1
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Walczak D, Sikorski A, Grzywacz D, Nowacki A, Liberek B. Identification of the furanose ring conformations and the factors driving their adoption. Carbohydr Res 2023; 526:108780. [PMID: 36944302 DOI: 10.1016/j.carres.2023.108780] [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: 01/12/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Three groups of furanoses with restricted freedom of rotation on the C3-C4, C2-C3, and C1-C2 bonds, respectively, are presented. Conformational analysis of these furanoses is conducted based on the proton nuclear magnetic resonance (1H NMR) spectroscopy, density functional theory (DFT) calculations, and X-ray analysis. It is shown that the particular group of the presented furanoses is locked in the specific conformation. These are the 1T2-like, the 0E-like, and the 3T4-like conformation, respectively. Characteristic 1H NMR spectra of these three conformations are presented and the factors influencing the conformational preferences of the analyzed furanoses are discussed.
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Affiliation(s)
- Dominik Walczak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Artur Sikorski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Daria Grzywacz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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2
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Sobrado P. Role of reduced flavin in dehalogenation reactions. Arch Biochem Biophys 2020; 697:108696. [PMID: 33245912 DOI: 10.1016/j.abb.2020.108696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Halogenated organic compounds are extensively used in the cosmetic, pharmaceutical, and chemical industries. Several naturally occurring halogen-containing natural products are also produced, mainly by marine organisms. These compounds accumulate in the environment due to their chemical stability and lack of biological pathways for their degradation. However, a few enzymes have been identified that perform dehalogenation reactions in specific biological pathways and others have been identified to have secondary activities toward halogenated compounds. Various mechanisms for dehalogenation of I, Cl, Br, and F containing compounds have been elucidated. These have been grouped into reductive, oxidative, and hydrolytic mechanisms. Flavin-dependent enzymes have been shown to catalyze oxidative dehalogenation reactions utilizing the C4a-hydroperoxyflavin intermediate. In addition, flavoenzymes perform reductive dehalogenation, forming transient flavin semiquinones. Recently, flavin-dependent enzymes have also been shown to perform dehalogenation reactions where the reduced form of the flavin produces a covalent intermediate. Here, recent studies on the reactions of flavoenzymes in dehalogenation reactions, with a focus on covalent catalytic dehalogenation mechanisms, are described.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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3
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Repositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning. Int J Mol Sci 2020; 21:ijms21228809. [PMID: 33233837 PMCID: PMC7699892 DOI: 10.3390/ijms21228809] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Chagas disease, caused by the parasite Trypanosoma cruzi, affects millions of people in South America. The current treatments are limited, have severe side effects, and are only partially effective. Drug repositioning, defined as finding new indications for already approved drugs, has the potential to provide new therapeutic options for Chagas. In this work, we conducted a structure-based drug repositioning approach with over 130,000 3D protein structures to identify drugs that bind therapeutic Chagas targets and thus represent potential new Chagas treatments. The screening yielded over 500 molecules as hits, out of which 38 drugs were prioritized following a rigorous filtering process. About half of the latter were already known to have trypanocidal activity, while the others are novel to Chagas disease. Three of the new drug candidates—ciprofloxacin, naproxen, and folic acid—showed a growth inhibitory activity in the micromolar range when tested ex vivo on T. cruzi trypomastigotes, validating the prediction. We show that our drug repositioning approach is able to pinpoint relevant drug candidates at a fraction of the time and cost of a conventional screening. Furthermore, our results demonstrate the power and potential of structure-based drug repositioning in the context of neglected tropical diseases where the pharmaceutical industry has little financial interest in the development of new drugs.
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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5
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Cossio-Pérez R, Pierdominici-Sottile G, Sobrado P, Palma J. Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. J Chem Inf Model 2019; 59:809-817. [PMID: 30608160 DOI: 10.1021/acs.jcim.8b00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes that both substrate and enzyme undergo during the process. It was determined that the galactopyranose portion of the substrate is highly mobile and that the opening/closing of the active site occurs in stages. Previously uncharacterized interactions with highly conserved residues were also identified. These findings provide new pieces of information that contribute to the rational design of drugs against T. cruzi.
