1
|
Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [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: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
Collapse
Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| |
Collapse
|
2
|
van Neer RHP, Dranchak PK, Liu L, Aitha M, Queme B, Kimura H, Katoh T, Battaile KP, Lovell S, Inglese J, Suga H. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. ACS Chem Biol 2022; 17:2284-2295. [PMID: 35904259 PMCID: PMC9900472 DOI: 10.1021/acschembio.2c00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.
Collapse
Affiliation(s)
- R H P van Neer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - P K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - L Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - M Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - B Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - H Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K P Battaile
- New York Structural Biology Center, NSLS-II, Upton, New York 11973, United States
| | - S Lovell
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - H Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| |
Collapse
|
3
|
Duminil P, Davanture M, Oury C, Boex-Fontvieille E, Tcherkez G, Zivy M, Hodges M, Glab N. Arabidopsis thaliana 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 activity requires serine 82 phosphorylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1478-1489. [PMID: 34174129 DOI: 10.1111/tpj.15395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Phosphoglycerate mutases (PGAMs) catalyse the reversible isomerisation of 3-phosphoglycerate and 2-phosphoglycerate, a step of glycolysis. PGAMs can be sub-divided into 2,3-bisphosphoglycerate-dependent (dPGAM) and -independent (iPGAM) enzymes. In plants, phosphoglycerate isomerisation is carried out by cytosolic iPGAM. Despite its crucial role in catabolism, little is known about post-translational modifications of plant iPGAM. In Arabidopsis thaliana, phosphoproteomics analyses have previously identified an iPGAM phosphopeptide where serine 82 is phosphorylated. Here, we show that this phosphopeptide is less abundant in dark-adapted compared to illuminated Arabidopsis leaves. In silico comparison of iPGAM protein sequences and 3D structural modelling of AtiPGAM2 based on non-plant iPGAM enzymes suggest a role for phosphorylated serine in the catalytic reaction mechanism. This is confirmed by the activity (or the lack thereof) of mutated recombinant Arabidopsis iPGAM2 forms, affected in different steps of the reaction mechanism. We thus propose that the occurrence of the S82-phosphopeptide reflects iPGAM2 steady-state catalysis. Based on this assumption, the metabolic consequences of a higher iPGAM activity in illuminated versus darkened leaves are discussed.
Collapse
Affiliation(s)
- Pauline Duminil
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Marlène Davanture
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, PAPPSO, GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Céline Oury
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Edouard Boex-Fontvieille
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, ACT, 2601, Australia
- Institut de Recherche en Horticulture et Semences, Université d'Angers, INRAe, 42 rue Georges Morel, Beaucouzé, 49070, France
| | - Michel Zivy
- INRAE, CNRS, AgroParisTech, Université Paris-Saclay, PAPPSO, GQE-Le Moulon, Gif-sur-Yvette, 91190, France
| | - Michael Hodges
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| | - Nathalie Glab
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAe, CNRS, Université Evry, Université Paris-Saclay, Bat 630, Gif sur Yvette, 91190, France
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Sun L, Vella P, Schnell R, Polyakova A, Bourenkov G, Li F, Cimdins A, Schneider TR, Lindqvist Y, Galperin MY, Schneider G, Römling U. Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium. J Mol Biol 2018; 430:3170-3189. [PMID: 30017920 DOI: 10.1016/j.jmb.2018.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/17/2022]
Abstract
Many bacteria secrete cellulose, which forms the structural basis for bacterial multicellular aggregates, termed biofilms. The cellulose synthase complex of Salmonella typhimurium consists of the catalytic subunits BcsA and BcsB and several auxiliary subunits that are encoded by two divergently transcribed operons, bcsRQABZC and bcsEFG. Expression of the bcsEFG operon is required for full-scale cellulose production, but the functions of its products are not fully understood. This work aimed to characterize the BcsG subunit of the cellulose synthase, which consists of an N-terminal transmembrane fragment and a C-terminal domain in the periplasm. Deletion of the bcsG gene substantially decreased the total amount of BcsA and cellulose production. BcsA levels were partially restored by the expression of the transmembrane segment, whereas restoration of cellulose production required the presence of the C-terminal periplasmic domain and its characteristic metal-binding residues. The high-resolution crystal structure of the periplasmic domain characterized BcsG as a member of the alkaline phosphatase/sulfatase superfamily of metalloenzymes, containing a conserved Zn2+-binding site. Sequence and structural comparisons showed that BcsG belongs to a specific family within alkaline phosphatase-like enzymes, which includes bacterial Zn2+-dependent lipopolysaccharide phosphoethanolamine transferases such as MCR-1 (colistin resistance protein), EptA, and EptC and the Mn2+-dependent lipoteichoic acid synthase (phosphoglycerol transferase) LtaS. These enzymes use the phospholipids phosphatidylethanolamine and phosphatidylglycerol, respectively, as substrates. These data are consistent with the recently discovered phosphoethanolamine modification of cellulose by BcsG and show that its membrane-bound and periplasmic parts play distinct roles in the assembly of the functional cellulose synthase and cellulose production.
