1
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Bayaraa T, Gaete J, Sutiono S, Kurz J, Lonhienne T, Harmer JR, Bernhardt PV, Sieber V, Guddat L, Schenk G. Dihydroxy‐Acid Dehydratases From Pathogenic Bacteria: Emerging Drug Targets to Combat Antibiotic Resistance. Chemistry 2022; 28:e202200927. [PMID: 35535733 PMCID: PMC9543379 DOI: 10.1002/chem.202200927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/30/2022]
Abstract
There is an urgent global need for the development of novel therapeutics to combat the rise of various antibiotic‐resistant superbugs. Enzymes of the branched‐chain amino acid (BCAA) biosynthesis pathway are an attractive target for novel anti‐microbial drug development. Dihydroxy‐acid dehydratase (DHAD) is the third enzyme in the BCAA biosynthesis pathway. It relies on an Fe−S cluster for catalytic activity and has recently also gained attention as a catalyst in cell‐free enzyme cascades. Two types of Fe−S clusters have been identified in DHADs, i.e. [2Fe−2S] and [4Fe−4S], with the latter being more prone to degradation in the presence of oxygen. Here, we characterise two DHADs from bacterial human pathogens, Staphylococcus aureus and Campylobacter jejuni (SaDHAD and CjDHAD). Purified SaDHAD and CjDHAD are virtually inactive, but activity could be reversibly reconstituted in vitro (up to ∼19,000‐fold increase with kcat as high as ∼6.7 s−1). Inductively‐coupled plasma‐optical emission spectroscopy (ICP‐OES) measurements are consistent with the presence of [4Fe−4S] clusters in both enzymes. N‐isopropyloxalyl hydroxamate (IpOHA) and aspterric acid are both potent inhibitors for both SaDHAD (Ki=7.8 and 51.6 μM, respectively) and CjDHAD (Ki=32.9 and 35.1 μM, respectively). These compounds thus present suitable starting points for the development of novel anti‐microbial chemotherapeutics.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jose Gaete
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Julia Kurz
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jeffrey R. Harmer
- Centre for Advanced Imaging The University of Queensland Brisbane 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Volker Sieber
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Luke Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Sustainable Minerals Institute The University of Queensland Brisbane 4072 Australia
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane 4072 Australia
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2
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Valera A, Wang S, Carr R, Trembleau L, Deng H. Characterization of a class II ketol-acid reductoisomerase from Mycobacterium tuberculosis. RSC Adv 2022; 12:10540-10544. [PMID: 35425013 PMCID: PMC8985424 DOI: 10.1039/d1ra08876a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/30/2022] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium tuberculosis ketol-acid reductoisomerases have been widely studied due to their metabolic importance towards development of drug-resistant bacteria treatment. We here report the biochemical characterization of a new KARI (MtKARI-II) from a Mycobacterium tuberculosis variant with a similar kinetic profile to class I KARIs. Phylogenetic analysis suggested that MtKARI-II is clustered into a class II KARI superfamily. Biochemical characterization of an unusual class II KARI (MtKARI-II) from a Mycobacterium tuberculosis variant.![]()
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Affiliation(s)
- Ane Valera
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | - Shan Wang
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | | | - Laurent Trembleau
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
| | - Hai Deng
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE Scotland UK
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3
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Pepi MJ, Chacko S, Marqus GM, Singh V, Wang Z, Planck K, Cullinane RT, Meka PN, Gollapalli DR, Ioerger TR, Rhee KY, Cuny GD, Boshoff HI, Hedstrom L. A d-Phenylalanine-Benzoxazole Derivative Reveals the Role of the Essential Enzyme Rv3603c in the Pantothenate Biosynthetic Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:330-342. [PMID: 35015509 DOI: 10.1021/acsinfecdis.1c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs and new targets are urgently needed to treat tuberculosis. We discovered that d-phenylalanine-benzoxazole Q112 displays potent antibacterial activity against Mycobacterium tuberculosis (Mtb) in multiple media and in macrophage infections. A metabolomic profiling indicates that Q112 has a unique mechanism of action. Q112 perturbs the essential pantothenate/coenzyme A biosynthetic pathway, depleting pantoate while increasing ketopantoate, as would be expected if ketopantoate reductase (KPR) were inhibited. We searched for alternative KPRs, since the enzyme annotated as PanE KPR is not essential in Mtb. The ketol-acid reductoisomerase IlvC catalyzes the KPR reaction in the close Mtb relative Corynebacterium glutamicum, but Mtb IlvC does not display KPR activity. We identified the essential protein Rv3603c as an orthologue of PanG KPR and demonstrated that a purified recombinant Rv3603c has KPR activity. Q112 inhibits Rv3603c, explaining the metabolomic changes. Surprisingly, pantothenate does not rescue Q112-treated bacteria, indicating that Q112 has an additional target(s). Q112-resistant strains contain loss-of-function mutations in the twin arginine translocase TatABC, further underscoring Q112's unique mechanism of action. Loss of TatABC causes a severe fitness deficit attributed to changes in nutrient uptake, suggesting that Q112 resistance may derive from a decrease in uptake.
