus CD, Kashipathy MM, Kanter L, Lamy L, Rogers JM, Tao D, Battaile KP, Rai G, Lovell S, Suga H, Inglese J. Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases. J Biol Chem 2021; 296:100628. [PMID: 33812994 PMCID: PMC8113725 DOI: 10.1016/j.jbc.2021.100628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/11/2023] Open
Abstract
Catalysis of human phosphoglycerate mutase is dependent on a 2,3-bisphosphoglycerate cofactor (dPGM), whereas the nonhomologous isozyme in many parasitic species is cofactor independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure–activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized Caenorhabditis elegans iPGM, measured as fold enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using cocrystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from Brugia malayi, Onchocerca volvulus, Dirofilaria immitis, and Escherichia coli, is achieved by a codependence between (1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ in the iPGM phosphatase domain and (2) shape complementarity surrounding the macrocyclic core at the phosphotransferase–phosphatase domain interface. Our results show that the high-affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.
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Affiliation(s)
- Mareike Wiedmann
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Mahesh Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Bryan Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Christopher D Collmus
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Maithri M Kashipathy
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Liza Kanter
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Laurence Lamy
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Joseph M Rogers
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kevin P Battaile
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Scott Lovell
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan.
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
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18
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Chan-Bacab MJ, Reyes-Estebanez MM, Camacho-Chab JC, Ortega-Morales BO. Microorganisms as a Potential Source of Molecules to Control Trypanosomatid Diseases. Molecules 2021; 26:molecules26051388. [PMID: 33806654 PMCID: PMC7962016 DOI: 10.3390/molecules26051388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022] Open
Abstract
Trypanosomatids are the causative agents of leishmaniasis and trypanosomiasis, which affect about 20 million people in the world’s poorest countries, leading to 95,000 deaths per year. They are often associated with malnutrition, weak immune systems, low quality housing, and population migration. They are generally recognized as neglected tropical diseases. New drugs against these parasitic protozoa are urgently needed to counteract drug resistance, toxicity, and the high cost of commercially available drugs. Microbial bioprospecting for new molecules may play a crucial role in developing a new generation of antiparasitic drugs. This article reviews the current state of the available literature on chemically defined metabolites of microbial origin that have demonstrated antitrypanosomatid activity. In this review, bacterial and fungal metabolites are presented; they originate from a range of microorganisms, including cyanobacteria, heterotrophic bacteria, and filamentous fungi. We hope to provide a useful overview for future research to identify hits that may become the lead compounds needed to accelerate the discovery of new drugs against trypanosomatids.
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19
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McNae IW, Kinkead J, Malik D, Yen LH, Walker MK, Swain C, Webster SP, Gray N, Fernandes PM, Myburgh E, Blackburn EA, Ritchie R, Austin C, Wear MA, Highton AJ, Keats AJ, Vong A, Dornan J, Mottram JC, Michels PAM, Pettit S, Walkinshaw MD. Fast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice. Nat Commun 2021; 12:1052. [PMID: 33594070 PMCID: PMC7887271 DOI: 10.1038/s41467-021-21273-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The parasitic protist Trypanosoma brucei is the causative agent of Human African Trypanosomiasis, also known as sleeping sickness. The parasite enters the blood via the bite of the tsetse fly where it is wholly reliant on glycolysis for the production of ATP. Glycolytic enzymes have been regarded as challenging drug targets because of their highly conserved active sites and phosphorylated substrates. We describe the development of novel small molecule allosteric inhibitors of trypanosome phosphofructokinase (PFK) that block the glycolytic pathway resulting in very fast parasite kill times with no inhibition of human PFKs. The compounds cross the blood brain barrier and single day oral dosing cures parasitaemia in a stage 1 animal model of human African trypanosomiasis. This study demonstrates that it is possible to target glycolysis and additionally shows how differences in allosteric mechanisms may allow the development of species-specific inhibitors to tackle a range of proliferative or infectious diseases.
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Affiliation(s)
- Iain W McNae
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - James Kinkead
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Divya Malik
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Li-Hsuan Yen
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Martin K Walker
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | | | - Scott P Webster
- Centre for Cardiovascular Science, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Nick Gray
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Peter M Fernandes
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Elizabeth A Blackburn
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Ryan Ritchie
- Institute of Infection Immunity and Inflammation, College of Medical Veterinary Life-Sciences, University of Glasgow, Glasgow, UK
| | - Carol Austin
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Martin A Wear
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Adrian J Highton
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Andrew J Keats
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Antonio Vong
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK
| | - Jacqueline Dornan
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Paul A M Michels
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Simon Pettit
- Selcia Ltd., Fyfield Business and Research Park, Fyfield Road, Ongar, Essex, UK.
| | - Malcolm D Walkinshaw
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.
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20
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Omolabi KF, Odeniran PO, Olotu FA, S Soliman ME. A Mechanistic Probe into the Dual Inhibition of T. cruzi Glucokinase and Hexokinase in Chagas Disease Treatment - A Stone Killing Two Birds? Chem Biodivers 2021; 18:e2000863. [PMID: 33411971 DOI: 10.1002/cbdv.202000863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/07/2021] [Indexed: 01/15/2023]
Abstract
Glucokinase (GLK) and Hexokinase (HK) have been characterized as essential targets in Trypanosoma cruzi (Tc)-mediated infection. A recent study reported the propensity of the concomitant inhibition of TcGLK and TcHK by compounds GLK2-003 and GLK2-004, thereby presenting an efficient approach in Chagas disease treatment. We investigated this possibility using atomic and molecular scaling methods. Sequence alignment of TcGLK and TcHK revealed that both proteins shared approximately 33.3 % homology in their glucose/inhibitor binding sites. The total binding free energies of GLK2-003 and GLK2-004 were favorable in both proteins. PRO92 and THR185 were pivotal to the binding and stabilization of the ligands in TcGLK, likewise their conserved counterparts, PRO163 and THR237 in TcHK. Both compounds also induced a similar pattern of perturbations in both TcGLK and TcHK secondary structure. Findings from this study therefore provide insights into the underlying mechanisms of dual inhibition exhibited by the compounds. These results can pave way to discover and optimize novel dual Tc inhibitors with favorable pharmacokinetics properties eventuating in the mitigation of Chagas disease.