Collapse
Affiliation(s)
- Lei Sun
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Peter Vella
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Anna Polyakova
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Annika Cimdins
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden.
| |
Collapse
|
6
|
Structural characterization, biochemical, inhibition and computational studies of Entamoeba histolytica phosphoglycerate mutase: finding hits for a new antiamoebic drug. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
7
|
Nayak A, Akpunarlieva S, Barrett M, Burchmore R. A defined medium for Leishmania culture allows definition of essential amino acids. Exp Parasitol 2018; 185:39-52. [PMID: 29326050 DOI: 10.1016/j.exppara.2018.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 10/18/2022]
Abstract
Axenic culture of Leishmania is generally performed in rich, serum-supplemented media which sustain robust growth over multiple passages. The use of such undefined media, however, obscures proteomic analyses and confounds the study of metabolism. We have established a simple, defined culture medium that supports the sustained growth of promastigotes over multiple passages and which yields parasites that have similar infectivity to macrophages to parasites grown in a conventional semi-defined medium. We have exploited this medium to investigate the amino acid requirements of promastigotes in culture and have found that phenylalanine, tryptophan, arginine, leucine, lysine and valine are essential for viability in culture. Most of the 20 proteogenic amino acids promote growth of Leishmania promastigotes, with the exception of alanine, asparagine, and glycine. This defined medium will be useful for further studies of promastigote substrate requirements, and will facilitate future proteomic and metabolomic analyses.
Collapse
Affiliation(s)
- Archana Nayak
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Snezhana Akpunarlieva
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michael Barrett
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
8
|
Co-factor-independent phosphoglycerate mutase of Leishmania donovani modulates macrophage signalling and promotes T-cell repertoires bearing epitopes for both MHC-I and MHC-II. Parasitology 2017; 145:292-306. [PMID: 29140228 DOI: 10.1017/s0031182017001494] [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] [Indexed: 11/07/2022]
Abstract
Immunoactivation depends upon the antigen potential to modulate T-cell repertoires. The present study has enumerated the effect of 61 kDa recombinant Leishmania donovani co-factor-independent phosphoglycerate mutase (rLd-iPGAM) on mononuclear cells of healthy and treated visceral leishmaniasis subjects as well as on THP-1 cell line. rLd-iPGAM stimulation induced higher expression of interleukin-1β (IL-1β) in the phagocytic cell, its receptor and CD69 on T-cell subsets. These cellular activations resulted in upregulation of host-protective cytokines IL-2, IL-12, IL-17, tumour necrosis factor-α and interferon-γ, and downregulation of IL-4, IL-10 and tumour growth factor-β. This immune polarization was also evidenced by upregulation of nuclear factor-κ light-chain enhancer of activated B cells p50 and regulated expression of suppressor of mother against decapentaplegic protein-4. rLd-iPGAM stimulation also promoted lymphocyte proliferation and boosted the leishmaniacidal activity of macrophages by upregulating reactive oxygen species. It also induced 1·8-fold higher release of nitric oxide (NO) by promoting the transcription of inducible nitric oxide synthase gene. Besides, in silico analysis suggested the presence of major histocompatibility complex class I and II restricted epitopes, which can proficiently trigger CD8+ and CD4+ cells, respectively. This study reports rLd-iPGAM as an effective immunoprophylactic agent, which can be used in future vaccine design.