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Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Juliana Palma
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
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6
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Dai Y, Valentino H, Sobrado P. Evidence for the Formation of a Radical-Mediated Flavin-N5 Covalent Intermediate. Chembiochem 2018; 19:1609-1612. [PMID: 29776001 DOI: 10.1002/cbic.201800123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 01/07/2023]
Abstract
The redox-neutral reaction catalyzed by 2-haloacrylate hydratase (2-HAH) leads to the conversion of 2-chloroacrylate to pyruvate. Previous mechanistic studies demonstrated the formation of a flavin-iminium ion as an important intermediate in the 2-HAH catalytic cycle. Time-resolved flavin absorbance studies were performed in this study, and the data showed that the enzyme is capable of stabilizing both anionic and neutral flavin semiquinone species. The presence of a radical scavenger decreases the activity in a concentration-dependent manner. These data are consistent with the flavin iminium intermediate occurring by radical recombination.
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Affiliation(s)
- Yumin Dai
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, 360 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Hannah Valentino
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, 360 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, 360 West Campus Drive, Blacksburg, VA, 24061, USA
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7
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Gadda G, Sobrado P. Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action. Biochemistry 2018; 57:3445-3453. [DOI: 10.1021/acs.biochem.8b00232] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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8
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Pierdominici-Sottile G, Cossio-Pérez R, Da Fonseca I, Kizjakina K, Tanner JJ, Sobrado P. Steric Control of the Rate-Limiting Step of UDP-Galactopyranose Mutase. Biochemistry 2018; 57:3713-3721. [PMID: 29757624 DOI: 10.1021/acs.biochem.8b00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Galactose is an abundant monosaccharide found exclusively in mammals as galactopyranose (Gal p), the six-membered ring form of this sugar. In contrast, galactose appears in many pathogenic microorganisms as the five-membered ring form, galactofuranose (Gal f). Gal f biosynthesis begins with the conversion of UDP-Gal p to UDP-Gal f catalyzed by the flavoenzyme UDP-galactopyranose mutase (UGM). Because UGM is essential for the survival and proliferation of several pathogens, there is interest in understanding the catalytic mechanism to aid inhibitor development. Herein, we have used kinetic measurements and molecular dynamics simulations to explore the features of UGM that control the rate-limiting step (RLS). We show that UGM from the pathogenic fungus Aspergillus fumigatus also catalyzes the isomerization of UDP-arabinopyranose (UDP-Ara p), which differs from UDP-Gal p by lacking a -CH2-OH substituent at the C5 position of the hexose ring. Unexpectedly, the RLS changed from a chemical step for the natural substrate to product release with UDP-Ara p. This result implicated residues that contact the -CH2-OH of UDP-Gal p in controlling the mechanistic path. The mutation of one of these residues, Trp315, to Ala changed the RLS of the natural substrate to product release, similar to the wild-type enzyme with UDP-Ara p. Molecular dynamics simulations suggest that steric complementarity in the Michaelis complex is responsible for this distinct behavior. These results provide new insight into the UGM mechanism and, more generally, how steric factors in the enzyme active site control the free energy barriers along the reaction path.
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Affiliation(s)
| | - Rodrigo Cossio-Pérez
- Sci-prot. Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , Bernal B1876BXD , Argentina
| | - Isabel Da Fonseca
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Karina Kizjakina
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry , University of Missouri-Columbia , Columbia , Missouri 65211 , United States
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
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9
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Dai Y, Kizjakina K, Campbell AC, Korasick DA, Tanner JJ, Sobrado P. Flavin-N5 Covalent Intermediate in a Nonredox Dehalogenation Reaction Catalyzed by an Atypical Flavoenzyme. Chembiochem 2017; 19:53-57. [PMID: 29116682 DOI: 10.1002/cbic.201700594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Indexed: 11/05/2022]
Abstract
The flavin-dependent enzyme 2-haloacrylate hydratase (2-HAH) catalyzes the conversion of 2-chloroacrylate, a major component in the manufacture of acrylic polymers, to pyruvate. The enzyme was expressed in Escherichia coli, purified, and characterized. 2-HAH was shown to be monomeric in solution and contained a non-covalent, yet tightly bound, flavin adenine dinucleotide (FAD). Although the catalyzed reaction was redox-neutral, 2-HAH was active only in the reduced state. A covalent flavin-substrate intermediate, consistent with the flavin-acrylate iminium ion, was trapped with cyanoborohydride and characterized by mass spectrometry. Small-angle X-ray scattering was consistent with 2-HAH belonging to the succinate dehydrogenase/fumarate reductase family of flavoproteins. These studies establish 2-HAH as a novel noncanonical flavoenzyme.