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Affiliation(s)
- Kehinde F Omolabi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Paul O Odeniran
- Department of Veterinary Parasitology and Entomology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, 200001, Nigeria
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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21
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de Castro Andreassa E, Santos MDMD, Wassmandorf R, Wippel HH, Carvalho PC, Fischer JDSDG, Souza TDACBD. Proteomic changes in Trypanosoma cruzi epimastigotes treated with the proapoptotic compound PAC-1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140582. [PMID: 33285319 DOI: 10.1016/j.bbapap.2020.140582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]
Abstract
Apoptosis is a highly regulated process of cell death in metazoans. Therefore, understanding the biochemical changes associated with apoptosis-like death in Trypanosoma cruzi is key to drug development. PAC-1 was recently shown to induce apoptosis in T. cruzi; with this as motivation, we used quantitative proteomics to unveil alterations of PAC-1-treated versus untreated epimastigotes. The PAC-1 treatment reduced the abundance of putative vesicle-associated membrane protein, putative eukaryotic translation initiation factor 1 eIF1, coatomer subunit beta, putative amastin, and a putative cytoskeleton-associated protein. Apoptosis-like signaling also increases the abundance of proteins associated with actin cytoskeleton remodeling, cell polarization, apoptotic signaling, phosphorylation, methylation, ergosterol biosynthesis, vacuolar proteins associated with autophagy, and flagellum motility. We shortlist seventeen protein targets for possible use in chemotherapy for Chagas disease. Almost all differentially abundant proteins belong to a family of proteins previously associated with apoptosis in metazoans, suggesting that the apoptotic pathway's key functions have been preserved from trypanosomatids and metazoans. SIGNIFICANCE: Approximately 8 million people worldwide are infected with Trypanosoma cruzi. The treatment of Chagas disease comprises drugs with severe side effects, thus limiting their application. Thus, developing new pharmaceutical solutions is relevant, and several molecules targeting apoptosis are therapeutically efficient for parasitic, cardiac, and neurological diseases. Apoptotic processes lead to specific morphological features that have been previously observed in T. cruzi. Here, we investigate changes in epimastigotes' proteomic profile treated with the proapoptotic compound PAC-1, providing data concerning the regulation of both metabolic and cellular processes in nonmetazoan apoptotic cells. We shortlist seventeen protein target candidates for use in chemotherapy for Chagas disease.
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Affiliation(s)
- Emanuella de Castro Andreassa
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Marlon Dias Mariano Dos Santos
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Rafaela Wassmandorf
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Helisa Helena Wippel
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
| | - Paulo Costa Carvalho
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, FIOCRUZ-PR, Curitiba, PR, 80320-290, Brazil
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22
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Galbiati A, Zana A, Conti P. Covalent inhibitors of GAPDH: From unspecific warheads to selective compounds. Eur J Med Chem 2020; 207:112740. [PMID: 32898762 DOI: 10.1016/j.ejmech.2020.112740] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/23/2020] [Accepted: 08/05/2020] [Indexed: 11/18/2022]
Abstract
Targeting glycolysis is an attractive approach for the treatment of a wide range of pathologies, such as various tumors and parasitic infections. Due to its pivotal role in the glycolysis, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) represents a rate-limiting enzyme in those cells that mostly, or exclusively rely on this pathway for energy production. In this context, GAPDH inhibition can be a valuable approach for the development of anticancer and antiparasitic drugs. In addition to its glycolytic role, GAPDH possesses several moonlight functions, whose deregulation is involved in some pathological conditions. Covalent modification on different amino acids of GAPDH, in particular on cysteine residues, can lead to a modulation of the enzyme activity. The selectivity towards specific cysteine residues is essential to achieve a specific phenotypic effect. In this work we report an extensive overview of the latest advances on the numerous compounds able to inhibit GAPDH through the covalent binding to cysteine residues, ranging from endogenous metabolites and xenobiotics, which may serve as pharmacological tools to actual drug-like compounds with promising therapeutic perspectives. Furthermore, we focused on the potentialities of the different warheads, shedding light on the possibility to exploit a combination of a finely tuned electrophilic group with a well-designed recognition moiety. These findings can provide useful information for the rational design of novel covalent inhibitors of GAPDH, with the final goal to expand the current treatment options.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy.
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milano, Italy
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23
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Forlemu NY, Sloop J. Molecular dynamics simulations of the interactions between triose phosphate isomerase and sulfonamides. PEERJ PHYSICAL CHEMISTRY 2020. [DOI: 10.7717/peerj-pchem.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malaria is a disease with debilitating health and negative economic impacts in regions at high risk of infection. Parasitic resistance and side effects of current antimalarial drugs are major setbacks to the successful campaigns that have reduced malaria incidence by 40% in the last decade. The parasite’s dependence on glycolysis for energy requirements makes pathway enzymes suitable targets for drug development. Specifically, triose phosphate isomerase (TPI) from Plasmodium falciparum (pTPI) and human (hTPI) cells show striking structural features that can be used in development of new antimalarial agents. In this study MD simulations were used to characterize binding sites on hTPI and pTPI interactions with sulfonamides. The molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method was used to estimate the interaction energies of four sulfonamide-TPI docked complexes. A unique combination of key residues at the dimer interface of pTPI is responsible for the observed selective affinity to pTPI compared to hTPI. The representative sulfonamide; 4-amino-N-(3,5-dimethylphenyl)-3-fluorbenzenesulfonamide (sulfaE) shows a strong affinity with pTPI (dimer interface, −42.91 kJ/mol and active site region, −71.62 kJ/mol), hTPI (dimer interface, −41.32 kJ/mol and active site region, −84.40 kJ/mol). Strong and favorable Van der Waals interactions and increases in non-polar solvation energies explain the difference in affinity between pTPI with sulfaE compared to hTPI at the dimer interface. This is an indication that the dimer interface of TPI glycolytic enzyme is vital for development of sulfonamide based antimalarial drugs.
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24
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Repurposing bioenergetic modulators against protozoan parasites responsible for tropical diseases. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:17-27. [PMID: 32829099 PMCID: PMC7452664 DOI: 10.1016/j.ijpddr.2020.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/30/2022]
Abstract
Malaria, leishmaniasis and trypanosomiasis are arthropod-borne, parasitic diseases that constitute a major global health problem. They are generally found in developing countries, where lack of access to preventive tools and treatment hinders their management. Because these parasites share an increased demand on glucose consumption with most cancer cells, six compounds used in anti-tumoral research were selected to be tested as antiparasitic agents in in vitro models of Leishmania infantum, Trypanosoma brucei, T. cruzi, and Plasmodium falciparum: dichloroacetic acid (DCA), 3-bromopyruvic acid (3BP), 2-deoxy-D-glucose (2DG), lonidamine (LND), metformin (MET), and sirolimus (SIR). No parasite-killing activity was found in L. infantum promastigotes, whereas DCA and 3BP reduced the burden of intra-macrophagic amastigotes. For T. brucei all selected compounds, but 2DG, decreased parasite survival. DCA, 2DG, LND and MET showed parasite-killing activity in T. cruzi. Finally, anti-plasmodial activity was found for DCA, 2DG, LND, MET and SIR. These results reinforce the hypothesis that drugs with proven efficacy in the treatment of cancer by interfering with ATP production, proliferation, and survival cell strategies might be useful in treating threatening parasitic diseases and provide new opportunities for their repurposing. Parasitic diseases are prevalent among the poorest of the poor. Some parasitic protists degrade glucose into CO2 even aerobically making this a target. Degrading glucose into CO2 (Warburg effect) is also characteristic for cancer cells. Repurposing cancer glycolysis blockers may provide cost-effective treatments for the poorest.