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Affiliation(s)
- Michael J. Pepi
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), and South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Zhe Wang
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Kyle Planck
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Ryan T. Cullinane
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | - Penchala N. Meka
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station 77843, Texas, United States
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York 10065, New York, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston 77204, Texas, United States
| | - Helena I.M. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda 20892, Maryland, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham 02453, Massachusetts, United States
- Department of Chemistry, Brandeis University, Waltham 02453, Massachusetts, United States
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4
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Lemaire ON, Müller MC, Kahnt J, Wagner T. Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen. Biomolecules 2021; 11:1679. [PMID: 34827677 PMCID: PMC8615647 DOI: 10.3390/biom11111679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.
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Affiliation(s)
- Olivier Nicolas Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
| | - Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
| | - Jörg Kahnt
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany;
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; (O.N.L.); (M.-C.M.)
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5
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Zhuang YC, Ye DS, Weng SU, Tsai HHG. Double Proton Transfer during a Novel Tertiary α-Ketol Rearrangement in Ketol-Acid Reductoisomerase: A Water-Mediated, Metal-Catalyzed, Base-Induced Mechanism. J Phys Chem B 2021; 125:11893-11906. [PMID: 34618450 DOI: 10.1021/acs.jpcb.1c07137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(KARI) catalyzes the conversion of (S)-2-acetolactate or (S)-2-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate, the second step in the biosynthesis of branched chain amino acids (BCAAs). Because the BCAA biosynthetic pathway is present in bacteria, plants, and fungi, but absent in animals, it is an excellent target for the development of new-generation antibiotics and herbicides. Nevertheless, the mechanism of the KARI-catalyzed reaction has not yet been fully solved. In this study, we used iterative molecular dynamics (MD) flexible fitting-Rosetta techniques to optimize the three-dimensional solution structure of archaea KARI from Sulfolobus solfataricus (Sso-KARI) determined from cryo-electron microscopy. On the basis of the structure of the Sso-KARI/2Mg2+/NADH/(S)-2-acetolactate complex, we deciphered the catalytic mechanism of the KARI-mediated reaction through hybrid quantum mechanics/molecular mechanics MD simulations in conjunction with umbrella sampling. With an activation energy of only 6.06 kcal/mol, a water-mediated, metal-catalyzed, base-induced (WMMCBI) mechanism was preferred for deprotonation of the tertiary OH group of (S)-2-acetolactate in Sso-KARI. The WMMCBI mechanism for double proton transfer occurred within a proton wire route with two steps involving the formation of hydroxide: (i) Glu233 served as a general base to deprotonate the Mg2+-bound water, forming a hydroxide-coordinated Mg2+ ion; (ii) this hydroxide ion acted as a strong base that rapidly deprotonated the ternary OH group of the substrate. In contrast, the direct deprotonation of the substrate by Glu233 was kinetically unfavorable. This mechanism suggests a novel approach for designing catalysts for deprotonation and provides clues for the development of new-generation antibiotics and herbicides.
