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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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2
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Hui X, Tian JM, Wang X, Zhang ZQ, Zhao YM, Gao WY, Li H. Overall analyses of the reactions catalyzed by acetohydroxyacid synthase/acetolactate synthase using a precolumn derivatization-HPLC method. Anal Biochem 2023; 660:114980. [PMID: 36368345 DOI: 10.1016/j.ab.2022.114980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
A precolumn derivatization-HPLC method using 2,4-dinitrophenylhydrazine and 4-nitro-o-phenylenediamine as respective labeling reagents for comprehensive analyses of the reactions catalyzed by acetohydroxyacid synthase (AHAS)/acetolactate synthase (ALS) is developed and evaluated in this research. Comparison with the classic Bauerle' UV assay which can analyze the enzymes only through measurement of acetoin production, the HPLC method shows advantages because it can analyze the enzymes not only via determination of consumption of the substrate pyruvate, but also via measurement of formation of the products including acetoin, 2,3-butanedione, and acetaldehyde in the enzymatic reactions. Thus the results deduced from the HPLC method can reflect the trait of each enzyme in a more precise manner. As far as we know, this is the first time that the reactions mediated by AHAS/ALS using pyruvate as a single substrate are globally analyzed and the features of the enzymes are properly discussed.
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Affiliation(s)
- Xian Hui
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Jin-Meng Tian
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Xin Wang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Zhen-Qian Zhang
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Ya-Mei Zhao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China
| | - Wen-Yun Gao
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Heng Li
- National Engineering Research Center for Miniaturized Detection Systems and College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, Shaanxi, 710069, China.
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3
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Wu S, Hu D, Wan X, Zhao J, He Q, Su Z, Cao H. Photocatalytic C-H Disulfuration for the Preparation of Indolizine-3-disulfides. J Org Chem 2022; 87:16297-16306. [PMID: 36417299 DOI: 10.1021/acs.joc.2c01871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A photocatalytic C-H disulfuration of indolizines was developed, giving an approach to a wide variety of indolizine-3-disulfides with good yields. Trisulfide dioxides were explored as a high-efficient disulfuration reagent. This disulfuration reaction could be scaled up to grams. Mechanistic studies support a photoinduced pathway involving the generation of indolizine cationic radicals. A bulky alkyl substituent on terminal sulfur of trisulfide dioxide A was necessary for selective formation of disulfide over monosulfide.
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Affiliation(s)
- Songxin Wu
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Dangzhong Hu
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Xuegui Wan
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Jiaji Zhao
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Qiuxing He
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Zhengquan Su
- Guangdong Engineering Research Centre of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Centre of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hua Cao
- School of Chemistry and Chemical Engineering and Guangdong Cosmetics Engineering & Technology Research Centre, Guangdong Pharmaceutical University, Zhongshan 528458, China.,Guangdong Pharmaceutical University-University of Hong Kong Joint Biomedical Innovation Platform, Zhongshan 528437, China
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4
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Berger A, Knak T, Kiffe-Delf AL, Mudrovcic K, Singh V, Njoroge M, Burckhardt BB, Gopalswamy M, Lungerich B, Ackermann L, Gohlke H, Chibale K, Kalscheuer R, Kurz T. Total Synthesis of the Antimycobacterial Natural Product Chlorflavonin and Analogs via a Late-Stage Ruthenium(II)-Catalyzed ortho-C(sp2)-H-Hydroxylation. Pharmaceuticals (Basel) 2022; 15:ph15080984. [PMID: 36015133 PMCID: PMC9415896 DOI: 10.3390/ph15080984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
The continuous, worldwide spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) endanger the World Health Organization’s (WHO) goal to end the global TB pandemic by the year 2035. During the past 50 years, very few new drugs have been approved by medical agencies to treat drug-resistant TB. Therefore, the development of novel antimycobacterial drug candidates to combat the threat of drug-resistant TB is urgent. In this work, we developed and optimized a total synthesis of the antimycobacterial natural flavonoid chlorflavonin by selective ruthenium(II)-catalyzed ortho-C(sp2)-H-hydroxylation of a substituted 3′-methoxyflavonoid skeleton. We extended our methodology to synthesize a small compound library of 14 structural analogs. The new analogs were tested for their antimycobacterial in vitro activity against Mycobacterium tuberculosis (Mtb) and their cytotoxicity against various human cell lines. The most promising new analog bromflavonin exhibited improved antimycobacterial in vitro activity against the virulent H37Rv strain of Mtb (Minimal Inhibitory Concentrations (MIC90) = 0.78 μm). In addition, we determined the chemical and metabolic stability as well as the pKa values of chlorflavonin and bromflavonin. Furthermore, we established a quantitative structure–activity relationship model using a thermodynamic integration approach. Our computations may be used for suggesting further structural changes to develop improved derivatives.
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Affiliation(s)
- Alexander Berger
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
| | - Talea Knak
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
| | - Anna-Lene Kiffe-Delf
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Korana Mudrovcic
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
| | - Vinayak Singh
- 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
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Mathew Njoroge
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Bjoern B. Burckhardt
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Mohanraj Gopalswamy
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
| | - Beate Lungerich
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Kelly Chibale
- 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
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany or
- Correspondence:
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5
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Zhang Y, Chen Z, Sun P, Xu Q, Chen N. Effect of low-level ultrasound treatment on the production of L-leucine by Corynebacterium glutamicum in fed-batch culture. Bioengineered 2021; 12:1078-1090. [PMID: 33775210 PMCID: PMC8806274 DOI: 10.1080/21655979.2021.1906028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022] Open
Abstract
Various process intensification methods were proposed to improve the yield, quality, and safety of fermented products. Here, we report the enhancement of L-leucine production by Corynebacterium glutamicum CP using ultrasound-assisted fed-batch fermentation. Response surface methodology was employed to optimize the sonication conditions. At an ultrasonic power density of 94 W/L, frequency of 25 kHz, interval of 31 min, and duration of 37 s, C. glutamicum CP produced 52.89 g/L of L-leucine in 44 h, representing a 21.6% increase compared with the control. The production performance of L-leucine was also improved under ultrasonic treatment. Moreover, the effects of ultrasound treatment on the fermentation performance of L-leucine were studied in terms of cell morphology, cell membrane permeability, and enzyme activity. The results indicate that ultrasonication is an efficient method for the intensification of L-leucine production by C. glutamicum CP.