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25
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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26
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Pinto Torres JE, Yuan M, Goossens J, Versées W, Caljon G, Michels PA, Walkinshaw MD, Magez S, Sterckx YGJ. Structural and kinetic characterization of Trypanosoma congolense pyruvate kinase. Mol Biochem Parasitol 2020; 236:111263. [PMID: 32084384 DOI: 10.1016/j.molbiopara.2020.111263] [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: 12/01/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 11/18/2022]
Abstract
Trypanosoma are blood-borne parasites and are the causative agents of neglected tropical diseases (NTDs) affecting both humans and animals. These parasites mainly rely on glycolysis for their energy production within the mammalian host, which is why trypanosomal glycolytic enzymes have been pursued as interesting targets for the development of trypanocidal drugs. The structure-function relationships of pyruvate kinases (PYKs) from trypanosomatids (Trypanosoma and Leishmania) have been well-studied within this context. In this paper, we describe the structural and enzymatic characterization of PYK from T. congolense (TcoPYK), the main causative agent of Animal African Trypanosomosis (AAT), by employing a combination of enzymatic assays, thermal unfolding studies and X-ray crystallography.
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Affiliation(s)
- Joar Esteban Pinto Torres
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Meng Yuan
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Julie Goossens
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Paul A Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Michael Swann Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Stefan Magez
- Research Unit for Cellular and Molecular Immunology (CMIM), Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Ghent University Global Campus, Songdomunhwa-Ro 119, Yeonsu-Gu, 406-840 Incheon, South Korea
| | - Yann G-J Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium.
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27
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Kwofie SK, Broni E, Dankwa B, Enninful KS, Kwarko GB, Darko L, Durvasula R, Kempaiah P, Rathi B, Miller Iii WA, Yaya A, Wilson MD. Outwitting an Old Neglected Nemesis: A Review on Leveraging Integrated Data-Driven Approaches to Aid in Unraveling of Leishmanicides of Therapeutic Potential. Curr Top Med Chem 2020; 20:349-366. [PMID: 31994465 DOI: 10.2174/1568026620666200128160454] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/20/2019] [Accepted: 09/12/2019] [Indexed: 11/22/2022]
Abstract
The global prevalence of leishmaniasis has increased with skyrocketed mortality in the past decade. The causative agent of leishmaniasis is Leishmania species, which infects populations in almost all the continents. Prevailing treatment regimens are consistently inefficient with reported side effects, toxicity and drug resistance. This review complements existing ones by discussing the current state of treatment options, therapeutic bottlenecks including chemoresistance and toxicity, as well as drug targets. It further highlights innovative applications of nanotherapeutics-based formulations, inhibitory potential of leishmanicides, anti-microbial peptides and organometallic compounds on leishmanial species. Moreover, it provides essential insights into recent machine learning-based models that have been used to predict novel leishmanicides and also discusses other new models that could be adopted to develop fast, efficient, robust and novel algorithms to aid in unraveling the next generation of anti-leishmanial drugs. A plethora of enriched functional genomic, proteomic, structural biology, high throughput bioassay and drug-related datasets are currently warehoused in both general and leishmania-specific databases. The warehoused datasets are essential inputs for training and testing algorithms to augment the prediction of biotherapeutic entities. In addition, we demonstrate how pharmacoinformatics techniques including ligand-, structure- and pharmacophore-based virtual screening approaches have been utilized to screen ligand libraries against both modeled and experimentally solved 3D structures of essential drug targets. In the era of data-driven decision-making, we believe that highlighting intricately linked topical issues relevant to leishmanial drug discovery offers a one-stop-shop opportunity to decipher critical literature with the potential to unlock implicit breakthroughs.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana.,West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana.,Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Bismark Dankwa
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra, Ghana
| | - Kweku S Enninful
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra, Ghana
| | - Gabriel B Kwarko
- West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Louis Darko
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Ravi Durvasula
- Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States
| | - Prakasha Kempaiah
- Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States
| | - Brijesh Rathi
- Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States.,Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi, 110007, India
| | - Whelton A Miller Iii
- Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States.,Department of Chemistry, Physics, & Engineering, Lincoln University, Lincoln University, PA 19352, United States.,Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, United States
| | - Abu Yaya
- Department of Materials Science and Engineering, College of Basic & Applied Sciences, University of Ghana, Legon, Ghana
| | - Michael D Wilson
- Department of Medicine, Loyola University Chicago, Loyola University Medical Center, Maywood, IL 60153, United States.,Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra, Ghana
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28
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Jimenez-Sandoval P, Castro-Torres E, González-González R, Díaz-Quezada C, Gurrola M, Camacho-Manriquez LD, Leyva-Navarro L, Brieba LG. Crystal structures of Triosephosphate Isomerases from Taenia solium and Schistosoma mansoni provide insights for vaccine rationale and drug design against helminth parasites. PLoS Negl Trop Dis 2020; 14:e0007815. [PMID: 31923219 PMCID: PMC6980832 DOI: 10.1371/journal.pntd.0007815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/23/2020] [Accepted: 09/27/2019] [Indexed: 12/18/2022] Open
Abstract
Triosephosphate isomerases (TPIs) from Taenia solium (TsTPI) and
Schistosoma mansoni (SmTPI) are potential vaccine and drug
targets against cysticercosis and schistosomiasis, respectively. This is due to
the dependence of parasitic helminths on glycolysis and because those proteins
elicit an immune response, presumably due to their surface localization. Here we
report the crystal structures of TsTPI and SmTPI in complex with
2-phosphoglyceric acid (2-PGA). Both TPIs fold into a dimeric (β-α)8
barrel in which the dimer interface consists of α-helices 2, 3, and 4, and
swapping of loop 3. TPIs from parasitic helminths harbor a region of three amino
acids knows as the SXD/E insert (S155 to E157 and S157 to D159 in TsTPI and
SmTPI, respectively). This insert is located between α5 and β6 and is proposed
to be the main TPI epitope. This region is part of a solvent-exposed
310–helix that folds into a hook-like structure. The crystal
structures of TsTPI and SmTPI predicted conformational epitopes that could be
used for vaccine design. Surprisingly, the epitopes corresponding to the SXD/E
inserts are not the ones with the greatest immunological potential. SmTPI, but
not TsTPI, habors a sole solvent exposed cysteine (SmTPI-S230) and alterations
in this residue decrease catalysis. The latter suggests that thiol-conjugating
agents could be used to target SmTPI. In sum, the crystal structures of SmTPI
and TsTPI are a blueprint for targeted schistosomiasis and cysticercosis drug
and vaccine development. Because of the worldwide prevalence of schistosomiasis and cysticercosis, it is
critical to develop drugs and vaccines against their causative agents. The
glycolytic enzyme triosephosphate isomerase (TPI) is a dual-edged sword against
diseases caused by parasitic helminths. This is because helminths heavily depend
on glycolysis for energy and because the surface localization exhibited by TPIs
that elicits an immune response against those organisms. Here we provide the
crystal structures TPIs from Taenia solium and
Schistosoma mansoni as a first step for vaccine and drug
design. As a proof of concept we found that modifications in the single solvent
exposed cysteine of TPI from S. mansoni
decreases catalysis, making this enzyme a novel target against
schistosomiasis.