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Affiliation(s)
- Yi-Chuan Zhuang
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Dong-Sheng Ye
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Sheng-Uei Weng
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
| | - Hui-Hsu Gavin Tsai
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan.,Research Center of New-Generation Light-Driven Photovoltaic Modules, National Central University, No. 300, Zhongda Rd., Zhongli District, Taoyuan City 32001, Taiwan
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6
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Singh N, Chauhan A, Kumar R, Singh SK. Biochemical and functional characterization of Mycobacterium tuberculosis ketol-acid reductoisomerase. MICROBIOLOGY-SGM 2021; 167. [PMID: 34515631 DOI: 10.1099/mic.0.001087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Branched-chain amino acids (BCAAs) are essential amino acids, but their biosynthetic pathway is absent in mammals. Ketol-acid reductoisomerase (IlvC) is a BCAA biosynthetic enzyme that is coded by Rv3001c in Mycobacterium tuberculosis H37Rv (Mtb-Rv) and MRA_3031 in M. tuberculosis H37Ra (Mtb-Ra). IlvCs are essential in Mtb-Rv as well as in Escherichia coli. Compared to wild-type and IlvC-complemented Mtb-Ra strains, IlvC knockdown strain showed reduced survival at low pH and under low pH+starvation stress conditions. Further, increased expression of IlvC was observed under low pH and starvation stress conditions. Confirmation of a role for IlvC in pH and starvation stress was achieved by developing E. coli BL21(DE3) IlvC knockout, which was defective for growth in M9 minimal medium, but growth could be rescued by isoleucine and valine supplementation. Growth was also restored by complementing with over-expressing constructs of Mtb-Ra and E. coli IlvCs. The E. coli knockout also had a survival deficit at pH=5.5 and 4.5 and was more susceptible to killing at pH=3.0. The biochemical characterization of Mtb-Ra and E. coli IlvCs confirmed that both have NADPH-dependent activity. In conclusion, this study demonstrates the functional complementation of E. coli IlvC by Mtb-Ra IlvC and also suggests that IlvC has a role in tolerance to low pH and starvation stress.
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Affiliation(s)
- Nirbhay Singh
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Lucknow-226031, UP, India
| | - Anu Chauhan
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Lucknow-226031, UP, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
| | - Ram Kumar
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Lucknow-226031, UP, India
| | - Sudheer Kumar Singh
- Molecular Microbiology and Immunology Division, CSIR - Central Drug Research Institute, BS 10/1, Sector 10, Jankipuram Extension, Lucknow-226031, UP, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
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7
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Liang YF, Long ZX, Zhang YJ, Luo CY, Yan LT, Gao WY, Li H. The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications. Biochimie 2021; 184:72-87. [PMID: 33607240 DOI: 10.1016/j.biochi.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Zi-Xian Long
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Ya-Jian Zhang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Cai-Yun Luo
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Le-Tian Yan
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
| | - Heng Li
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
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8
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Kandale A, Patel K, Hussein WM, Wun SJ, Zheng S, Tan L, West NP, Schenk G, Guddat LW, McGeary RP. Analogues of the Herbicide, N-Hydroxy- N-isopropyloxamate, Inhibit Mycobacterium tuberculosis Ketol-Acid Reductoisomerase and Their Prodrugs Are Promising Anti-TB Drug Leads. J Med Chem 2021; 64:1670-1684. [PMID: 33512163 DOI: 10.1021/acs.jmedchem.0c01919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs to treat tuberculosis (TB) are urgently needed to combat the increase in resistance observed among the current first-line and second-line treatments. Here, we propose ketol-acid reductoisomerase (KARI) as a target for anti-TB drug discovery. Twenty-two analogues of IpOHA, an inhibitor of plant KARI, were evaluated as antimycobacterial agents. The strongest inhibitor of Mycobacterium tuberculosis (Mt) KARI has a Ki value of 19.7 nM, fivefold more potent than IpOHA (Ki = 97.7 nM). This and four other potent analogues are slow- and tight-binding inhibitors of MtKARI. Three compounds were cocrystallized with Staphylococcus aureus KARI and yielded crystals that diffracted to 1.6-2.0 Å resolution. Prodrugs of these compounds possess antimycobacterial activity against H37Rv, a virulent strain of human TB, with the most active compound having an MIC90 of 2.32 ± 0.04 μM. This compound demonstrates a very favorable selectivity window and represents a highly promising lead as an anti-TB agent.