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Affiliation(s)
- Yufu Zhang
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, PR China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Zhichao Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, PR China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Pengjie Sun
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, PR China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Qingyang Xu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, PR China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, PR China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, PR China
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6
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Liang YF, Yan LT, Yue Q, Zhao JK, Luo CY, Gao F, Li H, Gao WY. Preparation of a whole cell catalyst overexpressing acetohydroxyacid synthase of Thermotoga maritima and its application in the syntheses of α-hydroxyketones. Sci Rep 2020; 10:15404. [PMID: 32958806 PMCID: PMC7505981 DOI: 10.1038/s41598-020-72416-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
The large catalytic subunit of acetohydroxyacid synthase (AHAS, EC 2.2.1.6) of Thermotoga maritima (TmcAHAS) was prepared in this study. It possesses high specific activity and excellent stability. The protein and a whole cell catalyst overexpressing the protein were applied to the preparation of α-hydroxyketones including acetoin (AC), 3-hydroxy-2-pentanone (HP), and (R)-phenylacetylcarbinol (R-PAC). The results show that AC and HP could be produced in high yields (84% and 62%, respectively), while R-PAC could be synthesized in a high yield (about 78%) with an R/S ratio of 9:1. Therefore, TmcAHAS and the whole cell catalyst overexpressing the protein could be practically useful bio-catalysts in the preparation of α-hydroxyketones including AC, HP, and R-PAC. To the best of our knowledge, this is the first time that bacterial AHAS was used as a catalyst to prepare HP with a good yield, and also the first time that TmcAHAS was employed to synthesize AC and R-PAC.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Le-Tian Yan
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Qiao Yue
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Ji-Kui Zhao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Cai-Yun Luo
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Feng Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China
| | - Heng Li
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
| | - Wen-Yun Gao
- College of Life Sciences, Northwest University, 229 North Taibai Road, Xi'an, 710069, Shaanxi, People's Republic of China.
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7
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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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8
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Wang B, Xu X, Gong S, Wang Q, Hu H, Xu D. Synthesis and Herbicidal Activity of O‐(2,6‐Bis(4,6‐dimethoxypyrimidin‐2‐yloxy) benzoyl)oxime 3‐Trifluoromethylacetophenone. ChemistrySelect 2019. [DOI: 10.1002/slct.201902806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Wang
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Xiangjian Xu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Shunze Gong
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Qin Wang
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Hang Hu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
| | - Defeng Xu
- School of pharmaceutical and Life SciencesChangzhou University Changzhou 213164 P.R. China
- National & Local Joint Engineering Research Center for High-efficiency Refining and High-quality Utilization of BiomassChangzhou University Changzhou 213164 P. R. China
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9
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Liu Y, Wang X, Zhan J, Hu J. The 138th residue of acetohydroxyacid synthase in Corynebacterium glutamicum is important for the substrate binding specificity. Enzyme Microb Technol 2019; 129:109357. [DOI: 10.1016/j.enzmictec.2019.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/12/2019] [Accepted: 06/01/2019] [Indexed: 11/28/2022]
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10
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Leitemberger A, Böhs LMC, Rosa CH, Silva CD, Galetto FZ, Godoi M. Synthesis of Symmetrical Diorganyl Disulfides Employing WEB as an Eco‐friendly Oxidative System. ChemistrySelect 2019. [DOI: 10.1002/slct.201901385] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Andrielli Leitemberger
- Escola de Química e AlimentosUniversidade Federal do Rio Grande, Santo Antônio da Patrulha Rio Grande do Sul Brazil
| | - Lucas Martins C. Böhs
- Escola de Química e AlimentosUniversidade Federal do Rio Grande, Santo Antônio da Patrulha Rio Grande do Sul Brazil
| | - Clarissa Helena Rosa
- Escola de Química e AlimentosUniversidade Federal do Rio Grande, Santo Antônio da Patrulha Rio Grande do Sul Brazil
| | - Cleiton Da Silva
- Departamento de QuímicaUniversidade Federal de Santa Catarina, Florianópolis Santa Catarina Brazil
| | - Fábio Z. Galetto
- Departamento de QuímicaUniversidade Federal de Santa Catarina, Florianópolis Santa Catarina Brazil
| | - Marcelo Godoi
- Escola de Química e AlimentosUniversidade Federal do Rio Grande, Santo Antônio da Patrulha Rio Grande do Sul Brazil
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Burke C, Abrahams KA, Richardson EJ, Loman NJ, Alemparte C, Lelievre J, Besra GS. Development of a whole-cell high-throughput phenotypic screen to identify inhibitors of mycobacterial amino acid biosynthesis. FASEB Bioadv 2019; 1:246-254. [PMID: 32123830 PMCID: PMC6996392 DOI: 10.1096/fba.2018-00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
Anti-tubercular drug discovery continues to be dominated by whole-cell high-throughput screening campaigns, enabling the rapid discovery of new inhibitory chemical scaffolds. Target-based screening is a popular approach to direct inhibitor discovery with a specified mode of action, eliminating the discovery of anti-tubercular agents against unsuitable targets. Herein, a screening method has been developed using Mycobacterium bovis BCG to identify inhibitors of amino acid biosynthesis. The methodology was initially optimized using the known branched-chain amino acid biosynthetic inhibitors metsulfuron-methyl (MSM) and sulfometuron-methyl (SMM), and subsequently, whole genome sequencing of resistant mutants and the use of over-expressor strains confirming their mode of action. The GlaxoSmithKline compound library of small molecule inhibitors with known activity against Mycobacterium tuberculosis was then used to validate the screen. In this paper, we have shown that media supplementation with amino acids can rescue M bovis BCG from known amino acid synthesis inhibitors, MSM and SMM, in a pathway specific manner. The therapeutic potential of amino acid biosynthesis inhibitors emphasizes the importance of this innovative screen, enabling the discovery of compounds targeting a multitude of related essential biochemical pathways, without limiting drug discovery toward a single target.