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Affiliation(s)
- Pedro Jimenez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Eduardo Castro-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Rogelio González-González
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Corina Díaz-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Misraim Gurrola
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Laura D. Camacho-Manriquez
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Lucia Leyva-Navarro
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad,
Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato,
México
- * E-mail:
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29
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In silico prediction of a new lead compound targeting enolase of trypanosomatids through structure-based virtual screening and molecular dynamic studies. J Mol Model 2020; 26:23. [PMID: 31912304 DOI: 10.1007/s00894-019-4284-0] [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: 01/17/2019] [Accepted: 12/20/2019] [Indexed: 10/25/2022]
Abstract
Enolase is one of the key glycolytic metalloenzyme in many organisms, and it is a potential therapeutic target including trypanosomatids. Sequence and structural analysis of enolase of Trypanosoma bruzi (TbENO), Trypanosoma cruzi (TcENO) and Leishmania donovani (LdENO) revealed conserved sequence pattern and structural features. Hence identification of an inhibitor against enolase of one trypanosomatid organism may have similar effects on enolase of homologous organisms belonging to same family. In the process to identify potent inhibitor compounds against TbENO by in silico methods, compounds containing the substructures of substrate, i.e. phosphoenolpyruvate (PEP) and the well-known inhibitors, fluoro-2-phosphono-acetohydroxamate (FPAH) and phosphono-acetohydroxamate (PAH), were collected. Virtual screening and induced fit docking studies were carried out to explore compounds that have better binding affinity than PEP and FPAH. PPPi was found to be the top hit exhibiting significant binding affinity towards enolase. Glide energy values of two other compounds represented by PubChem ID: 511392 and 101803456 was in good agreement with PEP and PAH. TbENO-PPPi complex was subjected to molecular orbital analysis and molecular dynamic studies by considering its remarkable binding affinity as it could be a potent inhibitor of enolase. Despite being an endogenous compound, based on the results of this study, we highlight PPPi to be a lead compound, and its structure can be treated as a model for further chemical modifications to obtain more potent antagonists.
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Voronin D, Schnall E, Grote A, Jawahar S, Ali W, Unnasch TR, Ghedin E, Lustigman S. Pyruvate produced by Brugia spp. via glycolysis is essential for maintaining the mutualistic association between the parasite and its endosymbiont, Wolbachia. PLoS Pathog 2019; 15:e1008085. [PMID: 31568486 PMCID: PMC6791551 DOI: 10.1371/journal.ppat.1008085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/14/2019] [Accepted: 09/16/2019] [Indexed: 01/01/2023] Open
Abstract
Human parasitic nematodes are the causative agents of lymphatic filariasis (elephantiasis) and onchocerciasis (river blindness), diseases that are endemic to more than 80 countries and that consistently rank in the top ten for the highest number of years lived with disability. These filarial nematodes have evolved an obligate mutualistic association with an intracellular bacterium, Wolbachia, a symbiont that is essential for the successful development, reproduction, and survival of adult filarial worms. Elimination of the bacteria causes adult worms to die, making Wolbachia a primary target for developing new interventional tools to combat filariases. To further explore Wolbachia as a promising indirect macrofilaricidal drug target, the essential cellular processes that define the symbiotic Wolbachia-host interactions need to be identified. Genomic analyses revealed that while filarial nematodes encode all the enzymes necessary for glycolysis, Wolbachia does not encode the genes for three glycolytic enzymes: hexokinase, 6-phosphofructokinase, and pyruvate kinase. These enzymes are necessary for converting glucose into pyruvate. Wolbachia, however, has the full complement of genes required for gluconeogenesis starting with pyruvate, and for energy metabolism via the tricarboxylic acid cycle. Therefore, we hypothesized that Wolbachia might depend on host glycolysis to maintain a mutualistic association with their parasitic host. We did conditional experiments in vitro that confirmed that glycolysis and its end-product, pyruvate, sustain this symbiotic relationship. Analysis of alternative sources of pyruvate within the worm indicated that the filarial lactate dehydrogenase could also regulate the local intracellular concentration of pyruvate in proximity to Wolbachia and thus help control bacterial growth via molecular interactions with the bacteria. Lastly, we have shown that the parasite's pyruvate kinase, the enzyme that performs the last step in glycolysis, could be a potential novel anti-filarial drug target. Establishing that glycolysis is an essential component of symbiosis in filarial worms could have a broader impact on research focused on other intracellular bacteria-host interactions where the role of glycolysis in supporting intracellular survival of bacteria has been reported.
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Affiliation(s)
- Denis Voronin
- Molecular Parasitology, New York Blood Center, New York, New York, United States of America
| | - Emily Schnall
- Molecular Parasitology, New York Blood Center, New York, New York, United States of America
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Shabnam Jawahar
- Molecular Parasitology, New York Blood Center, New York, New York, United States of America
| | - Waleed Ali
- Molecular Parasitology, New York Blood Center, New York, New York, United States of America
| | - Thomas R. Unnasch
- Center for Global Health Infectious Disease Research, University of South Florida, College of Public Health, Tampa, Florida, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- College of Global Public Health, New York University, New York, New York, United States of America
| | - Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, New York, United States of America
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Pomel S, Mao W, Ha-Duong T, Cavé C, Loiseau PM. GDP-Mannose Pyrophosphorylase: A Biologically Validated Target for Drug Development Against Leishmaniasis. Front Cell Infect Microbiol 2019; 9:186. [PMID: 31214516 PMCID: PMC6554559 DOI: 10.3389/fcimb.2019.00186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/15/2019] [Indexed: 01/02/2023] Open
Abstract
Leishmaniases are neglected tropical diseases that threaten about 350 million people in 98 countries around the world. In order to find new antileishmanial drugs, an original approach consists in reducing the pathogenic effect of the parasite by impairing the glycoconjugate biosynthesis, necessary for parasite recognition and internalization by the macrophage. Some proteins appear to be critical in this way, and one of them, the GDP-Mannose Pyrophosphorylase (GDP-MP), is an attractive target for the design of specific inhibitors as it is essential for Leishmania survival and it presents significant differences with the host counterpart. Two GDP-MP inhibitors, compounds A and B, have been identified in two distinct studies by high throughput screening and by a rational approach based on molecular modeling, respectively. Compound B was found to be the most promising as it exhibited specific competitive inhibition of leishmanial GDP-MP and antileishmanial activities at the micromolar range with interesting selectivity indexes, as opposed to compound A. Therefore, compound B can be used as a pharmacological tool for the development of new specific antileishmanial drugs.