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Affiliation(s)
- Ajit Kandale
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Khushboo Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia.,Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland 4072, Australia
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9
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Lin X, Kurz JL, Patel KM, Wun SJ, Hussein WM, Lonhienne T, West NP, McGeary RP, Schenk G, Guddat LW. Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase. Chemistry 2021; 27:3130-3141. [PMID: 33215746 DOI: 10.1002/chem.202004665] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/26/2022]
Abstract
New drugs aimed at novel targets are urgently needed to combat the increasing rate of drug-resistant tuberculosis (TB). Herein, the National Cancer Institute Developmental Therapeutic Program (NCI-DTP) chemical library was screened against a promising new target, ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid (BCAA) biosynthesis pathway. From this library, 6-hydroxy-2-methylthiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione (NSC116565) was identified as a potent time-dependent inhibitor of Mycobacterium tuberculosis (Mt) KARI with a Ki of 95.4 nm. Isothermal titration calorimetry studies showed that this inhibitor bound to MtKARI in the presence and absence of the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH), which was confirmed by crystal structures of the compound in complex with closely related Staphylococcus aureus KARI. It is also shown that NSC116565 inhibits the growth of H37Ra and H37Rv strains of Mt with MIC50 values of 2.93 and 6.06 μm, respectively. These results further validate KARI as a TB drug target and show that NSC116565 is a promising lead for anti-TB drug development.
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Affiliation(s)
- Xin Lin
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.,Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan University, Helwan, Egypt
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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10
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Wun SJ, Johnson LA, You L, McGeary RP, Brueck T, Schenk G, Guddat LW. Inhibition studies of ketol-acid reductoisomerases from pathogenic microorganisms. Arch Biochem Biophys 2020; 692:108516. [DOI: 10.1016/j.abb.2020.108516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 10/23/2022]
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11
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Bayaraa T, Kurz JL, Patel KM, Hussein WM, Bilyj JK, West NP, Schenk G, McGeary RP, Guddat LW. Discovery, Synthesis and Evaluation of a Ketol-Acid Reductoisomerase Inhibitor. Chemistry 2020; 26:8958-8968. [PMID: 32198779 DOI: 10.1002/chem.202000899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/13/2020] [Indexed: 11/10/2022]
Abstract
Ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway, is a potential drug target for bacterial infections including Mycobacterium tuberculosis. Here, we have screened the Medicines for Malaria Venture Pathogen Box against purified M. tuberculosis (Mt) KARI and identified two compounds that have Ki values below 200 nm. In Mt cell susceptibility assays one of these compounds exhibited an IC50 value of 0.8 μm. Co-crystallization of this compound, 3-((methylsulfonyl)methyl)-2H-benzo[b][1,4]oxazin-2-one (MMV553002), in complex with Staphylococcus aureus KARI, which has 56 % identity with Mt KARI, NADPH and Mg2+ yielded a structure to 1.72 Å resolution. However, only a hydrolyzed product of the inhibitor (i.e. 3-(methylsulfonyl)-2-oxopropanic acid, missing the 2-aminophenol attachment) is observed in the active site. Surprisingly, Mt cell susceptibility assays showed that the 2-aminophenol product is largely responsible for the anti-TB activity of the parent compound. Thus, 3-(methylsulfonyl)-2-oxopropanic acid was identified as a potent KARI inhibitor that could be further explored as a potential biocidal agent and we have shown 2-aminophenol, as an anti-TB drug lead, especially given it has low toxicity against human cells. The study highlights that careful analysis of broad screening assays is required to correctly interpret cell-based activity data.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.,Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Ein Helwan, Helwan University, Helwan, Egypt
| | - Jessica K Bilyj
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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12
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Krishna VS, Zheng S, Rekha EM, Nallangi R, Sai Prasad D, George SE, Guddat LW, Sriram D. Design and development of ((4-methoxyphenyl)carbamoyl) (5-(5-nitrothiophen-2-yl)-1,3,4-thiadiazol-2-yl)amide analogues as Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors. Eur J Med Chem 2020; 193:112178. [DOI: 10.1016/j.ejmech.2020.112178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 01/17/2023]
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13
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Endo S, Wako H. Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules. Biophys Physicobiol 2020; 16:205-212. [PMID: 31984173 PMCID: PMC6975923 DOI: 10.2142/biophysico.16.0_205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 12/01/2022] Open
Abstract
The number of degrees of freedom (DOF), N, in normal mode analysis (NMA) calculations of proteins is a crucial problem in huge systems because the eigenvalue problem of an N-by-N matrix must be solved. If it were possible to perform the analysis with a smaller number of DOF for the same system with minimal deterioration in accuracy, this would make a significant impact on the computational study of protein dynamics. We examined two models in which the number of DOF was reduced. Both of them adopted a full-atom model with dihedral angles as independent variables. In one model, side-chain dihedral angles, χ's, and a main-chain dihedral angle, ω, were fixed and only the main-chain dihedral angles, ϕ and ψ, were variable. In another model, the dihedral angles around virtual bonds that connect neighboring Cα atoms were tested. The number of DOFs for the two models was two and one per residue, respectively. The residue-by-residue fluctuation profiles for atoms and dihedral angles were well reproduced in both models. The motion of atoms in the individual lowest-frequency normal modes of the two models was also very similar to those of the original model in which all rotatable dihedral angles were variable. Consequently, these models could predict large-amplitude concerted motion. These results also imply that proteins in a full-atom model can undergo only limited large-scale conformational changes around the native conformation, and consequently, NMA results do not strongly depend on the independent variables adopted.
