1
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Min LJ, Shen ZH, Bajsa-Hirschel J, Cantrell CL, Han L, Hua XW, Liu XH, Duke SO. Synthesis, crystal structure, herbicidal activity and mode of action of new cyclopropane-1,1-dicarboxylic acid analogues. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105228. [PMID: 36464348 DOI: 10.1016/j.pestbp.2022.105228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 06/17/2023]
Abstract
A new series of cyclopropane-1,1-dicarboxylic (CPD) acid analogues were designed and synthesized. CPD is an inhibitor of ketol-acid reductoisomerase (KARI), an enzyme of the branched chain amino acid pathway in plants. The structures of CPD analogues were characterized by 1H NMR and HRMS. The structure of N,N'-bis(4-(tert-butyl)phenyl)cyclopropane-1,1-dicarboxamide was further elucidated by X-ray diffraction. The herbicidal activities of these compounds were tested against lettuce (Lactuca sativa) and bentgrass (Agrostis stolonifera). Most of these compounds exhibited low herbicidal activity against both plant species. Among them, N,N'-bis(2-ethylphenyl)cyclopropane-1,1-dicarboxamide displayed moderate activity against bentgrass. Inhibition of KARI activity by the CPD analogues was also assessed experimentally and by molecular docking simulation with results supporting inhibition of KARI as their mode of action. These results provide the basis for design of more effective KARI inhibitors.
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Affiliation(s)
- Li-Jing Min
- College of Life Science, Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, 313000, Zhejiang, China
| | - Zhong-Hua Shen
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, Agricultural Research Service, U.S. Department of Agriculture, P.O. Box 1848, MS 38677, USA
| | - Charles L Cantrell
- Natural Products Utilization Research Unit, Agricultural Research Service, U.S. Department of Agriculture, P.O. Box 1848, MS 38677, USA
| | - Liang Han
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Xue-Wen Hua
- College of Agriculture, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Xing-Hai Liu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
| | - Stephen O Duke
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS, 38677, USA.
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2
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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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3
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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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4
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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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5
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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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6
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Xiao C, Huang M, Gao J, Wang Z, Zhang D, Zhang Y, Yan L, Yu X, Li B, Shen Y. Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease. BMC Genomics 2020; 21:880. [PMID: 33297944 PMCID: PMC7727141 DOI: 10.1186/s12864-020-07286-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022] Open
Abstract
Background Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis. Results A total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot. Conclusions We found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07286-3.
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Affiliation(s)
- Chunfang Xiao
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianhua Gao
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Zhen Wang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Denghong Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Yuanxue Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Lei Yan
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Yanfen Shen
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China. .,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China.
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7
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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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8
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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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9
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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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10
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Wang BL, Zhang LY, Liu XH, Ma Y, Zhang Y, Li ZM, Zhang X. Synthesis, biological activities and SAR studies of new 3-substitutedphenyl-4-substitutedbenzylideneamino-1,2,4-triazole Mannich bases and bis-Mannich bases as ketol-acid reductoisomerase inhibitors. Bioorg Med Chem Lett 2017; 27:5457-5462. [DOI: 10.1016/j.bmcl.2017.10.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/20/2023]
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11
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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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12
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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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13
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Zhang Y, Liu XH, Zhan YZ, Zhang LY, Li ZM, Li YH, Zhang X, Wang BL. Synthesis and biological activities of novel 5-substituted-1,3,4-oxadiazole Mannich bases and bis-Mannich bases as ketol-acid reductoisomerase inhibitors. Bioorg Med Chem Lett 2016; 26:4661-4665. [DOI: 10.1016/j.bmcl.2016.08.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/04/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
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14
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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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15
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Lv Y, Kandale A, Wun SJ, McGeary RP, Williams SJ, Kobe B, Sieber V, Schembri MA, Schenk G, Guddat LW. Crystal structure of
Mycobacterium tuberculosis
ketol‐acid reductoisomerase at 1.0 Å resolution – a potential target for anti‐tuberculosis drug discovery. FEBS J 2016; 283:1184-96. [DOI: 10.1111/febs.13672] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/18/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Affiliation(s)