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Affiliation(s)
- Sébastien Pomel
- UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Wei Mao
- UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Tâp Ha-Duong
- UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Christian Cavé
- UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Philippe M Loiseau
- UMR 8076 CNRS BioCIS, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
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Landfear SM. Protean permeases: Diverse roles for membrane transport proteins in kinetoplastid protozoa. Mol Biochem Parasitol 2018; 227:39-46. [PMID: 30590069 DOI: 10.1016/j.molbiopara.2018.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 11/26/2022]
Abstract
Kinetoplastid parasites such as Trypanosoma brucei, Trypanosoma cruzi, and Leishmania species rely upon their insect and vertebrate hosts to provide a plethora of nutrients throughout their life cycles. Nutrients and ions critical for parasite survival are taken up across the parasite plasma membrane by transporters and channels, polytopic membrane proteins that provide substrate-specific pores across the hydrophobic barrier. However, transporters and channels serve a wide range of biological functions beyond uptake of nutrients. This article highlights the diversity of activities that these integral membrane proteins serve and underscores the emerging complexity of their functions.
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Affiliation(s)
- Scott M Landfear
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, 97239, USA.
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Buechner GS, Millington ME, Perry K, D'Antonio EL. The crystal structure of glucokinase from Leishmania braziliensis. Mol Biochem Parasitol 2018; 227:47-52. [PMID: 30571993 DOI: 10.1016/j.molbiopara.2018.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 11/30/2022]
Abstract
Glucokinase from pathogenic protozoa of the genus Leishmania is a potential drug target for the chemotherapeutic treatment against leishmaniasis because this enzyme is located at a nodal point between two critically important metabolic pathways, glycolysis and the pentose phosphate pathway (PPP). L. braziliensis glucokinase (LbGlcK) was evaluated for its structural characterization and enzymatic performance. The enzyme catalyzes the phosphorylation of d-glucose with co-substrate ATP to yield the products G6P and ADP. LbGlcK had KM values determined as 6.61 ± 2.63 mM and 0.338 ± 0.080 mM for d-glucose and ATP, respectively. The 1.85 Å resolution X-ray crystal structure of the apo form of LbGlcK was determined and a homodimer was revealed where each subunit (both in open conformations) included the typical small and large domains. Structural comparisons were assessed in relationship to Homo sapiens hexokinase IV and Trypanosoma cruzi glucokinase. Comparisons revealed that all residues important for making hydrogen bonding interactions with d-glucose in the active site and catalysis were strictly conserved. LbGlcK was screened against four glucosamine analogue inhibitors and the stronger inhibitor of the series, HPOP-GlcN, had a Ki value of 56.9 ± 16.6 μM that exhibited competitive inhibition. For the purpose of future structure-based drug design experimentation, L. braziliensis glucokinase was observed to be very similar to T. cruzi glucokinase even though there was a 44% protein sequence identity between the two enzymes.
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Affiliation(s)
- Gregory S Buechner
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC, 29909, USA
| | - Matthew E Millington
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC, 29909, USA
| | - Kay Perry
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
| | - Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC, 29909, USA.
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Heron PW, Abellán-Flos M, Salmon L, Sygusch J. Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase. J Med Chem 2018; 61:10558-10572. [PMID: 30418024 DOI: 10.1021/acs.jmedchem.8b01000] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The glycolytic enzyme aldolase is an emerging drug target in diseases such as cancer and protozoan infections which are dependent on a hyperglycolytic phenotype to synthesize adenosine 5'-triphosphate and metabolic precursors for biomass production. To date, structural information for the enzyme in complex with phosphate-derived inhibitors has been lacking. Thus, we determined the crystal structure of mammalian aldolase in complex with naphthalene 2,6-bisphosphate (1) that served as a template for the design of bisphosphonate-based inhibitors, namely, 2-phosphate-naphthalene 6-bisphosphonate (2), 2-naphthol 6-bisphosphonate (3), and 1-phosphate-benzene 4-bisphosphonate (4). All inhibitors targeted the active site, and the most promising lead, 2, exhibited slow-binding inhibition with an overall inhibition constant of ∼38 nM. Compound 2 inhibited proliferation of HeLa cancer cells, whereas HEK293 cells expressing a normal phenotype were not inhibited. The crystal structures delineated the essential features of high-affinity phosphate-derived inhibitors and provide a template for the development of inhibitors with prophylaxis potential.
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Affiliation(s)
- Paul W Heron
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
| | - Marta Abellán-Flos
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Laurent Salmon
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et des Matériaux D'Orsay (ICMMO) , Univ Paris-Saclay, Univ Paris-Sud, CNRS UMR8182, LabEx LERMIT , rue du doyen Georges Poitou , F-91405 Orsay , France
| | - Jurgen Sygusch
- Département de Biochimie et Médecine Moléculaire , Université de Montréal , CP 6128, Succursale Centre-Ville, Montréal , Québec H3C 3J7 , Canada
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Ong YC, Roy S, Andrews PC, Gasser G. Metal Compounds against Neglected Tropical Diseases. Chem Rev 2018; 119:730-796. [DOI: 10.1021/acs.chemrev.8b00338] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yih Ching Ong
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, 11 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Saonli Roy
- Department of Chemistry, University of Zurich, Wintherthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philip C. Andrews
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Gilles Gasser
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, 11 rue Pierre et Marie Curie, F-75005 Paris, France
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Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor. Biophys J 2018; 115:2114-2126. [PMID: 30467026 DOI: 10.1016/j.bpj.2018.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
Human African trypanosomiasis, or sleeping sickness, is a lethal disease caused by the protozoan parasite Trypanosoma brucei. However, although many efforts have been made to understand the biochemistry of this parasite, drug development has led to treatments that are of limited efficiency and of great toxicity. To develop new drugs, new targets must be identified, and among the several metabolic processes of trypanosomes that have been proposed as drug targets, carbohydrate metabolism (glycolysis and the pentose phosphate pathway (PPP)) appears as a promising one. As far as the PPP is concerned, a limited number of studies are related to the glucose-6-phosphate dehydrogenase. In this work, we have focused on the activity of the second PPP enzyme (6-phospho-gluconolactonase (6PGL)) that transforms 6-phosphogluconolactone into 6-phosphogluconic acid. A lactam analog of the natural substrate has been synthesized, and binding of the ligand to 6PGL has been investigated by NMR titration. The ability of this ligand to inhibit 6PGL has also been demonstrated using ultraviolet experiments, and protein-inhibitor interactions have been investigated through docking calculations and molecular dynamics simulations. In addition, a marginal inhibition of the third enzyme of the PPP (6-phosphogluconate dehydrogenase) was also demonstrated. Our results thus open new prospects for targeting T. brucei.