Collapse
|
9
|
Molecular, biochemical characterization and assessment of immunogenic potential of cofactor-independent phosphoglycerate mutase against Leishmania donovani: a step towards exploring novel vaccine candidate. Parasitology 2017; 145:508-526. [PMID: 28691653 DOI: 10.1017/s0031182017001160] [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] [Indexed: 11/06/2022]
Abstract
Despite immense efforts, vaccine against visceral leishmaniasis has yet not been developed. Earlier our proteomic study revealed a novel protein, cofactor-independent phoshoglycerate mutase (LdiPGAM), an important enzyme in glucose metabolism, in T helper cells type 1 (Th1) stimulatory region of soluble Leishmania donovani antigen. In this study, LdiPGAM was biochemically and molecularly characterized and evaluated for its immunogenicity and prophylactic efficacy against L. donovani. Immunogenicity of recombinant LdiPGAM (rLdiPGAM) was initially assessed in naïve hamsters immunized with it by analysing mRNA expression of inducible nitric oxide (NO) synthase (iNOS) and other Th1/T helper cells type 2 cytokines, which revealed an upregulation of Th1 cytokines along with iNOS. Immunogenicity of rLdiPGAM was further evaluated in lymphocytes of treated Leishmania-infected hamsters and peripheral blood mononuclear cells of Leishmania patients in clinical remission by various parameters, viz. lymphoproliferation assay and NO production (hamsters and patients) and levels of various cytokines (patients). rLdiPGAM induced remarkable Lymphoproliferative response and NO production in treated Leishmania-infected hamsters as well as in patients and increase in interferon gamma (IFN-γ), interleukin-12 (IL-12p40) responses in Leishmania patients in clinical remission. Vaccination with rLdiPGAM exerted considerable prophylactic efficacy (73%) supported by increase in mRNA expression of iNOS, IFN-γ and IL-12p40 with decrease in transforming growth factor beta and interleukin-10. Above results indicate the importance of rLdiPGAM protein as a potential vaccine candidate against visceral leishmaniasis.
Collapse
|
10
|
Yu H, Dranchak P, Li Z, MacArthur R, Munson MS, Mehzabeen N, Baird NJ, Battalie KP, Ross D, Lovell S, Carlow CKS, Suga H, Inglese J. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat Commun 2017; 8:14932. [PMID: 28368002 PMCID: PMC5382265 DOI: 10.1038/ncomms14932] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/13/2017] [Indexed: 11/22/2022] Open
Abstract
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
Collapse
Affiliation(s)
- Hao Yu
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Zhiru Li
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA
| | - Ryan MacArthur
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| | - Matthew S. Munson
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Nurjahan Mehzabeen
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | - Nathan J. Baird
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin P. Battalie
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Scott Lovell
- Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA
| |
Collapse
|
11
|
Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
Collapse
Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| |
Collapse
|
12
|
Tschoeke DA, Nunes GL, Jardim R, Lima J, Dumaresq AS, Gomes MR, de Mattos Pereira L, Loureiro DR, Stoco PH, de Matos Guedes HL, de Miranda AB, Ruiz J, Pitaluga A, Silva FP, Probst CM, Dickens NJ, Mottram JC, Grisard EC, Dávila AM. The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. Evol Bioinform Online 2014; 10:131-53. [PMID: 25336895 PMCID: PMC4182287 DOI: 10.4137/ebo.s13759] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the “Mexicana complex”, reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development.
Collapse
Affiliation(s)
- Diogo A Tschoeke
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Gisele L Nunes
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Jardim
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Joana Lima
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Aline Sr Dumaresq
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Monete R Gomes
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Leandro de Mattos Pereira
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Daniel R Loureiro
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil
| | - Patricia H Stoco
- Laboratório de Protozoologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Herbert Leonel de Matos Guedes
- Laboratório de Inflamação Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Antonio Basilio de Miranda
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jeronimo Ruiz
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Instituto René Rachou (Fiocruz/IRR), Belo Horizonte, MG, Brazil
| | - André Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Floriano P Silva
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Bioquímica de Proteínas e Peptídeos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Christian M Probst
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Instituto Carlos Chagas (Fiocruz/ICC), Curitiba, PR, Brazil
| | - Nicholas J Dickens
- Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Jeremy C Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Immunity, Infection and Inflammation, College of MVLS, University of Glasgow, Glasgow, UK
| | - Edmundo C Grisard
- Laboratório de Protozoologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Alberto Mr Dávila
- Pólo de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (Fiocruz/IOC), Rio de Janeiro, RJ, Brazil. ; Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
13
|
Trypanosomatid phosphoglycerate mutases have multiple conformational and oligomeric states. Biochem Biophys Res Commun 2014; 450:936-41. [DOI: 10.1016/j.bbrc.2014.06.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 06/15/2014] [Indexed: 12/31/2022]
|
14
|
Cofactor independent phosphoglycerate mutase of Brugia malayi induces a mixed Th1/Th2 type immune response and inhibits larval development in the host. BIOMED RESEARCH INTERNATIONAL 2014; 2014:590281. [PMID: 25061608 PMCID: PMC4100390 DOI: 10.1155/2014/590281] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/06/2014] [Accepted: 05/20/2014] [Indexed: 01/24/2023]
Abstract
Lymphatic filariasis is a major debilitating disease, endemic in 72 countries putting more than 1.39 billion people at risk and 120 million are already infected. Despite the significant progress in chemotherapeutic advancements, there is still need for other measures like development of an effective vaccine or discovery of novel drug targets. In this study, structural and immunological characterization of independent phosphoglycerate mutase of filarial parasite Brugia malayi was carried out. Protein was found to be expressed in all major parasite life stages and as an excretory secretory product of adult parasites. Bm-iPGM also reacted to all the categories of human bancroftian patient's sera including endemic normals. In vivo immunological behaviour of protein was determined in immunized BALB/c mice followed by prophylactic analysis in BALB/c mice and Mastomys coucha. Immunization with Bm-iPGM led to generation of a mixed Th1/Th2 type immune response offering 58.2% protection against larval challenge in BALB/c and 65–68% protection in M. coucha. In vitro studies confirmed participation of anti-Bm-iPGM antibodies in killing of B. malayi infective larvae and microfilariae through ADCC mechanism. The present findings reveal potential immunoprotective nature of Bm-iPGM advocating its worth as an antifilarial vaccine candidate.