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Affiliation(s)
- Yumin Dai
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
| | - Karina Kizjakina
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211, USA.,Department of Chemistry, University of Missouri, Columbia, Missouri, 65211, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, 360 West Campus Drive, Blacksburg, Virginia, 24061, USA
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10
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Kashif M, Tabrez S, Husein A, Arish M, Kalaiarasan P, Manna PP, Subbarao N, Akhter Y, Rub A. Identification of novel inhibitors against UDP‐galactopyranose mutase to combat leishmaniasis. J Cell Biochem 2017; 119:2653-2665. [DOI: 10.1002/jcb.26433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Mohammad Kashif
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
- Immunobiology Laboratory, Department of ZoologyInstitute of Science, Banaras Hindu UniversityVaranasiIndia
| | - Shams Tabrez
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Atahar Husein
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Mohd Arish
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
| | - Ponnusamy Kalaiarasan
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Partha P. Manna
- Immunobiology Laboratory, Department of ZoologyInstitute of Science, Banaras Hindu UniversityVaranasiIndia
| | - Naidu Subbarao
- School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal PradeshTemporary Academic BlockShahpurKangra (H.P.)India
| | - Abdur Rub
- Infection and Immunity Lab, Department of BiotechnologyJamia Millia Islamia (A Central University)New DelhiIndia
- Department of Medical Laboratory Sciences, College of Applied Medical ScienceMajmaah UniversityAl MajmaahKSA
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11
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Martin Del Campo JS, Eckshtain-Levi M, Vogelaar NJ, Sobrado P. Identification of Aspergillus fumigatus UDP-Galactopyranose Mutase Inhibitors. Sci Rep 2017; 7:10836. [PMID: 28883473 PMCID: PMC5589893 DOI: 10.1038/s41598-017-11022-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/17/2017] [Indexed: 01/08/2023] Open
Abstract
Aspergillus fumigatus is an opportunistic human pathogen responsible for deadly, invasive infections in immunocompromised patients. The A. fumigatus cell wall is a complex network of polysaccharides among them galactofuran, which is absent in humans. UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactofuranose (UDP-Galf) to UDP-galactopyranose (UDP-Galp) and is an important virulence factor. UGM is a flavin-dependent enzyme that requires the reduced flavin for activity; flavin reduction is achieved by reaction with NADPH. The aim of this work was to discover inhibitors of UGM by targeting the NADPH binding site using an ADP-TAMRA probe in a high-throughput screening assay. The flavonoids (2S)-hesperetin and (2S)-naringenin were validated as competitive inhibitors of UGM against NADPH with Ki values of 6 µM and 74 µM, respectively. To gain insight into the active chemical substituents involved in the inhibition of UGM, several derivatives of these inhibitors were studied. The results show that the hydroxyl groups of (2S)-hesperetin are important for inhibition, in particular the phenyl-chroman moiety. Congo red susceptibility assay and growth temperature effects showed that these compounds affected cell wall biosynthesis in A. fumigatus. This work is the first report of inhibition studies on UGM from eukaryotic human pathogens.
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Affiliation(s)
| | | | - Nancy J Vogelaar
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA. .,Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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12
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Sobrado P, Tanner JJ. Multiple functionalities of reduced flavin in the non-redox reaction catalyzed by UDP-galactopyranose mutase. Arch Biochem Biophys 2017; 632:59-65. [PMID: 28652025 DOI: 10.1016/j.abb.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/29/2022]
Abstract
Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Traditionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and reactivities of both traditional and noncanonical flavoenzymes. The major hot spots of reactivity include the N5, C4a, and C4O atoms of the isoalloxazine, and the 2' hydroxyl of the ribityl chain. The role of hot spots in traditional flavoenzymes, such as monooxygenases, is briefly reviewed. A more detailed description of flavin hot spots in noncanonical flavoenzymes is provided, with a focus on UDP-galactopyranose mutase, where the N5 functions as a nucleophile that attacks the anomeric carbon atom of the substrate. Recent results from mechanistic enzymology, kinetic crystallography, and computational chemistry provide a complete picture of the chemical mechanism of UDP-galactopyranose mutase.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211, USA.