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K R J, M R, M D, R S, Gad A, K J, P MI, Manuel AT, U C AJ. Feature optimization in high dimensional chemical space: statistical and data mining solutions. BMC Res Notes 2018; 11:463. [PMID: 30001749 PMCID: PMC6044099 DOI: 10.1186/s13104-018-3535-y] [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: 04/01/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022] Open
Abstract
Objectives The primary goal of this experiment is to prioritize molecular descriptors that control the activity of active molecules that could reduce the dimensionality produced during the virtual screening process. It also aims to: (1) develop a methodology for sampling large datasets and the statistical verification of the sampling process, (2) apply screening filter to detect molecules with polypharmacological or promiscuous activity. Results Sampling from large a dataset and its verification were done by applying Z-test. Molecular descriptors were prioritized using principal component analysis (PCA) by eliminating the least influencing ones. The original dimensions were reduced to one-twelfth by the application of PCA. There was a significant improvement in statistical parameter values of virtual screening model which in turn resulted in better screening results. Further improvement of screened results was done by applying Eli Lilly MedChem rules filter that removed molecules with polypharmacological or promiscuous activity. It was also shown that similarities in the activity of compounds were due to the molecular descriptors which were not apparent in prima facie structural studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-3535-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinuraj K R
- Research and Development Centre, Bharathiar University, Marudhamalai Rd, Coimbatore, TamilNadu, 641046, India
| | - Rakhila M
- Research and Development Centre, Bharathiar University, Marudhamalai Rd, Coimbatore, TamilNadu, 641046, India
| | - Dhanalakshmi M
- Research and Development Centre, Bharathiar University, Marudhamalai Rd, Coimbatore, TamilNadu, 641046, India
| | - Sajeev R
- Department of Chemistry, Malabar Christian College, Calicut, Kerala, 673001, India
| | - Akshata Gad
- OSPF-NIAS Drug Discovery Lab, NIAS, Indian Institute of Science Campus, Bengaluru, Karnataka, 560012, India
| | - Jayan K
- Department of Chemistry, Malabar Christian College, Calicut, Kerala, 673001, India
| | - Muhammed Iqbal P
- Department of Chemistry, University of Calicut, Malappuram, Kerala, 673635, India
| | - Andrew Titus Manuel
- OSPF-NIAS Drug Discovery Lab, NIAS, Indian Institute of Science Campus, Bengaluru, Karnataka, 560012, India
| | - Abdul Jaleel U C
- Principal Scientist , Cheminformatics, OSPF-NIAS Drug Discovery Lab, NIAS, Indian Institute of Science Campus, Bengaluru, Karnataka, 560012, India.
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Abstract
INTRODUCTION Parasitic diseases that pose a threat to human life include leishmaniasis - caused by protozoan parasite Leishmania species. Existing drugs have limitations due to deleterious side effects like teratogenicity, high cost and drug resistance. This calls for the need to have an insight into therapeutic aspects of disease. Areas covered: We have identified different drug targets via. molecular, imuunological, metabolic as well as by system biology approaches. We bring these promising drug targets into light so that they can be explored to their maximum. In an effort to bridge the gaps between existing knowledge and prospects of drug discovery, we have compiled interesting studies on drug targets, thereby paving the way for establishment of better therapeutic aspects. Expert opinion: Advancements in technology shed light on many unexplored pathways. Further probing of well established pathways led to the discovery of new drug targets. This review is a comprehensive report on current and emerging drug targets, with emphasis on several metabolic targets, organellar biochemistry, salvage pathways, epigenetics, kinome and more. Identification of new targets can contribute significantly towards strengthening the pipeline for disease elimination.
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Affiliation(s)
- Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221 005, UP, India
| | - Bhawana Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221 005, UP, India
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da Silva RA, Pereira LDM, Silveira MC, Jardim R, de Miranda AB. Mining of potential drug targets through the identification of essential and analogous enzymes in the genomes of pathogens of Glycine max, Zea mays and Solanum lycopersicum. PLoS One 2018; 13:e0197511. [PMID: 29799863 PMCID: PMC5969768 DOI: 10.1371/journal.pone.0197511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/03/2018] [Indexed: 01/19/2023] Open
Abstract
Pesticides are one of the most widely used pest and disease control measures in plant crops and their indiscriminate use poses a direct risk to the health of populations and environment around the world. As a result, there is a great need for the development of new, less toxic molecules to be employed against plant pathogens. In this work, we employed an in silico approach to study the genes coding for enzymes of the genomes of three commercially important plants, soybean (Glycine max), tomato (Solanum lycopersicum) and corn (Zea mays), as well as 15 plant pathogens (4 bacteria and 11 fungi), focusing on revealing a set of essential and non-homologous isofunctional enzymes (NISEs) that could be prioritized as drug targets. By combining sequence and structural data, we obtained an initial set of 568 cases of analogy, of which 97 were validated and further refined, revealing a subset of 29 essential enzymatic activities with a total of 119 different structural forms, most belonging to central metabolic routes, including the carbohydrate metabolism, the metabolism of amino acids, among others. Further, another subset of 26 enzymatic activities possess a tertiary structure specific for the pathogen, not present in plants, men and Apis mellifera, which may be of importance for the development of specific enzymatic inhibitors against plant diseases that are less harmful to humans and the environment.
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Affiliation(s)
| | | | | | - Rodrigo Jardim
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
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Roca C, Sebastián-Pérez V, Campillo NE. In silico Tools for Target Identification and Drug Molecular Docking in Leishmania. DRUG DISCOVERY FOR LEISHMANIASIS 2017. [DOI: 10.1039/9781788010177-00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neglected tropical diseases represent a significant health burden in large parts of the world. Drug discovery is currently a key bottleneck in the pipeline of these diseases. In this chapter, the in silico approaches used for the processes involved in drug discovery, identification and validation of druggable Leishmania targets, and design and optimisation of new anti-leishmanial drugs are discussed. We also provide a general view of the different computational tools that can be employed in pursuit of this aim, along with the most interesting cases found in the literature.
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Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
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Saidin S, Othman N, Noordin R. In Vitro Testing of Potential Entamoeba histolytica Pyruvate Phosphate Dikinase Inhibitors. Am J Trop Med Hyg 2017; 97:1204-1213. [PMID: 28820699 DOI: 10.4269/ajtmh.17-0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Adverse effects and resistance to metronidazole have motivated the search for new antiamoebic agents against Entamoeba histolytica. Control of amoeba growth may be achieved by inhibiting the function of the glycolytic enzyme and pyruvate phosphate dikinase (PPDK). In this study, we screened 10 compounds using an in vitro PPDK enzyme assay. These compounds were selected from a virtual screening of compounds in the National Cancer Institute database. The antiamoebic activity of the selected compounds was also evaluated by determining minimal inhibitory concentrations (MICs) and IC50 values using the nitro-blue tetrazolium reduction assay. Seven of the 10 compounds showed inhibitory activities against the adenosine triphosphate (ATP)/inorganic phosphate binding site of the ATP-grasp domain. Two compounds, NSC349156 (pancratistatin) and NSC228137 (7-ethoxy-4-[4-methylphenyl] sulfonyl-3-oxido-2, 1, 3-benzoxadiazol-3-ium), exhibited inhibitory effects on the growth of E. histolytica trophozoites with MIC values of 25 and 50 μM, and IC50 values of 14 and 20.7 μM, respectively.