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Affiliation(s)
| | | | | | | | | | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKlineMadridSpain
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12
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Uddin R, Zahra NUA, Azam SS. Identification of glucosyl-3-phosphoglycerate phosphatase as a novel drug target against resistant strain of Mycobacterium tuberculosis (XDR1219) by using comparative metabolic pathway approach. Comput Biol Chem 2019; 79:91-102. [PMID: 30743161 DOI: 10.1016/j.compbiolchem.2019.01.011] [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: 10/21/2018] [Revised: 01/13/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Tuberculosis (TB) is a major global health challenge. It has been afflicting human for thousands of years and is still severely affecting a huge population. The etiological agent of the disease is Mycobacterium tuberculosis (MTB) that survives in the human host in latent, dormant, and non-replicative state by evading the immune system. It is one of the leading causes of infection related death worldwide. The situation is exacerbated by the massive increase in the resistant strains such as multi-drug resistant TB (MDR-TB) and extensive drug-resistant TB (XDR-TB). The resistance is as severe that it resulted in failure of the current chemotherapy regimens (i.e. anti-tubercular drugs). It is therefore imperative to discover the new anti-tuberculosis drug targets and their potential inhibitors. Current study has made the use of in silico approaches to perform the comparative metabolic pathway analysis of the MTBXDR1219 with the host i.e. H. sapiens. We identified several metabolic pathways which are unique to pathogen only. By performing subtractive genomic analysis 05 proteins as potential drug target are retrieved. This study suggested that the identified proteins are essential for the bacterial survival and non-homolog to the host proteins. Furthermore, we selected glucosyl-3-phosoglycerate phosphatase (GpgP, EC 5.4.2.1) out of the 05 proteins for molecular docking analysis and virtual screening. The protein is involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs) which regulate the biosynthesis of mycolic acid. Mycolic acid is the building block of the unique cell wall of the MTB which is responsible for the resistance and pathogenicity. A relatively larger library consisting of 10,431 compounds was screened using AutoDock Vina to predict the binding modes and to rank the potential inhibitors. No potent inhibitor against MTB GpgP has been reported yet, therefore ranking of compounds is performed by making a comparison with the substrate i.e. glucosyl-3-phosphoglycerate. The obtained results provide the understanding of underlying mechanism of interactions of ligands with protein. Follow up study will include the study of the Protein-Protein Interactions (PPIs), and to propose the potential inhibitors against them.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Noor-Ul-Ain Zahra
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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13
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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: 32] [Impact Index Per Article: 6.4] [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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14
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Rehberg N, Akone HS, Ioerger TR, Erlenkamp G, Daletos G, Gohlke H, Proksch P, Kalscheuer R. Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:123-134. [PMID: 29108416 DOI: 10.1021/acsinfecdis.7b00055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavonoid natural compound chlorflavonin was isolated from the endophytic fungus Mucor irregularis, which was obtained from the Cameroonian medicinal plant Moringa stenopetala. Chlorflavonin exhibited strong growth inhibitory activity in vitro against Mycobacterium tuberculosis (MIC90 1.56 μM) while exhibiting no cytotoxicity toward the human cell lines MRC-5 and THP-1 up to concentrations of 100 μM. Mapping of resistance-mediating mutations employing whole-genome sequencing, chemical supplementation assays, and molecular docking studies as well as enzymatic characterization revealed that chlorflavonin specifically inhibits the acetohydroxyacid synthase catalytic subunit IlvB1, causing combined auxotrophies to branched-chain amino acids and to pantothenic acid. While exhibiting a bacteriostatic effect in monotreatment, chlorflavonin displayed synergistic effects with the first-line antibiotic isoniazid and particularly with delamanid, leading to a complete sterilization in liquid culture in combination treatment. Using a fluorescent reporter strain, intracellular activity of chlorflavonin against Mycobacterium tuberculosis inside infected macrophages was demonstrated and was superior to streptomycin treatment.
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Affiliation(s)
- Nidja Rehberg
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Herve Sergi Akone
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Faculty of Science, Department of Chemistry, University of Douala,
PO Box 24157, 2701 Douala, Cameroon
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, 710 Ross St., College Station, Texas 77843, United States
| | - German Erlenkamp
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Georgios Daletos
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Peter Proksch
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical
Biology and Biotechnology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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15
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Huang H, Ash J, Kang JY. Base-controlled Fe(Pc)-catalyzed aerobic oxidation of thiols for the synthesis of S–S and S–P(O) bonds. Org Biomol Chem 2018; 16:4236-4242. [DOI: 10.1039/c8ob00908b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Base-controlled Fe(Pc)-catalyzed S–S/S–P(O) bond formation.
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Affiliation(s)
- Hai Huang
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
- Department of Applied Chemistry
| | - Jeffrey Ash
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
| | - Jun Yong Kang
- Department of Chemistry and Biochemistry
- University of Nevada Las Vegas
- Las Vegas
- USA
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16
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Jia X, Liu Y, Han Y. A thermophilic cell-free cascade enzymatic reaction for acetoin synthesis from pyruvate. Sci Rep 2017; 7:4333. [PMID: 28659601 PMCID: PMC5489476 DOI: 10.1038/s41598-017-04684-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/18/2017] [Indexed: 11/09/2022] Open
Abstract
Acetoin (3-hydroxy-2-butanone) is an important bio-based platform chemical with wide applications. In vitro enzyme catalysed synthesis exhibits great feasibility in the production of chemicals with high purity. In the present work, a synthetic pathway involving a two-step continuous reaction was constructed in vitro for acetoin production from pyruvate at improved temperature. Thermostable candidates, acetolactate synthase (coAHASL1 and coAHASL2 from Caldicellulosiruptor owensensis OL) and α-acetolactate decarboxylase (bsALDC from Bacillus subtilis IPE5-4) were cloned, heterologously expressed, and characterized. All the enzymes showed maximum activities at 65–70 °C and pH of 6.5. Enzyme kinetics analysis showed that coAHASL1 had a higher activity but lower affinity against pyruvate than that of coAHASL2. In addition, the activities of coAHASL1 and bsALDC were promoted by Mn2+ and NADPH. The cascade enzymatic reaction was optimized by using coAHASL1 and bsALDC based on their kinetic properties. Under optimal conditions, a maximum concentration of 3.36 ± 0.26 mM acetoin was produced from 10 mM pyruvate after reaction for 24 h at 65 °C. The productivity of acetoin was 0.14 mM h−1, and the yield was 67.80% compared with the theoretical value. The results confirmed the feasibility of synthesis of acetoin from pyruvate with a cell-free enzyme catalysed system at improved temperature.
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Affiliation(s)
- Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ying Liu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China.