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Affiliation(s)
- Shigeru Endo
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Hiroshi Wako
- School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan
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14
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Chen CY, Chang YC, Lin BL, Huang CH, Tsai MD. Temperature-Resolved Cryo-EM Uncovers Structural Bases of Temperature-Dependent Enzyme Functions. J Am Chem Soc 2019; 141:19983-19987. [PMID: 31829582 DOI: 10.1021/jacs.9b10687] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein functions are temperature-dependent, but protein structures are usually solved at a single (often low) temperature because of limitations on the conditions of crystal growth or protein vitrification. Here we demonstrate the feasibility of solving cryo-EM structures of proteins vitrified at high temperatures, solve 12 structures of an archaeal ketol-acid reductoisomerase (KARI) vitrified at 4-70 °C, and show that structures of both the Mg2+ form (KARI:2Mg2+) and its ternary complex (KARI:2Mg2+:NADH:inhibitor) are temperature-dependent in correlation with the temperature dependence of enzyme activity. Furthermore, structural analyses led to dissection of the induced-fit mechanism into ligand-induced and temperature-induced effects and to capture of temperature-resolved intermediates of the temperature-induced conformational change. The results also suggest that it is preferable to solve cryo-EM structures of protein complexes at functional temperatures. These studies should greatly expand the landscapes of protein structure-function relationships and enhance the mechanistic analysis of enzymatic functions.
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Affiliation(s)
- Chin-Yu Chen
- Department of Life Sciences , National Central University , Taoyuan 32001 , Taiwan
| | | | | | - Chun-Hsiang Huang
- Experimental Facility Division , National Synchrotron Radiation Research Center , Hsinchu 30076 , Taiwan
| | - Ming-Daw Tsai
- Institute of Biochemical Sciences , National Taiwan University , Taipei 106 , Taiwan
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15
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Yu MJ, Wu J, Chen SL. Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids. Chembiochem 2019; 21:381-391. [PMID: 31309701 DOI: 10.1002/cbic.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jue Wu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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16
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Lee D, Hong J, Kim KJ. Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8527-8535. [PMID: 31298526 DOI: 10.1021/acs.jafc.9b03262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
l-Valine belongs to the branched-chain amino acids (BCAAs) and is an essential amino acid that is crucial for all living organisms. l-Valine is industrially produced by the nonpathogenic bacterium Corynebacterium glutamicum and is synthesized by the BCAA biosynthetic pathway. Ketol-acid reductoisomerase (KARI) is the second enzyme in the BCAA pathway and catalyzes the conversion of (S)-2-acetolactate into (R)-2,3-dihydroxy-isovalerate, or the conversion of (S)-2-aceto-2-hydroxybutyrate into (R)-2,3-dihydroxy-3-methylvalerate. To elucidate the enzymatic properties of KARI from C. glutamicum (CgKARI), we successfully produced CgKARI protein and determined its crystal structure in complex with NADP+ and two Mg2+ ions. Based on the complex structure, docking simulations, and site-directed mutagenesis experiments, we revealed that CgKARI belongs to Class I KARI and identified key residues involved in stabilization of the substrate, metal ions, and cofactor. Furthermore, we confirmed the difference in the binding of metal ions that depended on the conformational change.