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Affiliation(s)
- Syazwan Saidin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Nurulhasanah Othman
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang, Malaysia
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Olivares-Illana V, Riveros-Rosas H, Cabrera N, Tuena de Gómez-Puyou M, Pérez-Montfort R, Costas M, Gómez-Puyou A. A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease. Proteins 2017; 85:1190-1211. [PMID: 28378917 DOI: 10.1002/prot.25299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
Triosephosphate isomerase (TIM) is a ubiquitous enzyme, which appeared early in evolution. TIM is responsible for obtaining net ATP from glycolysis and producing an extra pyruvate molecule for each glucose molecule, under aerobic and anaerobic conditions. It is placed in a metabolic crossroad that allows a quick balance of the triose phosphate aldolase produced by glycolysis, and is also linked to lipid metabolism through the alternation of glycerol-3-phosphate and the pentose cycle. TIM is one of the most studied enzymes with more than 199 structures deposited in the PDB. The interest for this enzyme stems from the fact that it is involved in glycolysis, but also in aging, human diseases and metabolism. TIM has been a target in the search for chemical compounds against infectious diseases and is a model to study catalytic features. Until February 2017, 62% of all residues of the protein have been studied by mutagenesis and/or using other approaches. Here, we present a detailed and comprehensive recompilation of the reported effects on TIM catalysis, stability, druggability and human disease produced by each of the amino acids studied, contributing to a better understanding of the properties of this fundamental protein. The information reviewed here shows that the role of the noncatalytic residues depend on their molecular context, the delicate balance between the short and long-range interactions in concerted action determining the properties of the protein. Each protein should be regarded as a unique entity that has evolved to be functional in the organism to which it belongs. Proteins 2017; 85:1190-1211. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y Cáncer. Instituto de Física, Universidad Autónoma de San Luis Potosí, SLP, 78290, México
| | - Hector Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Marietta Tuena de Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Armando Gómez-Puyou
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
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Golldack A, Henke B, Bergmann B, Wiechert M, Erler H, Blancke Soares A, Spielmann T, Beitz E. Substrate-analogous inhibitors exert antimalarial action by targeting the Plasmodium lactate transporter PfFNT at nanomolar scale. PLoS Pathog 2017; 13:e1006172. [PMID: 28178358 PMCID: PMC5298233 DOI: 10.1371/journal.ppat.1006172] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/07/2017] [Indexed: 12/14/2022] Open
Abstract
Resistance against all available antimalarial drugs calls for novel compounds that hit unexploited targets in the parasite. Here, we show that the recently discovered Plasmodium falciparum lactate/proton symporter, PfFNT, is a valid druggable target, and describe a new class of fluoroalkyl vinylogous acids that potently block PfFNT and kill cultured parasites. The original compound, MMV007839, is derived from the malaria box collection of potent antimalarials with unknown targets and contains a unique internal prodrug principle that reversibly switches between a lipophilic transport form and a polar, substrate-analogous active form. Resistance selection of cultured P. falciparum parasites with sub-lethal concentrations of MMV007839 produced a single nucleotide exchange in the PfFNT gene; this, and functional characterization of the resulting PfFNT G107S validated PfFNT as a novel antimalarial target. From quantitative structure function relations we established the compound binding mode and the pharmacophore. The pharmacophore largely circumvents the resistance mutation and provides the basis for a medicinal chemistry program that targets lactate and proton transport as a new mode of antimalarial action.
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Affiliation(s)
- André Golldack
- Pharmaceutical Institute, Christian-Albrechts-University, Kiel, Germany
| | - Björn Henke
- Pharmaceutical Institute, Christian-Albrechts-University, Kiel, Germany
| | - Bärbel Bergmann
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Marie Wiechert
- Pharmaceutical Institute, Christian-Albrechts-University, Kiel, Germany
| | - Holger Erler
- Pharmaceutical Institute, Christian-Albrechts-University, Kiel, Germany
| | | | - Tobias Spielmann
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Eric Beitz
- Pharmaceutical Institute, Christian-Albrechts-University, Kiel, Germany
- * E-mail:
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Vermelho AB, Capaci GR, Rodrigues IA, Cardoso VS, Mazotto AM, Supuran CT. Carbonic anhydrases from Trypanosoma and Leishmania as anti-protozoan drug targets. Bioorg Med Chem 2017; 25:1543-1555. [PMID: 28161253 DOI: 10.1016/j.bmc.2017.01.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 01/24/2023]
Abstract
Trypanosoma cruzi and Leishmania spp. are protozoa of the Trypanosomatidae family, being the etiological agents of two widespread parasitic diseases, Chagas disease and leishmaniasis, respectively. Both parasites are the focus of worldwide research with the aim to find effective and less toxic drugs than the few ones available so far, and for controlling the spread of the diseases. Carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α- and β-class were recently identified in these protozoans and several studies suggested that they could be new targets for drug development. Sulfonamide, thiol and hydroxamate inhibitors effectively inhibited the α-CA from T. cruzi (TcCA) and the β-CA from L. donovani chagasi (LdccCA) in vitro, and some of them also showed in vivo efficacy in inhibiting the growth of the parasites in animal models of Chagas disease and leishmaniasis. As few therapeutic options are presently available for these orphan diseases, protozoan CA inhibition may represent a novel strategy to address this stringent health problem.
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Affiliation(s)
- Alane B Vermelho
- BIOINOVAR - Biotechnology Laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Giseli R Capaci
- School of Science and Technology and Graduate Studies in Science Education Program, University of Rio Grande, Duque de Caxias, RJ, Brazil
| | - Igor A Rodrigues
- Department of Natural Products and Food, School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Verônica S Cardoso
- BIOINOVAR - Biotechnology Laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Maria Mazotto
- BIOINOVAR - Biotechnology Laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudiu T Supuran
- Neurofarba Department and Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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Forlemu N, Watkins P, Sloop J. Molecular Docking of Selective Binding Affinity of Sulfonamide Derivatives as Potential Antimalarial Agents Targeting the Glycolytic Enzymes: GAPDH, Aldolase and TPI. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ojbiphy.2017.71004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Increased Abundance of Proteins Involved in Resistance to Oxidative and Nitrosative Stress at the Last Stages of Growth and Development of Leishmania amazonensis Promastigotes Revealed by Proteome Analysis. PLoS One 2016; 11:e0164344. [PMID: 27776144 PMCID: PMC5077082 DOI: 10.1371/journal.pone.0164344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/23/2016] [Indexed: 12/23/2022] Open
Abstract
Leishmania amazonensis is one of the major etiological agents of the neglected, stigmatizing disease termed american cutaneous leishmaniasis (ACL). ACL is a zoonosis and rodents are the main reservoirs. Most cases of ACL are reported in Brazil, Bolivia, Colombia and Peru. The biological cycle of the parasite is digenetic because sand fly vectors transmit the motile promastigote stage to the mammalian host dermis during blood meal intakes. The amastigote stage survives within phagocytes of the mammalian host. The purpose of this study is detection and identification of changes in protein abundance by 2DE/MALDI-TOF/TOF at the main growth phases of L. amazonensis promastigotes in axenic culture and the differentiation process that takes place simultaneously. The average number of proteins detected per gel is 202 and the non-redundant cumulative number is 339. Of those, 63 are differentially abundant throughout growth and simultaneous differentiation of L. amazonensis promastigotes. The main finding is that certain proteins involved in resistance to nitrosative and oxidative stress are more abundant at the last stages of growth and differentiation of cultured L. amazonensis promastigotes. These proteins are the arginase, a light variant of the tryparedoxin peroxidase, the iron superoxide dismutase, the regulatory subunit of the protein kinase A and a light HSP70 variant. These data taken together with the decrease of the stress-inducible protein 1 levels are additional evidence supporting the previously described pre-adaptative hypothesis, which consists of preparation in advance towards the amastigote stage.