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17
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Wang L, Bao BB, Song GQ, Chen C, Zhang XM, Lu W, Wang Z, Cai Y, Li S, Fu S, Song FH, Yang H, Wang JG. Discovery of unsymmetrical aromatic disulfides as novel inhibitors of SARS-CoV main protease: Chemical synthesis, biological evaluation, molecular docking and 3D-QSAR study. Eur J Med Chem 2017. [PMID: 28624700 PMCID: PMC7115414 DOI: 10.1016/j.ejmech.2017.05.045] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The worldwide outbreak of severe acute respiratory syndrome (SARS) in 2003 had caused a high rate of mortality. Main protease (Mpro) of SARS-associated coronavirus (SARS-CoV) is an important target to discover pharmaceutical compounds for the therapy of this life-threatening disease. During the course of screening new anti-SARS agents, we have identified that a series of unsymmetrical aromatic disulfides inhibited SARS-CoV Mpro significantly for the first time. Herein, 40 novel unsymmetrical aromatic disulfides were synthesized chemically and their biological activities were evaluated in vitro against SARS-CoV Mpro. These novel compounds displayed excellent IC50 data in the range of 0.516–5.954 μM. Preliminary studies indicated that these disulfides are reversible and mpetitive inhibitors. A possible binding mode was generated via molecular docking simulation and a comparative field analysis (CoMFA) model was constructed to understand the structure-activity relationships. The present research therefore has provided some meaningful guidance to design and identify anti-SARS drugs with totally new chemical structures. 40 novel unsymmetrical aromatic disulfides were synthesized. The synthesized disulfide compounds are potent inhibitors of SARS main protease. Possible binding mode and structure-activity relationships of the compounds were established.
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Affiliation(s)
- Li Wang
- State-Key Laboratory and Research Institute of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo-Bo Bao
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Guo-Qing Song
- State-Key Laboratory and Research Institute of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China.
| | - Xu-Meng Zhang
- State-Key Laboratory and Research Institute of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Wei Lu
- State-Key Laboratory and Research Institute of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Yan Cai
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Shuang Li
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Sheng Fu
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Fu-Hang Song
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jian-Guo Wang
- State-Key Laboratory and Research Institute of Elemento-Organic Chemistry, National Pesticide Engineering Research Center, College of Chemistry, Nankai University, Tianjin 300071, China.
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18
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Jung IP, Ha NR, Lee SC, Ryoo SW, Yoon MY. Development of potent chemical antituberculosis agents targeting Mycobacterium tuberculosis acetohydroxyacid synthase. Int J Antimicrob Agents 2016; 48:247-58. [DOI: 10.1016/j.ijantimicag.2016.04.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/27/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
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19
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Eram MS, Ma K. Pyruvate decarboxylase activity of the acetohydroxyacid synthase of Thermotoga maritima. Biochem Biophys Rep 2016; 7:394-399. [PMID: 28955930 PMCID: PMC5613635 DOI: 10.1016/j.bbrep.2016.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) catalyzes the production of acetolactate from pyruvate. The enzyme from the hyperthermophilic bacterium Thermotoga maritima has been purified and characterized (kcat ~100 s−1). It was found that the same enzyme also had the ability to catalyze the production of acetaldehyde and CO2 from pyruvate, an activity of pyruvate decarboxylase (PDC) at a rate approximately 10% of its AHAS activity. Compared to the catalytic subunit, reconstitution of the individually expressed and purified catalytic and regulatory subunits of the AHAS stimulated both activities of PDC and AHAS. Both activities had similar pH and temperature profiles with an optimal pH of 7.0 and temperature of 85 °C. The enzyme kinetic parameters were determined, however, it showed a non-Michaelis-Menten kinetics for pyruvate only. This is the first report on the PDC activity of an AHAS and the second bifunctional enzyme that might be involved in the production of ethanol from pyruvate in hyperthermophilic microorganisms. The acetohydroxyacid synthase of T. maritima has pyruvate decarboxylase activity The AHAS and PDC activities share the same temperature and pH optima Reconstitution of the catalytic and regulatory subunits increases both PDC and AHAS activities
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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20
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Liu YC, Qu RY, Chen Q, Yang JF, Cong-Wei N, Zhen X, Yang GF. Triazolopyrimidines as a New Herbicidal Lead for Combating Weed Resistance Associated with Acetohydroxyacid Synthase Mutation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4845-4857. [PMID: 27265721 DOI: 10.1021/acs.jafc.6b00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Acetohydroxyacid synthase (AHAS; also known as acetolactate synthase; EC 2.2.1.6, formerly EC 4.1.3.18) is the first common enzyme in the biosynthetic pathway leading to the branched-chain amino acids in plants and a wide range of microorganisms. Weed resistance to AHAS-inhibiting herbicides, increasing at an exponential rate, is becoming a global problem and leading to an urgent demand of developing novel compounds against both resistant and wild AHAS. In the present work, a series of novel 2-aroxyl-1,2,4-triazolopyrimidine derivatives (a total of 55) were designed and synthesized with the aim to discover an antiresistant lead compound. Fortunately, the screening results indicated that many of the newly synthesized compounds showed a better, even excellent, inhibition effect against both the wild-type Arabidopsis thaliana AHAS and P197L mutants. Among them, compounds 5-3 to 5-17, compounds 5-19 to 5-26, compounds 5-28 to 5-45, and compound 5-48 have the lower values of resistance factor (RF) and display a potential power to overcome resistance associated with the P197L mutation in the enzyme levels. Further greenhouse in vivo assay showed that compounds 5-15 and 5-20 displayed "moderate" to "good" herbicidal activity against both the wild type-and the resistant (P197L mutation) Descurainia sophia, even at a rate as low as 0.9375 (g of ai/ha). The above results indicated that these two compounds could be used as new leads for the future development of antiresistance herbicides.