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Affiliation(s)
- Donghoon Lee
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
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17
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Chen CY, Chang YC, Lin BL, Lin KF, Huang CH, Hsieh DL, Ko TP, Tsai MD. Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. J Am Chem Soc 2019; 141:6136-6140. [DOI: 10.1021/jacs.9b01354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chin-Yu Chen
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | | | - Kuan-Fu Lin
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Chun-Hsiang Huang
- Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Dong-Lin Hsieh
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | | | - Ming-Daw Tsai
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
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18
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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19
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Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors as therapeutic drug leads. J Comput Aided Mol Des 2019; 33:357-366. [PMID: 30666485 DOI: 10.1007/s10822-019-00184-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/02/2019] [Indexed: 01/11/2023]
Abstract
Tuberculosis (TB) remains a major threat to human health. This due to the fact that current drug treatments are less than optimal and the increasing occurrence of multi drug-resistant strains of etiological agent, Mycobacterium tuberculosis (Mt). Given the wide-spread significance of this disease, we have undertaken a design and evaluation program to discover new anti-TB drug leads. Here, we focused on ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway. Importantly, this enzyme is present in bacteria but not in humans, making it an attractive proposition for drug discovery. In the present work, we used molecular docking to identify seventeen potential inhibitors of KARI using an in-house database. Compounds were selected based on docking scores, which were assigned as the result of favourable interactions between the compound and the active site of KARI. The inhibitory constant values for two leads, compounds 14 and 16 are 3.71 and 3.06 µM respectively. To assess the mode of binding, 100 ns molecular dynamics simulations for these two compounds in association with Mt KARI were performed and showed that the complex was stable with an average root mean square deviation of less than 3.5 Å for all atoms. Furthermore, compound 16 showed a minimum inhibitory concentration of 2.06 ± 0.91 µM and a 1.9 fold logarithmic reduction in the growth of Mt in an infected macrophage model. The two compounds exhibited low toxicity against RAW 264.7 cell lines. Thus, both compounds are promising candidates for development as an anti-TB drug leads.
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20
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21
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Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA. Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol 2018; 14:696-705. [PMID: 29867142 DOI: 10.1038/s41589-018-0067-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.
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Affiliation(s)
- Michael S Carter
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xinshuai Zhang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hua Huang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Brian San Francisco
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nawar Al-Obaidi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi G Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Harvey M Andersen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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22
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NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius. Sci Rep 2018; 8:7176. [PMID: 29739976 PMCID: PMC5940873 DOI: 10.1038/s41598-018-25361-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
Ketol-acid reductoisomerase (KARI) is a bifunctional enzyme in the second step of branched-chain amino acids biosynthetic pathway. Most KARIs prefer NADPH as a cofactor. However, KARI with a preference for NADH is desirable in industrial applications including anaerobic fermentation for the production of branched-chain amino acids or biofuels. Here, we characterize a thermoacidophilic archaeal Sac-KARI from Sulfolobus acidocaldarius and present its crystal structure at a 1.75-Å resolution. By comparison with other holo-KARI structures, one sulphate ion is observed in each binding site for the 2′-phosphate of NADPH, implicating its NADPH preference. Sac-KARI has very high affinity for NADPH and NADH, with KM values of 0.4 μM for NADPH and 6.0 μM for NADH, suggesting that both are good cofactors at low concentrations although NADPH is favoured over NADH. Furthermore, Sac-KARI can catalyze 2(S)-acetolactate (2S-AL) with either cofactor from 25 to 60 °C, but the enzyme has higher activity by using NADPH. In addition, the catalytic activity of Sac-KARI increases significantly with elevated temperatures and reaches an optimum at 60 °C. Bi-cofactor utilization and the thermoactivity of Sac-KARI make it a potential candidate for use in metabolic engineering or industrial applications under anaerobic or harsh conditions.
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23
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Chenette EJ, Martin SJ. 50 years of The FEBS Journal: looking back as well as ahead. FEBS J 2018; 284:4162-4171. [PMID: 29251437 DOI: 10.1111/febs.14328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this last issue of 2017, we're celebrating the 50th anniversary of The FEBS Journal. This Editorial considers how the journal has grown and changed from volume 1, issue 1 and outlines our exciting plans for the future.