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13
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Piano V, Palfey BA, Mattevi A. Flavins as Covalent Catalysts: New Mechanisms Emerge. Trends Biochem Sci 2017; 42:457-469. [DOI: 10.1016/j.tibs.2017.02.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
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14
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Misra S, Valicherla GR, Mohd Shahab, Gupta J, Gayen JR, Misra-Bhattacharya S. UDP-galactopyranose mutase, a potential drug target against human pathogenic nematodeBrugia malayi. Pathog Dis 2016; 74:ftw072. [DOI: 10.1093/femspd/ftw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/02/2023] Open
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Mehra-Chaudhary R, Dai Y, Sobrado P, Tanner JJ. In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction. Biochemistry 2016; 55:833-6. [PMID: 26836146 PMCID: PMC4819441 DOI: 10.1021/acs.biochem.6b00035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
UDP-galactopyranose mutase (UGM)
plays an essential role in galactofuranose
biosynthesis in pathogens by catalyzing the conversion of UDP-galactopyranose
to UDP-galactofuranose. Here we report the first crystal structure
of a covalent intermediate in the UGM reaction. The 2.3 Å resolution
structure reveals UDP bound in the active site and galactopyranose
linked to the FAD through a covalent bond between the anomeric C of
galactopyranose and N5 of the FAD. The structure confirms the role
of the flavin as nucleophile and supports the hypothesis that the
proton destined for O5 of galactofuranose is shuttled from N5 of the
FAD via O4 of the FAD.
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Affiliation(s)
- Ritcha Mehra-Chaudhary
- Structural Biology Core, University of Missouri-Columbia , Columbia, Missouri 65211, United States
| | - Yumin Dai
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States
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16
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Eppe G, El Bkassiny S, Vincent SP. Galactofuranose Biosynthesis: Discovery, Mechanisms and Therapeutic Relevance. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Galactofuranose, the atypical and thermodynamically disfavored form of d-galactose, has in reality a very old history in chemistry and biochemistry. The purpose of this book chapter is to give an overview on the fundamental aspects of the galactofuranose biosynthesis, from the biological occurrence to the search of inhibitors.
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Affiliation(s)
- Guillaume Eppe
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
| | - Sandy El Bkassiny
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
| | - Stéphane P. Vincent
- University of Namur, Département de Chimie, Laboratoire de Chimie Bio-Organique rue de Bruxelles 61 B-5000 Namur Belgium
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17
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van Straaten KE, Kuttiyatveetil JRA, Sevrain CM, Villaume SA, Jiménez-Barbero J, Linclau B, Vincent SP, Sanders DAR. Structural basis of ligand binding to UDP-galactopyranose mutase from Mycobacterium tuberculosis using substrate and tetrafluorinated substrate analogues. J Am Chem Soc 2015; 137:1230-44. [PMID: 25562380 DOI: 10.1021/ja511204p] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
UDP-Galactopyranose mutase (UGM) is a flavin-containing enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf) and plays a key role in the biosynthesis of the mycobacterial cell wall galactofuran. A soluble, active form of UGM from Mycobacterium tuberculosis (MtUGM) was obtained from a dual His6-MBP-tagged MtUGM construct. We present the first complex structures of MtUGM with bound substrate UDP-Galp (both oxidized flavin and reduced flavin). In addition, we have determined the complex structures of MtUGM with inhibitors (UDP and the dideoxy-tetrafluorinated analogues of both UDP-Galp (UDP-F4-Galp) and UDP-Galf (UDP-F4-Galf)), which represent the first complex structures of UGM with an analogue in the furanose form, as well as the first structures of dideoxy-tetrafluorinated sugar analogues bound to a protein. These structures provide detailed insight into ligand recognition by MtUGM and show an overall binding mode similar to those reported for other prokaryotic UGMs. The binding of the ligand induces conformational changes in the enzyme, allowing ligand binding and active-site closure. In addition, the complex structure of MtUGM with UDP-F4-Galf reveals the first detailed insight into how the furanose moiety binds to UGM. In particular, this study confirmed that the furanoside adopts a high-energy conformation ((4)E) within the catalytic pocket. Moreover, these investigations provide structural insights into the enhanced binding of the dideoxy-tetrafluorinated sugars compared to unmodified analogues. These results will help in the design of carbohydrate mimetics and drug development, and show the enormous possibilities for the use of polyfluorination in the design of carbohydrate mimetics.