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Affiliation(s)
- Yu-Chao Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, PR China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, PR China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, PR China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, PR China
| | - Niu Cong-Wei
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, PR China
| | - Xi Zhen
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, PR China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjing 30071, PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , Wuhan 430079, PR China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, PR China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjing 30071, PR China
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21
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Kaur P, Datta S, Shandil RK, Kumar N, Robert N, Sokhi UK, Guptha S, Narayanan S, Anbarasu A, Ramaiah S. Unravelling the Secrets of Mycobacterial Cidality through the Lens of Antisense. PLoS One 2016; 11:e0154513. [PMID: 27144597 PMCID: PMC4856384 DOI: 10.1371/journal.pone.0154513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/14/2016] [Indexed: 01/13/2023] Open
Abstract
One of the major impediments in anti-tubercular drug discovery is the lack of a robust grammar that governs the in-vitro to the in-vivo translation of efficacy. Mycobacterium tuberculosis (Mtb) is capable of growing both extracellular as well as intracellular; encountering various hostile conditions like acidic milieu, free radicals, starvation, oxygen deprivation, and immune effector mechanisms. Unique survival strategies of Mtb have prompted researchers to develop in-vitro equivalents to simulate in-vivo physiologies and exploited to find efficacious inhibitors against various phenotypes. Conventionally, the inhibitors are screened on Mtb under the conditions that are unrelated to the in-vivo disease environments. The present study was aimed to (1). Investigate cidality of Mtb targets using a non-chemical inhibitor antisense-RNA (AS-RNA) under in-vivo simulated in-vitro conditions.(2). Confirm the cidality of the targets under in-vivo in experimental tuberculosis. (3). Correlate in-vitro vs. in-vivo cidality data to identify the in-vitro condition that best predicts in-vivo cidality potential of the targets. Using cidality as a metric for efficacy, and AS-RNA as a target-specific inhibitor, we delineated the cidality potential of five target genes under six different physiological conditions (replicating, hypoxia, low pH, nutrient starvation, nitrogen depletion, and nitric oxide).In-vitro cidality confirmed in experimental tuberculosis in BALB/c mice using the AS-RNA allowed us to identify cidal targets in the rank order of rpoB>aroK>ppk>rpoC>ilvB. RpoB was used as the cidality control. In-vitro and in-vivo studies feature aroK (encoding shikimate kinase) as an in-vivo mycobactericidal target suitable for anti-TB drug discovery. In-vitro to in-vivo cidality correlations suggested the low pH (R = 0.9856) in-vitro model as best predictor of in-vivo cidality; however, similar correlation studies in pathologically relevant (Kramnik) mice are warranted. In the acute infection phase for the high fidelity translation, the compound efficacy may also be evaluated in the low pH, in addition to the standard replication condition.
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Affiliation(s)
- Parvinder Kaur
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
- * E-mail:
| | | | | | - Naveen Kumar
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Nanduri Robert
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Upneet K. Sokhi
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, United States of America
| | - Supreeth Guptha
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Shridhar Narayanan
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Anand Anbarasu
- School of Biosciences and Technology, VIT University, Vellore, India
| | - Sudha Ramaiah
- School of Biosciences and Technology, VIT University, Vellore, India
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22
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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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23
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Li H, Liu N, Wang WT, Wang JY, Gao WY. Cloning and characterization of GST fusion tag stabilized large subunit of Escherichia coli acetohydroxyacid synthase I. J Biosci Bioeng 2016; 121:21-26. [DOI: 10.1016/j.jbiosc.2015.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 10/22/2022]
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24
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Functional evaluation of residues in the herbicide-binding site of Mycobacterium tuberculosis acetohydroxyacid synthase by site-directed mutagenesis. Enzyme Microb Technol 2015. [DOI: 10.1016/j.enzmictec.2015.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Eram MS, Sarafuddin B, Gong F, Ma K. Characterization of acetohydroxyacid synthase from the hyperthermophilic bacterium Thermotoga maritima. Biochem Biophys Rep 2015; 4:89-97. [PMID: 29124191 PMCID: PMC5668897 DOI: 10.1016/j.bbrep.2015.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/30/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is the key enzyme in branched chain amino acid biosynthesis pathway. The enzyme activity and properties of a highly thermostable AHAS from the hyperthermophilic bacterium Thermotoga maritima is being reported. The catalytic and regulatory subunits of AHAS from T. maritima were over-expressed in Escherichia coli. The recombinant subunits were purified using a simplified procedure including a heat-treatment step followed by chromatography. A discontinuous colorimetric assay method was optimized and used to determine the kinetic parameters. AHAS activity was determined to be present in several Thermotogales including T. maritima. The catalytic subunit of T. maritima AHAS was purified approximately 30-fold, with an AHAS activity of approximately 160±27 U/mg and native molecular mass of 156±6 kDa. The regulatory subunit was purified to homogeneity and showed no catalytic activity as expected. The optimum pH and temperature for AHAS activity were 7.0 and 85 °C, respectively. The apparent Km and Vmax for pyruvate were 16.4±2 mM and 246±7 U/mg, respectively. Reconstitution of the catalytic and regulatory subunits led to increased AHAS activity. This is the first report on characterization of an isoleucine, leucine, and valine operon (ilv operon) enzyme from a hyperthermophilic microorganism and may contribute to our understanding of the physiological pathways in Thermotogales. The enzyme represents the most active and thermostable AHAS reported so far. First report of AHAS from a hyperthermophilic bacterium. Catalytic and regulatory subunits of AHAS of T. maritima was expressed in E. coli. Recombinant proteins were purified using a simplified procedure. Enzyme represents the most active and thermostable AHAS reported so far. Kinetic parameters were determined for the purified recombinant enzyme
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Key Words
- AHAS, acetohydroxyacid synthase
- Acetohydroxyacid synthase
- BCAA, branched chain amino acid
- Branched-chain amino acids
- CCE, crude cell extract
- CFE, cell-free extract
- HTCCE, heat-treated crude cell extract
- Hyperthermophiles
- IB, inclusion body
- IMAC, immobilized metal affinity chromatography
- TPP, thiamine pyrophosphate
- Thermotogales
- TmAHAS, Thermotoga maritima acetohydroxyacid synthase
- ilv, isoleucine, leucine, valine
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Affiliation(s)
- Mohammad S Eram
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Benozir Sarafuddin
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Frank Gong
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kesen Ma
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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26
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Development of ssDNA aptamers as potent inhibitors of Mycobacterium tuberculosis acetohydroxyacid synthase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1338-50. [PMID: 25988243 DOI: 10.1016/j.bbapap.2015.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/22/2015] [Accepted: 05/09/2015] [Indexed: 01/01/2023]
Abstract
Acetohydroxyacid synthase (AHAS) from Mycobacterium tuberculosis (Mtb) is a promising potential drug target for an emerging class of new anti-tuberculosis agents. In this study, we identify short (30-mer) single-stranded DNA aptamers as a novel class of potent inhibitors of Mtb-AHAS through an in vitro DNA-SELEX method. Among all tested aptamers, two candidate aptamers (Mtb-Apt1 and Mtb-Apt6) demonstrated the greatest inhibitory potential against Mtb-AHAS activity with IC50 values in the low nanomolar range (28.94±0.002 and 22.35±0.001 nM respectively). Interestingly, inhibition kinetics analysis of these aptamers showed different modes of enzyme inhibition (competitive and mixed type of inhibition respectively). Secondary structure-guided mutational modification analysis of Mtb-Apt1 and Mtb-Apt6 identified the minimal region responsible for their inhibitory action and consequently led to 17-mer and 20-mer shortened aptamers that retained equivalent or greater inhibitory potential. Notably, a modeling and docking exercise investigated the binding site of these two potent inhibitory aptamers on the target protein and showed possible involvement of some key catalytic dimer interface residues of AHAS in the DNA-protein interactions that lead to its potent inhibition. Importantly, these two short candidate aptamers, Mtb-Apt1 (17-mer) and Mtb-Apt6 (20-mer), also demonstrated significant growth inhibition against multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains of tuberculosis with very low MIC of 5.36 μg/ml and 6.24 μg/ml, respectively and no significant cytotoxicity against mammalian cell line. This is the first report of functional inhibitory aptamers against Mtb-AHAS and provides the basis for development of these aptamers as novel and strong anti-tuberculosis agents.