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Affiliation(s)
| | - Seamus J Martin
- The FEBS Journal Editorial Office, Cambridge, UK.,Department of Genetics, The Smurfit Institute, Trinity College, Dublin, Ireland
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24
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Patel KM, Teran D, Zheng S, Kandale A, Garcia M, Lv Y, Schembri MA, McGeary RP, Schenk G, Guddat LW. Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity. Chemistry 2017; 23:18289-18295. [PMID: 28975665 DOI: 10.1002/chem.201704481] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 01/19/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is an NAD(P)H and Mg2+ -dependent enzyme of the branched-chain amino acid (BCAA) biosynthesis pathway. Here, the first crystal structures of Staphylococcus aureus (Sa) KARI in complex with two transition state analogues, cyclopropane-1,1-dicarboxylate (CPD) and N-isopropyloxalyl hydroxamate (IpOHA) are reported. These compounds bind competitively and in multi-dentate manner to KARI with Ki values of 2.73 μm and 7.9 nm, respectively; however, IpOHA binds slowly to the enzyme. Interestingly, intact IpOHA is present in only ≈25 % of binding sites, whereas its deoxygenated form is present in the remaining sites. This deoxy form of IpOHA binds rapidly to Sa KARI, but with much weaker affinity (Ki =21 μm). Thus, our data pinpoint the origin of the slow binding mechanism of IpOHA. Furthermore, we propose that CPD mimics the early stage of the catalytic reaction (preceding the reduction step), whereas IpOHA mimics the late stage (after the reduction took place). These structural insights will guide strategies to design potent and rapidly binding derivatives of these compounds for the development of novel biocides.
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Affiliation(s)
- Khushboo M Patel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - David Teran
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Shan Zheng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ajit Kandale
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Mario Garcia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - You Lv
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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25
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Amorim Franco TM, Blanchard JS. Bacterial Branched-Chain Amino Acid Biosynthesis: Structures, Mechanisms, and Drugability. Biochemistry 2017; 56:5849-5865. [PMID: 28977745 DOI: 10.1021/acs.biochem.7b00849] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eight enzymes responsible for the biosynthesis of the three branched-chain amino acids (l-isoleucine, l-leucine, and l-valine) were identified decades ago using classical genetic approaches based on amino acid auxotrophy. This review will highlight the recent progress in the determination of the three-dimensional structures of these enzymes, their chemical mechanisms, and insights into their suitability as targets for the development of antibacterial agents. Given the enormous rise in bacterial drug resistance to every major class of antibacterial compound, there is a clear and present need for the identification of new antibacterial compounds with nonoverlapping targets to currently used antibacterials that target cell wall, protein, mRNA, and DNA synthesis.
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Affiliation(s)
- Tathyana M Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
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26
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Xu CG, Yang YB, Zhou YH, Hao MQ, Ren YZ, Wang XT, Chen JQ, Muhammad I, Wang S, Liu D, Li XB, Li YH. Comparative Proteomic Analysis Provides insight into the Key Proteins as Possible Targets Involved in Aspirin Inhibiting Biofilm Formation of Staphylococcus xylosus. Front Pharmacol 2017; 8:543. [PMID: 28871227 PMCID: PMC5566577 DOI: 10.3389/fphar.2017.00543] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Staphylococcus xylosus is an opportunistic pathogen that causes infection in humans and cow mastitis. And S. xylosus possesses a strong ability to form biofilms in vitro. As biofilm formation facilitates resistance to antimicrobial agents, the discovery of new medicinal properties for classic drugs is highly desired. Aspirin, which is the most common active component of non-steroidal anti-inflammatory compounds, affects the biofilm-forming capacity of various bacterial species. We have found that aspirin effectively inhibits biofilm formation of S. xylosus by Crystal violet (CV) staining and scanning electron microscopy analyses. The present study sought to elucidate possible targets of aspirin in suppressing S. xylosus biofilm formation. Based on an isobaric tag for relative and absolute quantitation (iTRAQ) fold-change of >1.2 or <0.8 (P-value < 0.05), 178 differentially expressed proteins, 111 down-regulated and 67 up-regulated, were identified after application of aspirin to cells at a 1/2 minimal inhibitory concentration. Gene ontology analysis indicated enrichment in metabolic processes for the majority of the differentially expressed proteins. We then used the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database to analyze a large number of differentially expressed proteins and identified genes involved in biosynthesis of amino acids pathway, carbon metabolism (pentose phosphate and glycolytic pathways, tricarboxylic acid cycle) and nitrogen metabolism (histidine metabolism). These novel proteins represent candidate targets in aspirin-mediated inhibition of S. xylosus biofilm formation at sub-MIC levels. The findings lay the foundation for further studies to identify potential aspirin targets.