- You Lv
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Ajit Kandale
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Shun Jie Wun
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
- Institute for Molecular Bioscience University of Queensland Brisbane Australia
| | - Volker Sieber
- Straubing Center of Science Technische Universität München Straubing Germany
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences and Australian Infectious Disease Research Centre University of Queensland Brisbane Australia
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16
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Identification and optimization of a novel thermo- and solvent stable ketol-acid reductoisomerase for cell free isobutanol biosynthesis. Biochimie 2015; 108:76-84. [DOI: 10.1016/j.biochi.2014.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 10/27/2014] [Indexed: 11/22/2022]
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17
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Zhu H, Wang B, Zhang X, Xiong L, Yu S, Li Z. Syntheses and biological activities of novel 3-bromo-1-(3-chloropyridin-2-yl)-N-hydroxy-N-aryl-1H-pyrazole-5-carboxamides. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-3376-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Liu X, Wang J, Xu J, Shi J. FgIlv5 is required for branched-chain amino acid biosynthesis and full virulence in Fusarium graminearum. Microbiology (Reading) 2014; 160:692-702. [DOI: 10.1099/mic.0.075333-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In this study, we characterized FgIlv5, a homologue of the Saccharomyces cerevisiae keto-acid reductoisomerase (KARI) from the important wheat head scab fungus Fusarium graminearum. KARI is a key enzyme in the branched-chain amino acid (BCAA, including leucine, isoleucine and valine) biosynthetic pathway that exists in a variety of organisms from bacteria to fungi and higher plants, but not in mammals. The FgILV5 deletion mutant ΔFgIlv5-4 failed to grow when the culture medium was nutritionally limited for BCAAs. When grown on potato-dextrose agar plates, ΔFgIlv5-4 exhibited a significant decrease in aerial hyphae formation and red pigmentation. Conidia formation was also blocked in ΔFgIlv5-4. Exogenous addition of 1 mM isoleucine and valine was able to rescue the defects of mycelial growth and conidial morphogenesis. Cellular stress assays showed that ΔFgIlv5-4 was more sensitive to osmotic and oxidative stresses than the wild-type strain. In addition, virulence of ΔFgIlv5-4 was dramatically reduced on wheat heads, and a low level of deoxynivalenol production was detected in ΔFgIlv5-4 in wheat kernels. The results of this study indicate that FgIlv5 is involved in valine and isoleucine biosynthesis and is required for full virulence in F. graminearum.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality (Nanjing), Ministry of Agriculture/Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, PR China
| | - Jian Wang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality (Nanjing), Ministry of Agriculture/Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, PR China
| | - Jianhong Xu
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality (Nanjing), Ministry of Agriculture/Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, PR China
| | - Jianrong Shi
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality (Nanjing), Ministry of Agriculture/Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, PR China
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General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH. Proc Natl Acad Sci U S A 2013; 110:10946-51. [PMID: 23776225 DOI: 10.1073/pnas.1306073110] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To date, efforts to switch the cofactor specificity of oxidoreductases from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) have been made on a case-by-case basis with varying degrees of success. Here we present a straightforward recipe for altering the cofactor specificity of a class of NADPH-dependent oxidoreductases, the ketol-acid reductoisomerases (KARIs). Combining previous results for an engineered NADH-dependent variant of Escherichia coli KARI with available KARI crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specificity determinants and used this information to construct five KARIs with reversed cofactor preference. Additional directed evolution generated two enzymes having NADH-dependent catalytic efficiencies that are greater than the wild-type enzymes with NADPH. High-resolution structures of a wild-type/variant pair reveal the molecular basis of the cofactor switch.
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20
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Zabalza A, Zulet A, Gil-Monreal M, Igal M, Royuela M. Branched-chain amino acid biosynthesis inhibitors: herbicide efficacy is associated with an induced carbon-nitrogen imbalance. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:814-21. [PMID: 23394788 DOI: 10.1016/j.jplph.2013.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 05/08/2023]
Abstract
Acetolactate synthase (ALS; EC 4.1.3.18) and ketol-acid reductoisomerase (KARI; EC 1.1.1.86) are two consecutive enzymes in the biosynthesis of branched-chain amino acids. Several commercial herbicides inhibit ALS as their primary site of action. KARI has also attracted attention as a potential target for herbicides. Although potent and selective inhibitors of KARI have been discovered, these inhibitors display less herbicidal activity than ALS-inhibiting herbicides. To obtain a better understanding of these findings, we have compared the physiological effects induced in pea plants after KARI or ALS inhibition. Although, both types of inhibitors induce growth arrest and photosynthesis inhibition, plant death occurs more rapidly under ALS inhibition than KARI inhibition. Carbohydrates accumulated in the leaves and roots following treatments with both inhibitors. The carbohydrate accumulation in the leaves occurred as a consequence of a decrease in sink strength. In contrast, the free amino acid content was only affected through ALS inhibition. These results indicate that although KARI and ALS inhibition block the same biosynthetic pathway and exert common effects on carbon metabolism, nitrogen metabolism is more affected via ALS than KARI inhibition. Thus, metabolic alterations in nitrogen metabolism induced through ALS inhibitors might contribute to the increased efficacy of these chemicals as herbicides.