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Affiliation(s)
- Karin E van Straaten
- Department of Chemistry, University of Saskatchewan , 110 Science Place, Saskatoon S7N 5C9, Canada
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18
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Keenan M, Chaplin JH. A New Era for Chagas Disease Drug Discovery? PROGRESS IN MEDICINAL CHEMISTRY 2015; 54:185-230. [DOI: 10.1016/bs.pmch.2014.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Da Fonseca I, Qureshi IA, Mehra-Chaudhary R, Kizjakina K, Tanner JJ, Sobrado P. Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry 2014; 53:7794-804. [PMID: 25412209 PMCID: PMC4270374 DOI: 10.1021/bi501008z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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UDP-galactopyranose mutase (UGM)
catalyzes the interconversion
between UDP-galactopyranose and UDP-galactofuranose. Absent in humans,
galactofuranose is found in bacterial and fungal cell walls and is
a cell surface virulence factor in protozoan parasites. For these
reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis
and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on
active site residues that are conserved in eukaryotic UGMs but are
absent or different in bacterial UGMs. Kinetic analysis of the variants
F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in kcat/KM values of 200–1000-fold for the mutase
reaction. In contrast, none of the mutations significantly affect
the kinetics of enzyme activation by NADPH. These results indicate
that the targeted residues are important for promoting the transition
state conformation for UDP-galactofuranose formation. Crystal structures
of the A. fumigatus mutant enzymes
were determined in the presence and absence of UDP to understand the
structural consequences of the mutations. The structures suggest important
roles for Asn207 in stabilizing the closed active site, and Tyr317
in positioning of the uridine ring. Phe66 and the corresponding residue
in Mycobacterium tuberculosis UGM (His68)
play a role as the backstop, stabilizing the galactopyranose group
for nucleophilic attack. Together, these results provide insight into
the essentiality of the targeted residues for realizing maximal catalytic
activity and a proposal for how conformational changes that close
the active site are temporally related and coupled together.
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Affiliation(s)
- Isabel Da Fonseca
- Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
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20
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Pierdominici-Sottile G, Cossio Pérez R, Galindo JF, Palma J. QM/MM molecular dynamics study of the galactopyranose → galactofuranose reaction catalysed by Trypanosoma cruzi UDP-galactopyranose mutase. PLoS One 2014; 9:e109559. [PMID: 25299056 PMCID: PMC4192007 DOI: 10.1371/journal.pone.0109559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/25/2014] [Indexed: 12/18/2022] Open
Abstract
The enzyme UDP-Galactopyranose Mutase (UGM) catalyses the conversion of galactopyranose into galactofuranose. It is known to be critical for the survival and proliferation of several pathogenic agents, both prokaryotic and eukaryotic. Among them is Trypanosoma cruzi, the parasite responsible for Chagas' disease. Since the enzyme is not present in mammals, it appears as a promising target for the design of drugs to treat this illness. A precise knowledge of the mechanism of the catalysed reaction would be crucial to assist in such design. In this article we present a detailed study of all the putative steps of the mechanism. The study is based on QM/MM free energy calculations along properly selected reaction coordinates, and on the analysis of the main structural changes and interactions taking place at every step. The results are discussed in connection with the experimental evidence and previous theoretical studies.
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Affiliation(s)
| | - Rodrigo Cossio Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Johan F. Galindo
- Quantum and Computational Chemistry Group, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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21
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El Bkassiny S, N'Go I, Sevrain CM, Tikad A, Vincent SP. Synthesis of a novel UDP-carbasugar as UDP-galactopyranose mutase inhibitor. Org Lett 2014; 16:2462-5. [PMID: 24746099 DOI: 10.1021/ol500848q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The multistep synthesis of a novel UDP-C-cyclohexene, designed as a high energy intermediate analogue of the UDP-galactopyranose mutase (UGM) catalyzed isomerization reaction, is reported. The synthesis of the central carbasugar involved the preparation of a galactitol derivative bearing two olefins necessary for the construction of the cyclohexene ring by a ring-closing metathesis as a key step. Further successive phosphonylation, deprotection, and UMP coupling provided the target molecule. The final molecule was assayed against UGM and compared with UDP-C-Galf, the C-glycosidic UGM substrate analogue.