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27
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Lu W, Baig IA, Sun HJ, Cui CJ, Guo R, Jung IP, Wang D, Dong M, Yoon MY, Wang JG. Synthesis, crystal structure and biological evaluation of substituted quinazolinone benzoates as novel antituberculosis agents targeting acetohydroxyacid synthase. Eur J Med Chem 2015; 94:298-305. [DOI: 10.1016/j.ejmech.2015.03.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/03/2015] [Accepted: 03/05/2015] [Indexed: 11/17/2022]
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Lee SC, Jung IP, Baig IA, Chien PN, La IJ, Yoon MY. Mutational analysis of critical residues of FAD-independent catabolic acetolactate synthase from Enterococcus faecalis V583. Int J Biol Macromol 2014; 72:104-9. [PMID: 25128823 DOI: 10.1016/j.ijbiomac.2014.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/02/2014] [Accepted: 08/04/2014] [Indexed: 10/24/2022]
Abstract
Catabolic acetolactate synthase (cALS) from Enterococcus faecalis is a FAD-independent enzyme, which catalyzes the condensation of two molecules of pyruvate to produce acetolactate. Mutational and kinetic analyses of variants suggested the importance of H111, Q112, and Q411 residues for catalysis in cALS. The wild-type and variants were expressed as equally soluble proteins and co-migrated to a size of 60 kDa on SDS-PAGE. Importantly, H111 in cALS, which is widely present as phenylalanine in many other ThDP-dependent enzymes, plays a crucial role in substrate binding. Interestingly, the H111 variants, H111R and H111F, demonstrated altered specific activity of H111 variants with 17- and 26-fold increases in Km, respectively, compared to wild-type cALS. Furthermore, Q112 variants, Q112E, Q112N, and Q112V, exhibited significantly lower specific activity with 70-, 15-, and 10-fold higher Ks for ThDP, respectively. In the case of Q411, the variant Q411E showed a 10-fold rise in Km and a 20-fold increase in Ks for ThDP. Further, the molecular docking results indicated that the binding mode of ThDP was slightly affected in the variants of cALS. Based on these results, we suggest that H111 plays a role in substrate binding, and further suggest that Q112 and Q411 might be involved in ThDP binding of cALS.
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Affiliation(s)
- Sang-Choon Lee
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
| | - In-Pil Jung
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
| | - Irshad Ahmed Baig
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
| | - Pham Ngoc Chien
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
| | - Im-Joung La
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea
| | - Moon-Young Yoon
- Department of Chemistry, College of Natural Science, Hanyang University, Seoul 133-791, Republic of Korea.
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29
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Baig IA, Moon JY, Kim MS, Koo BS, Yoon MY. Structural and functional significance of the highly-conserved residues in Mycobacterium tuberculosis acetohydroxyacid synthase. Enzyme Microb Technol 2014; 58-59:52-9. [DOI: 10.1016/j.enzmictec.2014.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/05/2014] [Accepted: 02/18/2014] [Indexed: 10/25/2022]
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30
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Dover LG, Bhatt A, Bhowruth V, Willcox BE, Besra GS. New drugs and vaccines for drug-resistantMycobacterium tuberculosisinfections. Expert Rev Vaccines 2014; 7:481-97. [DOI: 10.1586/14760584.7.4.481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Liu Y, Bao P, Wang D, Li Z, Li Y, Tang L, Zhou Y, Zhao W. Evaluation of the In Vivo Efficacy of Novel Monosubstituted Sulfonylureas against H37Rv and Extensively Drug-Resistant Tuberculosis. Jpn J Infect Dis 2014; 67:485-7. [DOI: 10.7883/yoken.67.485] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Biochemical characterization and evaluation of potent inhibitors of the Pseudomonas aeruginosa PA01 acetohydroxyacid synthase. Biochimie 2013; 95:1411-21. [DOI: 10.1016/j.biochi.2013.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 03/10/2013] [Indexed: 11/17/2022]
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33
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Balakrishnan A, Jordan F, Nathan CF. Influence of allosteric regulators on individual steps in the reaction catalyzed by Mycobacterium tuberculosis 2-hydroxy-3-oxoadipate synthase. J Biol Chem 2013; 288:21688-702. [PMID: 23760263 DOI: 10.1074/jbc.m113.465419] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Allosteric regulation often controls key branch points in metabolic processes. Mycobacterium tuberculosis 2-hydroxy-3-oxoadipate synthase (HOAS), a thiamin diphosphate (ThDP)-dependent enzyme, produces 2-hydroxy-3-oxoadipate using 2-ketoglutarate and glyoxylate. The proposed chemical mechanism in analogy with other ThDP-dependent carboligases involves multiple ThDP-bound covalent intermediates. Acetyl coenzyme A is an activator, and GarA, a forkhead association domain-containing protein known to regulate glutamate metabolism, is an allosteric inhibitor of HOAS. Steady state kinetics using assays to study the first half and the full catalytic cycle suggested that the regulators act at different steps in the overall mechanism. To explore the modes of regulation and to test the effects on individual catalytic steps, we performed circular dichroism (CD) studies using a non-decarboxylatable 2-ketoglutarate analog and determined the distribution of ThDP-bound covalent intermediates during the steady state of the HOAS reaction using one-dimensional (1)H gradient carbon heteronuclear single quantum coherence NMR. The results suggest that acetyl coenzyme A acts as a mixed V and K type activator and predominantly affects the predecarboxylation steps. GarA does not inhibit the formation of the predecarboxylation analog and does not affect the accumulation of the postdecarboxylation covalent intermediate derived from 2-ketoglutarate; however, it decreases the abundance of the product ThDP adduct in the HOAS pathway. Thus, the two regulators act on different halves of the catalytic cycle in an unusual regulatory regime.