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Affiliation(s)
- Ana Zabalza
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Campus de Arrosadia, E-31006, Pamplona, Spain
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21
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Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle. J Mol Biol 2012; 424:168-79. [PMID: 23036858 DOI: 10.1016/j.jmb.2012.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/09/2012] [Accepted: 09/24/2012] [Indexed: 11/21/2022]
Abstract
Ketol-acid reductoisomerase (KARI) is the second enzyme in the branched-chain amino acid biosynthesis pathway, which is found in plants, fungi and bacteria but not in animals. This difference in metabolism between animals and microorganisms makes KARI an attractive target for the development of antimicrobial agents. Herein we report the crystal structure of Escherichia coli KARI in complex with Mg(2+) and NADPH at 2.3Å resolution. Ultracentrifugation studies confirm that the enzyme exists as a tetramer in solution, and isothermal titration calorimetry shows that the binding of Mg(2+) increases structural disorder while the binding of NADPH increases the structural rigidity of the enzyme. Comparison of the structure of the E. coli KARI-Mg(2+)-NADPH complex with that of enzyme in the absence of cofactors shows that the binding of Mg(2+) and NADPH opens the interface between the N- and C-domains, thereby allowing access for the substrates to bind: the existence of only a small opening between the domains in the crystal structure of the unliganded enzyme signifies restricted access to the active site. This observation contrasts with that in the plant enzyme, where the N-domain can rotate freely with respect to the C-domain until the binding of Mg(2+) and/or NADPH stabilizes the relative positions of these domains. Support is thereby provided for the idea that plant and bacterial KARIs have evolved different mechanisms of induced fit to prepare the active site for catalysis.
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22
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Synthesis, bioactivity and DFT structure–activity relationship study of novel 1,2,3-thiadiazole derivatives. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0521-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis. Clin Proteomics 2012; 9:1. [PMID: 22300397 PMCID: PMC3298717 DOI: 10.1186/1559-0275-9-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 02/03/2012] [Indexed: 01/20/2023] Open
Abstract
Aspergillus is a leading causative agent for fungal morbidity and mortality in immuno-compromised patients. To identify a putative target to design or identify new antifungal drug, against Aspergillus is required. In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target. This enzyme was found to be unique by comparing to host proteome through BLASTp analysis. A homology based model of KARI was generated by Swiss model server. The generated model had been validated by PROCHECK and WHAT IF programs. The Zinc library was generated within the limitation of the Lipinski rule of five, for docking study. Based on the dock-score six molecules have been studied for ADME/TOX analysis and subjected for pharmacophore model generation. The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI. This study is an attempt to Insilco evaluation of the KARI as a drug target and the screened inhibitors could help in the development of the better drug against Aspergillus.
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24
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Synthesis, structure, and biological activity of novel (oxdi/tri)azoles derivatives containing 1,2,3-thiadiazole or methyl moiety. Mol Divers 2012; 16:251-60. [PMID: 22249419 DOI: 10.1007/s11030-011-9352-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 12/22/2011] [Indexed: 10/14/2022]
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25
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Wang BL, Liu XH, Zhang XL, Zhang JF, Song HB, Li ZM. Synthesis, Structure and Biological Activity of Novel 1,2,4-Triazole Mannich Bases Containing a Substituted Benzylpiperazine Moiety. Chem Biol Drug Des 2011; 78:42-9. [DOI: 10.1111/j.1747-0285.2011.01132.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Liu XH, Chen PQ, Wang BL, Dong WL, Li YH, Xie XQ, Li ZM. High Throughput Receptor-Based Virtual Screening Under ZINC Database, Synthesis, and Biological Evaluation of Ketol-Acid Reductoisomerase Inhibitors. Chem Biol Drug Des 2010; 75:228-32. [DOI: 10.1111/j.1747-0285.2009.00924.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Liu XH, Zhang CY, Guo WC, Li YH, Chen PQ, Wang T, Dong WL, Wang BL, Sun HW, Li ZM. Synthesis, Bioactivity and SAR study of N′-(5-substituted-1,3,4-thiadiazol-2-yl)-N-cyclopropylformyl-thioureas as ketol-acid reductoisomerase Inhibitors. J Enzyme Inhib Med Chem 2009; 24:545-52. [DOI: 10.1080/14756360802234943] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xing-Hai Liu
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Chuan-Yu Zhang
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Wan-Cheng Guo
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Yong-Hong Li