Collapse
|
15
|
Peysselon F, Launay G, Lisacek F, Duclos B, Ricard-Blum S. Comparative analysis of Leishmania exoproteomes: Implication for host–pathogen interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2653-62. [DOI: 10.1016/j.bbapap.2013.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/06/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
|
16
|
Mercaldi GF, Pereira HM, Cordeiro AT, Michels PAM, Thiemann OH. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase. FEBS J 2012; 279:2012-21. [PMID: 22458781 DOI: 10.1111/j.1742-4658.2012.08586.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphoglycerate mutases (PGAMs) participate in both the glycolytic and the gluconeogenic pathways in reversible isomerization of 3-phosphoglycerate and 2-phosphoglycerate. PGAMs are members of two distinct protein families: enzymes that are dependent on or independent of the 2,3-bisphosphoglycerate cofactor. We determined the X-ray structure of the monomeric Trypanosoma brucei independent PGAM (TbiPGAM) in its apoenzyme form, and confirmed this observation by small angle X-ray scattering data. Comparing the TbiPGAM structure with the Leishmania mexicana independent PGAM structure, previously reported with a phosphoglycerate molecule bound to the active site, revealed the domain movement resulting from active site occupation. The structure reported here shows the interaction between Asp319 and the metal bound to the active site, and its contribution to the domain movement. Substitution of the metal-binding residue Asp319 by Ala resulted in complete loss of independent PGAM activity, and showed for the first time its involvement in the enzyme's function. As TbiPGAM is an attractive molecular target for drug development, the apoenzyme conformation described here provides opportunities for its use in structure-based drug design approaches. Database Structural data for the Trypanosoma brucei 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) has been deposited with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank under code 3NVL.
Collapse
Affiliation(s)
- Gustavo F Mercaldi
- Instituto de Física de São Carlos, Grupo de Cristalografia, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
17
|
Fuad FAA, Fothergill-Gilmore LA, Nowicki MW, Eades LJ, Morgan HP, McNae IW, Michels PAM, Walkinshaw MD. Phosphoglycerate mutase from Trypanosoma brucei is hyperactivated by cobalt in vitro, but not in vivo. Metallomics 2011; 3:1310-7. [PMID: 21993954 DOI: 10.1039/c1mt00119a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Production of ATP by the glycolytic pathway in the mammalian pathogenic stage of protists from the genus Trypanosoma is required for the survival of the parasites. Cofactor-independent phosphoglycerate mutase (iPGAM) is particularly attractive as a drug target because it shows no similarity to the corresponding enzyme in humans, and has also been genetically validated as a target by RNAi experiments. It has previously been shown that trypanosomatid iPGAMs require Co(2+) to reach maximal activity, but the biologically relevant metal has remained unclear. In this paper the metal content in the cytosol of procyclic and bloodstream-form T. brucei (analysed by inductively coupled plasma-optical emission spectroscopy) shows that Mg(2+), Zn(2+) and Fe(2+) were the most abundant, whereas Co(2+) was below the limit of detection (<0.035 μM). The low concentration indicates that Co(2+) is unlikely to be the biologically relevant metal, but that instead, Mg(2+) and/or Zn(2+) may assume this role. Results from metal analysis of purified Leishmania mexicana iPGAM by inductively coupled plasma-mass spectrometry also show high concentrations of Mg(2+) and Zn(2+), and are consistent with this proposal. Our data suggest that in vivo cellular conditions lacking Co(2+) are unable to support the maximal activity of iPGAM, but instead maintain its activity at a relatively low level by using Mg(2+) and/or Zn(2+). The physiological significance of these observations is being pursued by structural, biochemical and biophysical studies.
Collapse
|
18
|
Harding MM, Nowicki MW, Walkinshaw MD. Metals in protein structures: a review of their principal features. CRYSTALLOGR REV 2010. [DOI: 10.1080/0889311x.2010.485616] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Marjorie M. Harding
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Matthew W. Nowicki
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Malcolm D. Walkinshaw
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| |
Collapse
|