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Affiliation(s)
- Sandy El Bkassiny
- University of Namur , Département de Chimie, Laboratoire de Chimie Bio-Organique, rue de Bruxelles 61, B-5000 Namur, Belgium
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22
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Tanner JJ, Boechi L, Andrew McCammon J, Sobrado P. Structure, mechanism, and dynamics of UDP-galactopyranose mutase. Arch Biochem Biophys 2014; 544:128-41. [PMID: 24096172 PMCID: PMC3946560 DOI: 10.1016/j.abb.2013.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 11/16/2022]
Abstract
The flavoenzyme UDP-galactopyranose mutase (UGM) is a key enzyme in galactofuranose biosynthesis. The enzyme catalyzes the 6-to-5 ring contraction of UDP-galactopyranose to UDP-galactofuranose. Galactofuranose is absent in humans yet is an essential component of bacterial and fungal cell walls and a cell surface virulence factor in protozoan parasites. Thus, inhibition of galactofuranose biosynthesis is a valid strategy for developing new antimicrobials. UGM is an excellent target in this effort because the product of the UGM reaction represents the first appearance of galactofuranose in the biosynthetic pathway. The UGM reaction is redox neutral, which is atypical for flavoenzymes, motivating intense examination of the chemical mechanism and structural features that tune the flavin for its unique role in catalysis. These studies show that the flavin functions as nucleophile, forming a flavin-sugar adduct that facilitates galactose-ring opening and contraction. The 3-dimensional fold is novel and conserved among all UGMs, however the larger eukaryotic enzymes have additional secondary structure elements that lead to significant differences in quaternary structure, substrate conformation, and conformational flexibility. Here we present a comprehensive review of UGM three-dimensional structure, provide an update on recent developments in understanding the mechanism of the enzyme, and summarize computational studies of active site flexibility.
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Affiliation(s)
- John J Tanner
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, United States.
| | - Leonardo Boechi
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| | - J Andrew McCammon
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States; Howard Hughes Medical Institute, Department of Pharmacology, University of California San Diego, La Jolla, CA, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States; Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
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23
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Comparative genome analysis of Campylobacter fetus subspecies revealed horizontally acquired genetic elements important for virulence and niche specificity. PLoS One 2014; 9:e85491. [PMID: 24416416 PMCID: PMC3887049 DOI: 10.1371/journal.pone.0085491] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/28/2013] [Indexed: 01/03/2023] Open
Abstract
Campylobacter fetus are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of C. fetus subsp. venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40. Functional analysis of genes predicted to be involved in C. fetus virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of C. fetus pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens.
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24
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N'Go I, Golten S, Ardá A, Cañada J, Jiménez-Barbero J, Linclau B, Vincent SP. Tetrafluorination of sugars as strategy for enhancing protein-carbohydrate affinity: application to UDP-Galp mutase inhibition. Chemistry 2013; 20:106-12. [PMID: 24311368 DOI: 10.1002/chem.201303693] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Indexed: 01/16/2023]
Abstract
Tetrafluorinated analogues of both UDP-galactopyranose and UDP-galactofuranose have been synthesized and assayed against UDP-galactopyranose mutase, a key enzyme for Mycobacterium tuberculosis cell wall biosynthesis. Competition assays and STD-NMR spectroscopy techniques have evidenced not only the first unambiguous case of affinity enhancement through local sugar polyfluorination, but also showed that tetrafluorination can still have a beneficial effect on binding when monofluorination at the same position does not.