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Pei-Quan Chen
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Teng Wang
- 2Department of Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Wei-Li Dong
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Bao-Lei Wang
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
| | - Hong-Wei Sun
- 2Department of Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Zheng-Ming Li
- 1State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, China
- 3National Pesticide Engineering Research Center, Nankai University, Tianjin, 300071, China
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28
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Wang BL, Li YH, Wang JG, Ma Y, Li ZM. Molecular design, synthesis and biological activities of amidines as new ketol-acid reductoisomerase inhibitors. CHINESE CHEM LETT 2008. [DOI: 10.1016/j.cclet.2008.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Liu XH, Chen PQ, Guo WC, Wang SH, Li ZM. High Throughput Screening Under Zinc-Database and Synthesis a Dialkylphosphinic Acid as a Potential Kari Inhibitor. PHOSPHORUS SULFUR 2008. [DOI: 10.1080/10426500701807897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Xing-Hai Liu
- a The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center , Nankai University , Tianjin, China
| | - Pei-Quan Chen
- a The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center , Nankai University , Tianjin, China
| | - Wan-Cheng Guo
- a The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center , Nankai University , Tianjin, China
| | - Su-Hua Wang
- a The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center , Nankai University , Tianjin, China
| | - Zheng-Ming Li
- a The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center , Nankai University , Tianjin, China
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30
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Brandes N, Rinck A, Leichert LI, Jakob U. Nitrosative stress treatment of E. coli targets distinct set of thiol-containing proteins. Mol Microbiol 2007; 66:901-14. [PMID: 17919278 DOI: 10.1111/j.1365-2958.2007.05964.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Reactive nitrogen species (RNS) function as powerful antimicrobials in host defence, but so far little is known about their bacterial targets. In this study, we set out to identify Escherichia coli proteins with RNS-sensitive cysteines. We found that only a very select set of proteins contain cysteines that undergo reversible thiol modifications upon nitric oxide (NO) treatment in vivo. Of the 10 proteins that we identified, six (AtpA, AceF, FabB, GapA, IlvC, TufA) have been shown to harbour functionally important thiol groups and are encoded by genes that are considered essential under our growth conditions. Media supplementation studies suggested that inactivation of AceF and IlvC is, in part, responsible for the observed NO-induced growth inhibition, indicating that RNS-mediated modifications play important physiological roles. Interestingly, the majority of RNS-sensitive E. coli proteins differ from E. coli proteins that harbour H2O2-sensitive thiol groups, implying that reactive oxygen and nitrogen species affect distinct physiological processes in bacteria. We confirmed this specificity by analysing the activity of one of our target proteins, the small subunit of glutamate synthase. In vivo and in vitro activity studies confirmed that glutamate synthase rapidly inactivates upon NO treatment but is resistant towards other oxidative stressors.
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Affiliation(s)
- Nicolas Brandes
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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31
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Liu XH, Chen PQ, Wang BL, Li YH, Wang SH, Li ZM. Synthesis, bioactivity, theoretical and molecular docking study of 1-cyano-N-substituted-cyclopropanecarboxamide as ketol-acid reductoisomerase inhibitor. Bioorg Med Chem Lett 2007; 17:3784-8. [PMID: 17512731 DOI: 10.1016/j.bmcl.2007.04.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 03/15/2007] [Accepted: 04/02/2007] [Indexed: 11/24/2022]
Abstract
Ketol-acid reductoisomerase (KARI; EC 1.1.1.86) catalyzes the second common step in branched-chain amino acid biosynthesis. The catalyzed process consists of two stages, the first of which is an alkyl migration from one carbon atom to its neighbouring atom. The likely transition state is a cyclopropane derivative, thus a series of new cyclopropane derivatives, such as 1-cyano-N-substituted-cyclopropanecarboxamide, were designed and synthesized. Their structures were verified by (1)H NMR, FTIR spectrum, MS and elemental analysis. The K(i) values of active compounds 2, 4b against rice KARI were 95.30+/-13.71, 207.9+/-21.99 microM, respectively. The X-ray crystal structure of compound 4a was also determined. Auto-Dock was used to predict the binding mode of 4a. This was done by analyzing the interaction of the compounds 4a with the active sites of spinach KARI. This result was in accord with the result analyzed by the frontier molecular orbital theory.