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Affiliation(s)
- Chang-Geng Xu
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yan-Bei Yang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yong-Hui Zhou
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Mei-Qi Hao
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yong-Zhi Ren
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Xiao-Ting Wang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Jian-Qing Chen
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Ishfaq Muhammad
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Shuai Wang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Di Liu
- Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Xiu-Bo Li
- Feed Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical DevelopmentHarbin, China
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27
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Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Meneguello JE, Seixas FAV, Lopes-Ortiz MA, Scodro RBL, Pires CTA, da Silva RZ, Siqueira VLD, Nakamura CV, Cardoso RF. Proteomic profile of Mycobacterium tuberculosis after eupomatenoid-5 induction reveals potential drug targets. Future Microbiol 2017; 12:867-879. [DOI: 10.2217/fmb-2017-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: We investigated a proteome profile, protein–protein interaction and morphological changes of Mycobacterium tuberculosis after different times of eupomatenoid-5 (EUP-5) induction to evaluate the cellular response to the drug-induced damages. Methods: The bacillus was induced to sub-minimal inhibitory concentration of EUP-5 at 12 h, 24 h and 48 h. The proteins were separated by 2D gel electrophoresis, identified by LC/MS-MS. Scanning electron microscopy and Search Tool for the Retrieval of Interacting Genes/Proteins analyses were performed. Results: EUP-5 impacts mainly in M. tuberculosis proteins of intermediary metabolism and interactome suggests a multisite disturbance that contributes to bacilli death. Scanning electron microscopy revealed the loss of bacillary form. Conclusion: Some of the differentially expressed proteins have the potential to be drug targets such as citrate synthase (Rv0896), phosphoglycerate kinase (Rv1437), ketol-acid reductoisomerase (Rv3001c) and ATP synthase alpha chain (Rv1308).
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Affiliation(s)
- Luciana D Ghiraldi-Lopes
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Paula AZ Campanerut-Sá
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Jean E Meneguello
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Flávio AV Seixas
- Department of Biochemistry, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Mariana A Lopes-Ortiz
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Uningá University Center, Rod PR 317, 6114, 87035-510, Maringá, Paraná, Brazil
| | - Regiane BL Scodro
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Claudia TA Pires
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosi Z da Silva
- State University of Ponta Grossa, Avenida General Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Paraná, Brazil
| | - Vera LD Siqueira
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Celso V Nakamura
- Postgraduate Program in Pharmaceutical Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
| | - Rosilene F Cardoso
- Postgraduate Program in Health Sciences, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
- Postgraduate Program in Biosciences & Phisiopatology, Department of Clinical Analyses & Biomedicine, State University of Maringá, Avenida Colombo, 5790, 87020-900, Maringá, Paraná, Brazil
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Tadrowski S, Pedroso MM, Sieber V, Larrabee JA, Guddat LW, Schenk G. Metal Ions Play an Essential Catalytic Role in the Mechanism of Ketol-Acid Reductoisomerase. Chemistry 2016; 22:7427-36. [PMID: 27136273 DOI: 10.1002/chem.201600620] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 01/13/2023]
Abstract
Ketol-acid reductoisomerase (KARI) is a Mg(2+) -dependent enzyme in the branched-chain amino acid biosynthesis pathway. It catalyses a complex two-part reaction: an alkyl migration followed by a NADPH-dependent reduction. Both reactions occur within the one active site, but in particular, the mechanism of the isomerisation step is poorly understood. Here, using a combination of kinetic, thermodynamic and spectroscopic techniques, the reaction mechanisms of both Escherichia coli and rice KARI have been investigated. We propose a conserved mechanism of catalysis, whereby a hydroxide, bridging the two Mg(2+) ions in the active site, initiates the reaction by abstracting a proton from the C2 alcohol group of the substrate. While the μ-hydroxide-bridged dimetallic centre is pre-assembled in the bacterial enzyme, in plant KARI substrate binding leads to a reduction of the metal-metal distance with the concomitant formation of a hydroxide bridge. Only Mg(2+) is capable of promoting the isomerisation reaction, likely to be due to non-competent substrate binding in the presence of other metal ions.
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Affiliation(s)
- Sonya Tadrowski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo M Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Volker Sieber
- Straubing Center of Science, Technische Universität München, Straubing, Germany
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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