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D'Antonio EL, Deinema MS, Kearns SP, Frey TA, Tanghe S, Perry K, Roy TA, Gracz HS, Rodriguez A, D'Antonio J. Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase. Mol Biochem Parasitol 2016; 204:64-76. [PMID: 26778112 DOI: 10.1016/j.molbiopara.2015.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 12/10/2015] [Accepted: 12/16/2015] [Indexed: 01/29/2023]
Abstract
Glucokinase and hexokinase from pathogenic protozoa Trypanosoma cruzi are potential drug targets for antiparasitic chemotherapy of Chagas' disease. These glucose kinases phosphorylate d-glucose with co-substrate ATP and yield glucose 6-phosphate and are involved in essential metabolic pathways, such as glycolysis and the pentose phosphate pathway. An inhibitor class was conceived that is selective for T. cruzi glucokinase (TcGlcK) using structure-based drug design involving glucosamine having a linker from the C2 amino that terminates with a hydrophobic group either being phenyl, p-hydroxyphenyl, or dioxobenzo[b]thiophenyl groups. The synthesis and characterization for two of the four compounds are presented while the other two compounds were commercially available. Four high-resolution X-ray crystal structures of TcGlcK inhibitor complexes are reported along with enzyme inhibition constants (Ki) for TcGlcK and Homo sapiens hexokinase IV (HsHxKIV). These glucosamine analogue inhibitors include three strongly selective TcGlcK inhibitors and a fourth inhibitor, benzoyl glucosamine (BENZ-GlcN), which is a similar variant exhibiting a shorter linker. Carboxybenzyl glucosamine (CBZ-GlcN) was found to be the strongest glucokinase inhibitor known to date, having a Ki of 0.71±0.05μM. Also reported are two biologically active inhibitors against in vitro T. cruzi culture that were BENZ-GlcN and CBZ-GlcN, with intracellular amastigote growth inhibition IC50 values of 16.08±0.16μM and 48.73±0.69μM, respectively. These compounds revealed little to no toxicity against mammalian NIH-3T3 fibroblasts and provide a key starting point for further drug development with this class of compound.
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Affiliation(s)
- Edward L D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA.
| | - Mason S Deinema
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Sean P Kearns
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Tyler A Frey
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Scott Tanghe
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | - Kay Perry
- NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Timothy A Roy
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
| | - Hanna S Gracz
- Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, North Carolina 27695, USA
| | - Ana Rodriguez
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | - Jennifer D'Antonio
- Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, South Carolina 29909, USA
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Fluorine-containing benzothiazole as a novel trypanocidal agent: design, in silico study, synthesis and activity evaluation. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1475-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PLoS One 2015; 10:e0137976. [PMID: 26367006 PMCID: PMC4569355 DOI: 10.1371/journal.pone.0137976] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 08/24/2015] [Indexed: 01/02/2023] Open
Abstract
Leishmania infantum, causative agent of visceral leishmaniasis in humans, illustrates a complex lifecycle pertaining to two extreme environments, namely, the gut of the sandfly vector and human macrophages. Leishmania is capable of dynamically adapting and tactically switching between these critically hostile situations. The possible metabolic routes ventured by the parasite to achieve this exceptional adaptation to its varying environments are still poorly understood. In this study, we present an extensively reconstructed energy metabolism network of Leishmania infantum as an attempt to identify certain strategic metabolic routes preferred by the parasite to optimize its survival in such dynamic environments. The reconstructed network consists of 142 genes encoding for enzymes performing 237 reactions distributed across five distinct model compartments. We annotated the subcellular locations of different enzymes and their reactions on the basis of strong literature evidence and sequence-based detection of cellular localization signal within a protein sequence. To explore the diverse features of parasite metabolism the metabolic network was implemented and analyzed as a constraint-based model. Using a systems-based approach, we also put forth an extensive set of lethal reaction knockouts; some of which were validated using published data on Leishmania species. Performing a robustness analysis, the model was rigorously validated and tested for the secretion of overflow metabolites specific to Leishmania under varying extracellular oxygen uptake rate. Further, the fate of important non-essential amino acids in L. infantum metabolism was investigated. Stage-specific scenarios of L. infantum energy metabolism were incorporated in the model and key metabolic differences were outlined. Analysis of the model revealed the essentiality of glucose uptake, succinate fermentation, glutamate biosynthesis and an active TCA cycle as driving forces for parasite energy metabolism and its optimal growth. Finally, through our in silico knockout analysis, we could identify possible therapeutic targets that provide experimentally testable hypotheses.
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50
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Ethyl Pyruvate Emerges as a Safe and Fast Acting Agent against Trypanosoma brucei by Targeting Pyruvate Kinase Activity. PLoS One 2015; 10:e0137353. [PMID: 26340747 PMCID: PMC4560413 DOI: 10.1371/journal.pone.0137353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/14/2015] [Indexed: 12/25/2022] Open
Abstract
Background Human African Trypanosomiasis (HAT) also called sleeping sickness is an infectious disease in humans caused by an extracellular protozoan parasite. The disease, if left untreated, results in 100% mortality. Currently available drugs are full of severe drawbacks and fail to escape the fast development of trypanosoma resistance. Due to similarities in cell metabolism between cancerous tumors and trypanosoma cells, some of the current registered drugs against HAT have also been tested in cancer chemotherapy. Here we demonstrate for the first time that the simple ester, ethyl pyruvate, comprises such properties. Results The current study covers the efficacy and corresponding target evaluation of ethyl pyruvate on T. brucei cell lines using a combination of biochemical techniques including cell proliferation assays, enzyme kinetics, phasecontrast microscopic video imaging and ex vivo toxicity tests. We have shown that ethyl pyruvate effectively kills trypanosomes most probably by net ATP depletion through inhibition of pyruvate kinase (Ki = 3.0±0.29 mM). The potential of ethyl pyruvate as a trypanocidal compound is also strengthened by its fast acting property, killing cells within three hours post exposure. This has been demonstrated using video imaging of live cells as well as concentration and time dependency experiments. Most importantly, ethyl pyruvate produces minimal side effects in human red cells and is known to easily cross the blood-brain-barrier. This makes it a promising candidate for effective treatment of the two clinical stages of sleeping sickness. Trypanosome drug-resistance tests indicate irreversible cell death and a low incidence of resistance development under experimental conditions. Conclusion Our results present ethyl pyruvate as a safe and fast acting trypanocidal compound and show that it inhibits the enzyme pyruvate kinase. Competitive inhibition of this enzyme was found to cause ATP depletion and cell death. Due to its ability to easily cross the blood-brain-barrier, ethyl pyruvate could be considered as new candidate agent to treat the hemolymphatic as well as neurological stages of sleeping sickness.
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