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Affiliation(s)
- Xing-Hai Liu
- The Research Institute of Elemento-Organic Chemistry, The State-Key Laboratory of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, Nankai University, Tianjin 300071, China
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McCourt JA, Duggleby RG. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 2006; 31:173-210. [PMID: 16699828 DOI: 10.1007/s00726-005-0297-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.
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Affiliation(s)
- J A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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33
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Moberg WK, Cross B. Herbicides inhibiting branched-chain amino acid biosynthesis. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ps.2780290302] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Zabalza A, González EM, Arrese-Igor C, Royuela M. Fermentative metabolism is induced by inhibiting different enzymes of the branched-chain amino acid biosynthesis pathway in pea plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:7486-93. [PMID: 16159177 DOI: 10.1021/jf050654x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The inhibition of branched-chain amino acid (BCAA) biosynthesis was evaluated in pea plants in relation to the ability for induction of fermentative metabolism under aerobic conditions. Chlorsulfuron and imazethapyr (inhibitors of acetolactate synthase, ALS, EC 4.1.3.18) produced a strong induction of pyruvate decarboxylase (PDC, EC 4.1.1.1) and alcohol dehydrogenase (ADH, EC 1.1.1.1) activities and a lesser induction of lactate dehydrogenase (LDH, EC 1.1.1.27) and alanine aminotransferase (AlaAT, EC 2.6.1.2) activities in roots. Inhibition of the second enzyme of the BCAA biosynthesis (ketol-acid reductoisomerase, KARI, EC 1.1.1.86) by Hoe 704 (2-dimethylphosphinoyl-2-hydroxyacetic acid) and CPCA (1,1-cyclopropanedicarboxylic acid) enhanced fermentative enzyme activities including PDC, ADH, and AlaAT. Fermentative metabolism induction occurring with ALS- and KARI-inhibitors was related to a higher expression of PDC. In the case of KARI inhibition, it is proposed that fermentation induction is due to an inhibition of ALS activity resulted from an increase in acetolactate concentration. Fermentative metabolism induction in roots, or at least ethanolic fermentation, appeared to be a general physiological response to the BCAA biosynthesis inhibition.
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Affiliation(s)
- Ana Zabalza
- Departamento Ciencias del Medio Natural, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, Spain
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Kuntz L, Tritsch D, Grosdemange-Billiard C, Hemmerlin A, Willem A, Bach T, Rohmer M. Isoprenoid biosynthesis as a target for antibacterial and antiparasitic drugs: phosphonohydroxamic acids as inhibitors of deoxyxylulose phosphate reducto-isomerase. Biochem J 2005; 386:127-35. [PMID: 15473867 PMCID: PMC1134774 DOI: 10.1042/bj20041378] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Isoprenoid biosynthesis via the methylerythritol phosphate pathway is a target against pathogenic bacteria and the malaria parasite Plasmodium falciparum. 4-(Hydroxyamino)-4-oxobutylphosphonic acid and 4-[hydroxy(methyl)amino]-4-oxobutyl phosphonic acid, two novel inhibitors of DXR (1-deoxy-D-xylulose 5-phosphate reducto-isomerase), the second enzyme of the pathway, have been synthesized and compared with fosmidomycin, the best known inhibitor of this enzyme. The latter phosphonohydroxamic acid showed a high inhibitory activity towards DXR, much like fosmidomycin, as well as significant antibacterial activity against Escherichia coli in tests on Petri dishes.
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Affiliation(s)
- Lionel Kuntz
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Denis Tritsch
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | | | - Andréa Hemmerlin
- †CNRS-UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Audrey Willem
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Thomas J. Bach
- †CNRS-UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Michel Rohmer
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
- To whom correspondence should be addressed (email )
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Wang BL, Duggleby RG, Li ZM, Wang JG, Li YH, Wang SH, Song HB. Synthesis, crystal structure and herbicidal activity of mimics of intermediates of the KARI reaction. PEST MANAGEMENT SCIENCE 2005; 61:407-412. [PMID: 15751008 DOI: 10.1002/ps.972] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two mimics of the intermediate in the reaction catalyzed by ketol-acid reductoisomerase (KARI) were synthesized. Their structures were established on the basis of elemental analyses, IR, 1H NMR and GC/mass detector. The crystal structure of compound 2 was found to be a substituted dioxane, formed by the condensation of two molecules. The two compounds showed some herbicidal activity on the basis of tests using rape root and barnyard grass growth inhibition. However, the herbicidal effect was weaker in greenhouse tests.