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Affiliation(s)
- Inès N'Go
- Department of Chemistry, University of Namur, Rue de Bruxelles 61, 5000 Namur (Belgium)
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25
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Kizjakina K, Tanner JJ, Sobrado P. Targeting UDP-galactopyranose mutases from eukaryotic human pathogens. Curr Pharm Des 2013; 19:2561-73. [PMID: 23116395 PMCID: PMC3624792 DOI: 10.2174/1381612811319140007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 12/19/2022]
Abstract
UDP-Galactopyranose mutase (UGM) is a unique flavin-dependent enzyme that catalyzes the conversion of UDP-galactopyranose(UDP-Galp) to UDP-galactofuranose (UDP-Galf). The product of this reaction is the precursor to Galf, a major component of the cell wall and of cell surface glycoproteins and glycolipids in many eukaryotic and prokaryotic human pathogens. The function of UGM is important in the virulence of fungi, parasites, and bacteria. Its role in virulence and its absence in humans suggest that UGM is an ideal drug target. Significant structural and mechanistic information has been accumulated on the prokaryotic UGMs; however, in the past few years the research interest has shifted to UGMs from eukaryotic human pathogens such as fungi and protozoan parasites. It has become clear that UGMs from prokaryotic and eukaryotic organisms have different structural and mechanistic features. The amino acid sequence identity between these two classes of enzymes is low, resulting in differences in oligomeric states, substrate binding, active site flexibility, and interaction with redox partners. However, the unique role of the flavin cofactor in catalysis is conserved among this enzyme family. In this review, recent findings on eukaryotic UGMs are discussed and presented in comparison with prokaryotic UGMs.
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Affiliation(s)
- Karina Kizjakina
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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26
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Boechi L, de Oliveira CAF, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Sci 2013; 22:1490-501. [PMID: 23934860 DOI: 10.1002/pro.2332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 02/04/2023]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that represents one of the major health challenges of the Latin American countries. Successful efforts were made during the last few decades to control the transmission of this disease, but there is still no treatment for the 10 million adults in the chronic phase of the disease. In T. cruzi, as well as in other pathogens, the flavoenzyme UDP-galactopyranose mutase (UGM) catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, a precursor of the cell surface β-galactofuranose that is involved in the virulence of the pathogen. The fact that UGM is not present in humans makes inhibition of this enzyme a good approach in the design of new Chagas therapeutics. By performing a series of computer simulations of T. cruzi UGM in the presence or absence of an active site ligand, we address the molecular details of the mechanism that controls the uptake and retention of the substrate. The simulations suggest a modular mechanism in which each moiety of the substrate controls the flexibility of a different protein loop. Furthermore, the calculations indicate that interactions with the substrate diphosphate moiety are especially important for stabilizing the closed active site. This hypothesis is supported with kinetics measurements of site-directed mutants of T. cruzi UGM. Our results extend our knowledge of UGM dynamics and offer new alternatives for the prospective design of drugs.
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Affiliation(s)
- Leonardo Boechi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
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27
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Fonseca IO, Kizjakina K, Sobrado P. UDP-galactopyranose mutases from Leishmania species that cause visceral and cutaneous leishmaniasis. Arch Biochem Biophys 2013; 538:103-10. [PMID: 24012809 DOI: 10.1016/j.abb.2013.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/21/2013] [Accepted: 08/24/2013] [Indexed: 01/18/2023]
Abstract
Leishmaniasis is a vector-borne, neglected tropical disease caused by parasites from the genus Leishmania. Galactofuranose (Galf) is found on the cell surface of Leishmania parasites and is important for virulence. The flavoenzyme that catalyzes the isomerization of UDP-galactopyranose to UDP-Galf, UDP-galactopyranose mutase (UGM), is a validated drug target in protozoan parasites. UGMs from L. mexicana and L. infantum were recombinantly expressed, purified, and characterized. The isolated enzymes contained tightly bound flavin cofactor and were active only in the reduced form. NADPH is the preferred redox partner for both enzymes. A kcat value of 6 ± 0.4s(-1) and a Km value of 252 ± 42 μM were determined for L. infantum UGM. For L. mexicana UGM, these values were ∼4-times lower. Binding of UDP-Galp is enhanced 10-20 fold in the reduced form of the enzymes. Changes in the spectra of the reduced flavin upon interaction with the substrate are consistent with formation of a flavin-iminium ion intermediate.