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Affiliation(s)
- Anand Balakrishnan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
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34
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Baig IA, Gedi V, Lee SC, Koh SH, Yoon MY. Role of a highly conserved proline-126 in ThDP binding of Mycobacterium tuberculosis acetohydroxyacid synthase. Enzyme Microb Technol 2013; 53:243-9. [PMID: 23931689 DOI: 10.1016/j.enzmictec.2013.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 05/12/2013] [Accepted: 05/14/2013] [Indexed: 11/30/2022]
Abstract
Acetohydroxyacid synthase (AHAS) of Mycobacterium tuberculosis is a promising target for the development of anti-tuberculosis agents. With the absence of an available bacterial AHAS crystal structure, that of M. tuberculosis, site-directed mutagenesis has been a useful tool for determining its structural and functional features. In this study, a highly conserved proline residue (P126 of M. tuberculosis AHAS) was selected, and the possible role was evaluated by site-directed mutagenesis. P126 was replaced by valine, threonine, alanine, and glutamate to yield P126V, P126T, P126A, and P126E, respectively. All variants were expressed in their soluble forms in Escherichia coli and purified to near homogeneity. The molecular mass (SDS-PAGE) of the purified variants was ∼68 kDa, which is similar to that of wild-type AHAS. The P126V, P126T, and P126A variants exhibited significantly lower activity than wild-type AHAS, whereas P126E was inactive under the tested assay conditions. Furthermore, the P126V and P126T variants showed a significantly decreased preference toward pyruvate and ThDP as substrate and cofactor respectively, whereas the P126A showed similar kinetics to that of wild-type AHAS. Like in AHAS from yeast Saccharomyces cerevisiae (PDB ID: 1N0H), residue P126 is located in the ThDP binding pocket of M. tuberculosis AHAS homology model. Collectively, these results suggest that the conserved P126 plays a significant role in the ThDP binding of M. tuberculosis AHAS.
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35
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Li ZS, Wang WM, Lu W, Niu CW, Li YH, Li ZM, Wang JG. Synthesis and biological evaluation of nonsymmetrical aromatic disulfides as novel inhibitors of acetohydroxyacid synthase. Bioorg Med Chem Lett 2013; 23:3723-7. [PMID: 23726033 DOI: 10.1016/j.bmcl.2013.05.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/03/2013] [Accepted: 05/07/2013] [Indexed: 11/15/2022]
Abstract
46 Novel nonsymmetrical aromatic disulfides containing [1,3,4]thiadiazole or [1,3,4]oxadiazole groups were synthesized and their biological activities were evaluated as inhibitors of acetohydroxyacid synthase (AHAS, EC 2.2.1.6). Besides their strong in vitro inhibition against plant AHAS, compounds 3e and 3f also display 80-100% post-emergence herbicidal activities in greenhouse bioassay at 1500g /ha dosage. The assay of exogenous branched-chain amino acids supplementation on rape root growth of 3e suggests that the herbicidal activity has relationship with AHAS inhibition.
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Affiliation(s)
- Zai-Shun Li
- State-Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, PR China
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36
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Zhao Y, Niu C, Wen X, Xi Z. The minimum activation peptide from ilvH can activate the catalytic subunit of AHAS from different species. Chembiochem 2013; 14:746-52. [PMID: 23512804 DOI: 10.1002/cbic.201200680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 11/10/2022]
Abstract
Acetohydroxyacid synthases (AHASs), which catalyze the first step in the biosynthesis of branched-chain amino acids, are composed of a catalytic subunit (CSU) and a regulatory subunit (RSU). The CSU harbors the catalytic site, and the RSU is responsible for the activation and feedback regulation of the CSU. Previous results from Chipman and co-workers and our lab have shown that heterologous activation can be achieved among isozymes of Escherichia coli AHAS. It would be interesting to find the minimum peptide of ilvH (the RSU of E. coli AHAS III) that could activate other E. coli CSUs, or even those of ## species. In this paper, C-terminal, N-terminal, and C- and N-terminal truncation mutants of ilvH were constructed. The minimum peptide to activate ilvI (the CSU of E. coli AHAS III) was found to be ΔN 14-ΔC 89. Moreover, this peptide could not only activate its homologous ilvI and heterologous ilvB (CSU of E. coli AHAS I), but also heterologously activate the CSUs of AHAS from Saccharomyces cerevisiae, Arabidopsis thaliana, and Nicotiana plumbaginifolia. However, this peptide totally lost its ability for feedback regulation by valine, thus suggesting different elements for enzymatic activation and feedback regulation. Additionally, the apparent dissociation constant (Kd ) of ΔN 14-ΔC 89 when binding CSUs of different species was found to be 9.3-66.5 μM by using microscale thermophoresis. The ability of this peptide to activate different CSUs does not correlate well with its binding ability (Kd ) to these CSUs, thus implying that key interactions by specific residues is more important than binding ability in promoting enzymatic reactions. The high sequence similarity of the peptide ΔN 14-ΔC 89 to RSUs across species hints that this peptide represents the minimum activation motif in RSU and that it regulates all AHASs.