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Affiliation(s)
- Bao-Lei Wang
- Elemento-Organic Chemistry Institute, State-Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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Tyagi R, Lee YT, Guddat LW, Duggleby RG. Probing the mechanism of the bifunctional enzyme ketol-acid reductoisomerase by site-directed mutagenesis of the active site. FEBS J 2005; 272:593-602. [PMID: 15654896 DOI: 10.1111/j.1742-4658.2004.04506.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ketol-acid reductoisomerase (EC 1.1.1.86) is involved in the biosynthesis of the branched-chain amino acids. It is a bifunctional enzyme that catalyzes two quite different reactions at a common active site; an isomerization consisting of an alkyl migration, followed by an NADPH-dependent reduction of a 2-ketoacid. The 2-ketoacid formed by the alkyl migration is not released. Using the pure recombinant Escherichia coli enzyme, we show that the isomerization reaction has a highly unfavourable equilibrium constant. The reductase activity is shown to be relatively nonspecific and is capable of utilizing a variety of 2-ketoacids. The active site of the enzyme contains eight conserved polar amino acids and we have mutated each of these in order to dissect their contributions to the isomerase and reductase activities. Several mutations result in loss of the isomerase activity with retention of reductase activity. However, none of the 17 mutants examined have the isomerase activity only. We suggest a reason for this, involving direct reduction of a transition state formed during the isomerization, which is necessitated by the unfavourable equilibrium position of the isomerization. Our mechanism explains why the two activities must occur in a single active site without release of a 2-ketoacid and provides a rationale for the requirement for NADPH by the isomerase.
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Affiliation(s)
- Rajiv Tyagi
- Department of Biochemistry and Molecular Biology, The University of Queensland, Brisbane, Qld 4072, Australia
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Fox DT, Poulter CD. Synthesis and Evaluation of 1-Deoxy-d-xylulose 5-Phosphoric Acid Analogues as Alternate Substrates for Methylerythritol Phosphate Synthase. J Org Chem 2005; 70:1978-85. [PMID: 15760175 DOI: 10.1021/jo048022h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] Four deoxyxylulose phosphate (DXP) analogues were synthesized and evaluated as substrates/inhibitors for methylerythritol phosphate (MEP) synthase. In analogues CF(3)-DXP (1), CF(2)-DXP (2), and CF-DXP (3), the three methyl hydrogens at C1 of DXP were sequentially replaced by fluorine. In the fourth analogue, Et-DXP (4), the methyl group in DXP was replaced by an ethyl moiety. Analogues 1, 2, and 4 were not substrates for MEP synthase under normal catalytic conditions and were instead modest inhibitors with IC(50) values of 2.0, 3.4, and 6.2 mM, respectively. In contrast, 3 was a good substrate (k(cat) = 38 s(-)(1), K(m) = 227 muM) with a turnover rate similar to that of the natural substrate. These results are consistent with a retro-aldol/aldol mechanism rather than an alpha-ketol rearrangement for the enzyme-catalyzed conversion of DXP to MEP.
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Affiliation(s)
- David T Fox
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Engel S, Vyazmensky M, Vinogradov M, Berkovich D, Bar-Ilan A, Qimron U, Rosiansky Y, Barak Z, Chipman DM. Role of a Conserved Arginine in the Mechanism of Acetohydroxyacid Synthase. J Biol Chem 2004; 279:24803-12. [PMID: 15044456 DOI: 10.1074/jbc.m401667200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thiamin diphosphate (ThDP)-dependent bio-synthetic enzyme acetohydroxyacid synthase (AHAS) catalyzes decarboxylation of pyruvate and specific condensation of the resulting ThDP-bound two-carbon intermediate, hydroxyethyl-ThDP anion/enamine (HEThDP(-)), with a second ketoacid, to form acetolactate or acetohydroxybutyrate. Whereas the mechanism of formation of HEThDP(-) from pyruvate is well understood, the role of the enzyme in control of the carboligation reaction of HEThDP(-) is not. Recent crystal structures of yeast AHAS from Duggleby's laboratory suggested that an arginine residue might interact with the second ketoacid substrate. Mutagenesis of this completely conserved residue in Escherichia coli AHAS isozyme II (Arg(276)) confirms that it is required for rapid and specific reaction of the second ketoacid. In the mutant proteins, the normally rapid second phase of the reaction becomes rate-determining. A competing alternative nonnatural but stereospecific reaction of bound HEThDP(-) with benzaldehyde to form phenylacetylcarbinol (Engel, S., Vyazmensky, M., Geresh, S., Barak, Z., and Chipman, D. M. (2003) Biotechnol. Bioeng. 84, 833-840) provides a new tool for studying the fate of HEThDP(-) in AHAS, since the formation of the new product has a very different dependence on active site modifications than does acetohydroxyacid acid formation. The effects of mutagenesis of four different residues in the site on the rates and specificities of the normal and unnatural reactions support a critical role for Arg(276) in the stabilization of the transition states for ligation of the incoming second ketoacid with HEThDP(-) and/or for the breaking of the product-ThDP bond. This information makes it possible to engineer the active site so that it efficiently and preferentially catalyzes a new reaction.