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Affiliation(s)
- Isabel O Fonseca
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States
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28
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Abstract
Nematodes represent a diverse phylum of both free living and parasitic species. While the species Caenorhabditis elegans is a valuable model organism, parasitic nematodes or helminths pose a serious threat to human health. Indeed, helminths cause many neglected tropical diseases that afflict humans. Nematode glycoconjugates have been implicated in evasive immunomodulation, a hallmark of nematode infections. One monosaccharide residue present in the glycoconjugates of several human pathogens is galactofuranose (Galf). This five-membered ring isomer of galactose has not been detected in mammals, making Galf metabolic enzymes attractive therapeutic targets. The only known pathway for biosynthetic incorporation of Galf into glycoconjugates depends upon generation of the glycosyl donor UDP-Galf by the flavoenzyme uridine 5'-diphosphate (UDP) galactopyranose mutase (UGM or Glf). A putative UGM encoding gene (glf-1) was recently identified in C. elegans. We sought to assess the catalytic activity of the corresponding gene product (CeUGM). CeUGM catalyzes the isomerization of UDP-Galf and UDP-galactopyranose (UDP-Galp). In the presence of enzyme, substrate, and a hydride source, a galactose-N5-FAD adduct was isolated, suggesting the CeUGM flavin adenine dinucleotide (FAD) cofactor serves as a nucleophile in covalent catalysis. Homology modeling and protein variants indicate that CeUGM possesses an active site similar to that of prokaryotic enzymes, despite the low sequence identity (∼15%) between eukaryotic and prokaryotic UGM proteins. Even with the primary sequence differences, heterocyclic UGM inhibitors developed against prokaryotic proteins also inhibit CeUGM activity. We postulate that inhibitors of CeUGM can serve as chemical probes of Galf in nematodes and as anthelmintic leads. The available data suggest that CeUGM facilitates the biosynthetic incorporation of Galf into nematode glycoconjugates through generation of the glycosyl donor UDP-Galf.
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Affiliation(s)
- Darryl A. Wesener
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
| | - John F. May
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
| | - Elizabeth M. Huffman
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 USA
| | - Laura L. Kiessling
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 USA
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 USA
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29
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Abstract
Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a "molecular scaffold" in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
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30
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Dhatwalia R, Singh H, Solano LM, Oppenheimer M, Robinson RM, Ellerbrock JF, Sobrado P, Tanner JJ. Identification of the NAD(P)H binding site of eukaryotic UDP-galactopyranose mutase. J Am Chem Soc 2012; 134:18132-8. [PMID: 23036087 PMCID: PMC3493617 DOI: 10.1021/ja308188z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UDP-galactopyranose mutase (UGM) plays an essential role in galactofuranose biosynthesis in microorganisms by catalyzing the conversion of UDP-galactopyranose to UDP-galactofuranose. The enzyme has gained attention recently as a promising target for the design of new antifungal, antitrypanosomal, and antileishmanial agents. Here we report the first crystal structure of UGM complexed with its redox partner NAD(P)H. Kinetic protein crystallography was used to obtain structures of oxidized Aspergillus fumigatus UGM (AfUGM) complexed with NADPH and NADH, as well as reduced AfUGM after dissociation of NADP(+). NAD(P)H binds with the nicotinamide near the FAD isoalloxazine and the ADP moiety extending toward the mobile 200s active site flap. The nicotinamide riboside binding site overlaps that of the substrate galactopyranose moiety, and thus NADPH and substrate binding are mutually exclusive. On the other hand, the pockets for the adenine of NADPH and uracil of the substrate are distinct and separated by only 6 Å, which raises the possibility of designing novel inhibitors that bind both sites. All 12 residues that contact NADP(H) are conserved among eukaryotic UGMs. Residues that form the AMP pocket are absent in bacterial UGMs, which suggests that eukaryotic and bacterial UGMs have different NADP(H) binding sites. The structures address the longstanding question of how UGM binds NAD(P)H and provide new opportunities for drug discovery.
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Affiliation(s)
- Richa Dhatwalia
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Luis M. Solano
- Department of Biology, Costa Rica Institute of Technology, Cartago, Costa Rica
| | | | | | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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31
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Ansiaux C, N'Go I, Vincent SP. Reversible and Efficient Inhibition of UDP-Galactopyranose Mutase by Electrophilic, Constrained and Unsaturated UDP-Galactitol Analogues. Chemistry 2012; 18:14860-6. [DOI: 10.1002/chem.201202302] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 11/09/2022]
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32
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Dhatwalia R, Singh H, Oppenheimer M, Sobrado P, Tanner JJ. Crystal structures of Trypanosoma cruzi UDP-galactopyranose mutase implicate flexibility of the histidine loop in enzyme activation. Biochemistry 2012; 51:4968-79. [PMID: 22646091 PMCID: PMC3426654 DOI: 10.1021/bi300498c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 Å movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k(cat). Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.
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Affiliation(s)
- Richa Dhatwalia
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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