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Affiliation(s)
- Stanislav Engel
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, 84105 Beer-Sheva, Israel
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Dumas R, Biou V, Halgand F, Douce R, Duggleby RG. Enzymology, structure, and dynamics of acetohydroxy acid isomeroreductase. Acc Chem Res 2001; 34:399-408. [PMID: 11352718 DOI: 10.1021/ar000082w] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetohydroxy acid isomeroreductase is a key enzyme involved in the biosynthetic pathway of the amino acids isoleucine, valine, and leucine. This enzyme is of great interest in agrochemical research because it is present only in plants and microorganisms, making it a potential target for specific herbicides and fungicides. Moreover, it catalyzes an unusual two-step reaction that is of great fundamental interest. With a view to characterizing both the mechanism of inhibition by potential herbicides and the complex reaction mechanism, various techniques of enzymology, molecular biology, mass spectrometry, X-ray crystallography, and theoretical simulation have been used. The results and conclusions of these studies are described briefly in this paper.
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Affiliation(s)
- R Dumas
- Laboratoire Mixte CNRS/INRA/Aventis, Aventis CropScience, 14-20 rue Pierre Baizet, 69263 Lyon, France.
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Epelbaum S, Chipman DM, Barak Z. Analysis of intracellular metabolites as tool for studying branched-chain amino acid biosynthesis and its inhibition in bacteria. Methods Enzymol 2001; 324:10-23. [PMID: 10989413 DOI: 10.1016/s0076-6879(00)24214-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- S Epelbaum
- Central Research and Development Department, E.I. duPont de Nemours and Company, Wilmington, Delaware 19880-0173, USA
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Liao DI, Calabrese JC, Wawrzak Z, Viitanen PV, Jordan DB. Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 2001; 9:11-8. [PMID: 11342130 DOI: 10.1016/s0969-2126(00)00550-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND 3,4-Dihydroxy-2-butanone-4-phosphate synthase catalyzes a commitment step in the biosynthesis of riboflavin. On the enzyme, ribulose 5-phosphate is converted to 3,4-dihydroxy-2-butanone 4-phosphate and formate in steps involving enolization, ketonization, dehydration, skeleton rearrangement, and formate elimination. The enzyme is absent in humans and an attractive target for the discovery of antimicrobials for pathogens incapable of acquiring sufficient riboflavin from their hosts. The homodimer of 23 kDa subunits requires Mg(2+) for activity. RESULTS The first three-dimensional structure of the enzyme was determined at 1.4 A resolution using the multiwavelength anomalous diffraction (MAD) method on Escherichia coli protein crystals containing gold. The protein consists of an alpha + beta fold having a complex linkage of beta strands. Intersubunit contacts are mediated by numerous hydrophobic interactions and three hydrogen bond networks. CONCLUSIONS A proposed active site was identified on the basis of amino acid residues that are conserved among the enzyme from 19 species. There are two well-separated active sites per dimer, each of which comprise residues from both subunits. In addition to three arginines and two threonines, which may be used for recognizing the phosphate group of the substrate, the active site consists of three glutamates, two aspartates, two histidines, and a cysteine which may provide the means for general acid and base catalysis and for coordinating the Mg(2+) cofactor within the active site.
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Affiliation(s)
- D I Liao
- DuPont Central Research and Development Experimental Station, Wilmington, DE 19880, USA.
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Metzler DE, Metzler CM, Sauke DJ. Enzymatic Addition, Elimination, Condensation, and Isomerization. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Proust-De Martin F, Dumas R, Field MJ. A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction. J Am Chem Soc 2000. [DOI: 10.1021/ja000414s] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Flavien Proust-De Martin
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale, Jean-Pierre Ebel 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France, and Unité Mixte CNRS/Aventis Crop Science (UMR 1932), 14-20, rue Pierre Baizet, 69263 Lyon Cedex 09, France
| | - Renaud Dumas
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale, Jean-Pierre Ebel 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France, and Unité Mixte CNRS/Aventis Crop Science (UMR 1932), 14-20, rue Pierre Baizet, 69263 Lyon Cedex 09, France
| | - Martin J. Field
- Contribution from the Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale, Jean-Pierre Ebel 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France, and Unité Mixte CNRS/Aventis Crop Science (UMR 1932), 14-20, rue Pierre Baizet, 69263 Lyon Cedex 09, France
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Miyata R, Yonehara T. Breeding of high-pyruvate-producing Torulopsis glabrata and amino acid auxotrophic mutants. J Biosci Bioeng 2000. [DOI: 10.1016/s1389-1723(00)80100-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hill CM, Duggleby RG. Purified recombinant Escherichia coli ketol-acid reductoisomerase is unsuitable for use in a coupled assay of acetohydroxyacid synthase activity due to an unexpected side reaction. Protein Expr Purif 1999; 15:57-61. [PMID: 10024470 DOI: 10.1006/prep.1998.0988] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ketol-acid reductoisomerase (EC 1.1.1.86) catalyzes the conversion of 2-aceto-2-hydroxyacids to 2-keto-3-hydroxyacids and their subsequent reduction by NADPH to 2,3-dihydroxyacids. The gene encoding the Escherichia coli enzyme was cloned and expressed as a hexahistidine-tagged fusion protein and the recombinant enzyme purified by metal-ligand affinity chromatography. The pure enzyme was tested for its ability to provide a sensitive and continuous coupled assay for acetohydroxyacid synthase (EC 4.1.3.18), the preceding enzyme in the pathway of branched-chain amino acid biosynthesis. An unexpected side reaction of ketol-acid reductoisomerase was observed in which it catalyzes the reduction of pyruvate. Although relatively slow, this side reaction is high enough to prohibit the use of this enzyme in a coupled assay for acetohydroxyacid synthase.
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Affiliation(s)
- C M Hill
- Centre for Protein Structure, Function, and Engineering, Department of Biochemistry, University of Queensland, Brisbane, Queensland, 4072, Australia
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Laprévote O, Serani L, Das BC, Halgand F, Forest E, Dumas R. Stepwise building of a 115-kDa macromolecular edifice monitored by electrospray mass spectrometry. The case of acetohydroxy acid isomeroreductase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 259:356-9. [PMID: 9914514 DOI: 10.1046/j.1432-1327.1999.00046.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The macromolecular complexes formed by the enzyme acetohydroxy acid isomeroreductase with NADPH, magnesium ions and the competitive inhibitor N-hydroxy-N-isopropyloxamate (IpOHA) were analysed by electrospray mass spectrometry. Each ligand was added successively to a protein solution, allowing the stoichiometry of the whole macromolecular edifice (115 583 Da) to be unambiguously determined. The combination of an electrospray ion source with the high mass range magnetic instrument used in the present studies proved to be a very powerful tool for characterizing, in a specific manner, the quaternary structures of proteins by single mass measurements.
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Affiliation(s)
- O Laprévote
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette Cedex, France.
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Hardré R, Bonnette C, Salmon L, Gaudemer A. Synthesis and evaluation of a new inhibitor of phosphoglucose isomerases: the enediolate analogue 5-phospho-D-arabinohydroxamate. Bioorg Med Chem Lett 1998; 8:3435-8. [PMID: 9873748 DOI: 10.1016/s0960-894x(98)00621-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Designed as a high energy intermediate analogue inhibitor of the potent chemotherapeutic target phosphoglucose isomerases, 5-phospho-D-arabinohydroxamate was efficiently synthesized in a two steps procedure. To date, it proved to be the strongest competitive inhibitor with respect to substrate D-fructose-6-phosphate (Ki down to 98 nM and Km/Ki values up to 513). A comparative inhibition study of this compound and other known strong inhibitors on phosphoglucose isomerases from three different sources is also reported.
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Affiliation(s)
- R Hardré
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-URA 1384, ICMO, Université Paris-XI, Orsay, France
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Vogel KW, Drueckhammer DG. A Reversed Thioester Analogue of Acetyl-Coenzyme A: An Inhibitor of Thiolase and a Synthon for Other Acyl-CoA Analogues. J Am Chem Soc 1998. [DOI: 10.1021/ja971758u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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