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Affiliation(s)
- Yuefang Zhao
- Department of Chemical Biology and State Key Laboratory of Elemento-organic Chemistry, Nankai University, Weijin 94, Tianjin 300071, China
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37
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Wang D, Zhu X, Cui C, Dong M, Jiang H, Li Z, Liu Z, Zhu W, Wang JG. Discovery of Novel Acetohydroxyacid Synthase Inhibitors as Active Agents against Mycobacterium tuberculosis by Virtual Screening and Bioassay. J Chem Inf Model 2013; 53:343-53. [PMID: 23316686 DOI: 10.1021/ci3004545] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Di Wang
- Department of Clinical Laboratory,
309 Hospital of Chinese People’s Liberation Army, Beijing 100091,
China
| | - Xuelian Zhu
- State Key Laboratory
of Drug
Research, Drug Discovery and Design Center, Shanghai Institute of
Materia Medica, Shanghai 201203, China
| | - Changjun Cui
- State Key Laboratory and Institute
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071,
China
| | - Mei Dong
- Department of Clinical Laboratory,
309 Hospital of Chinese People’s Liberation Army, Beijing 100091,
China
| | - Hualiang Jiang
- State Key Laboratory
of Drug
Research, Drug Discovery and Design Center, Shanghai Institute of
Materia Medica, Shanghai 201203, China
| | - Zhengming Li
- State Key Laboratory and Institute
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071,
China
| | - Zhen Liu
- Department of Clinical Laboratory,
309 Hospital of Chinese People’s Liberation Army, Beijing 100091,
China
| | - Weiliang Zhu
- State Key Laboratory
of Drug
Research, Drug Discovery and Design Center, Shanghai Institute of
Materia Medica, Shanghai 201203, China
| | - Jian-Guo Wang
- State Key Laboratory and Institute
of Elemento-Organic Chemistry, Nankai University, Tianjin 300071,
China
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38
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Development of a new generation of vectors for gene expression, gene replacement, and protein-protein interaction studies in mycobacteria. Appl Environ Microbiol 2013; 79:1718-29. [PMID: 23315736 DOI: 10.1128/aem.03695-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli-mycobacterium shuttle vectors are important tools for gene expression and gene replacement in mycobacteria. However, most of the currently available vectors are limited in their use because of the lack of extended multiple cloning sites (MCSs) and convenience of appending an epitope tag(s) to the cloned open reading frames (ORFs). Here we report a new series of vectors that allow for the constitutive and regulatable expression of proteins, appended with peptide tag sequences at their N and C termini, respectively. The applicability of these vectors is demonstrated by the constitutive and induced expression of the Mycobacterium tuberculosis pknK gene, coding for protein kinase K, a serine-threonine protein kinase. Furthermore, a suicide plasmid with expanded MCS for creating gene replacements, a plasmid for chromosomal integrations at the commonly used L5 attB site, and a hypoxia-responsive vector, for expression of a gene(s) under hypoxic conditions that mimic latency, have also been created. Additionally, we have created a vector for the coexpression of two proteins controlled by two independent promoters, with each protein being in fusion with a different tag. The shuttle vectors developed in the present study are excellent tools for the analysis of gene function in mycobacteria and are a valuable addition to the existing repertoire of vectors for mycobacterial research.
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39
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Chien PN, Jung IP, Reddy KV, Yoon MY. Mechanism Studies of Substituted Triazol-1-yl-pyrimidine Derivatives Inhibition on Mycobacterium tuberculosis Acetohydroxyacid Synthase. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.12.4074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Zhao Y, Wen X, Niu C, Xi Z. Arginine 26 and Aspartic Acid 69 of the Regulatory Subunit are Key Residues of Subunits Interaction of Acetohydroxyacid Synthase Isozyme III fromE. coli. Chembiochem 2012; 13:2445-54. [DOI: 10.1002/cbic.201200362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Indexed: 11/08/2022]
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41
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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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42
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Shang J, Wang WM, Li YH, Song HB, Li ZM, Wang JG. Synthesis, crystal structure, in vitro acetohydroxyacid synthase inhibition, in vivo herbicidal activity, and 3D-QSAR of new asymmetric aryl disulfides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:8286-8293. [PMID: 22905906 DOI: 10.1021/jf302206x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Acetohydroxyacid synthase (AHAS; EC 2.2.1.6) is an important bioactive target for the design of environmentally benign herbicides. On the basis of previous virtual screening, 50 asymmetric aryl disulfides containing [1,2,4]triazole groups were synthesized and characterized by (1)H NMR, HRMS, and crystal structure. Compounds I-a, I-b, and I-p show Ki values of 1.70, 4.69, and 5.57 μM, respectively, for wild type Arabidopsis thaliana AHAS (AtAHAS) and low resistance against mutant type AtAHAS W574L. At 100 mg L(-1) concentration, compounds I-a, II-a, and II-b exhibit 86.6, 81.7, and 87.5% in vivo rape root growth inhibition. CoMFA steric and electrostatic contour maps were established, and a possible binding mode was suggested from molecular docking, which provide valuable information to understand the key structural features of these disulfide compounds. To the authors' knowledge, this is the first comprehensive case suggesting that asymmetric aryl disulfides are novel AHAS inhibitors.
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Affiliation(s)
- Jun Shang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University , Tianjin 300071, China
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43
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Synthesis and evaluation of novel monosubstituted sulfonylurea derivatives as antituberculosis agents. Eur J Med Chem 2012; 50:18-26. [DOI: 10.1016/j.ejmech.2012.01.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 12/27/2011] [Accepted: 01/06/2012] [Indexed: 11/17/2022]
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44
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Gedi V, Yoon MY. Bacterial acetohydroxyacid synthase and its inhibitors - a summary of their structure, biological activity and current status. FEBS J 2012; 279:946-63. [DOI: 10.1111/j.1742-4658.2012.08505.x] [Citation(s) in RCA: 37] [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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45
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Cloning, characterization and evaluation of potent inhibitors of Shigella sonnei acetohydroxyacid synthase catalytic subunit. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1825-31. [DOI: 10.1016/j.bbapap.2011.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 09/21/2011] [Accepted: 09/26/2011] [Indexed: 11/20/2022]
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46
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Gedi V, Moon JY, Lim WM, Lee MY, Lee SC, Koo BS, Govindwar S, Yoon MY. Identification and characterization of inhibitors of Haemophilus influenzae acetohydroxyacid synthase. Enzyme Microb Technol 2011; 49:1-5. [PMID: 22112263 DOI: 10.1016/j.enzmictec.2011.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 03/24/2011] [Accepted: 04/02/2011] [Indexed: 11/18/2022]
Abstract
Acetohydroxyacid synthase (AHAS), a potential target for antimicrobial agents, catalyzes the first common step in the biosynthesis of branched-chain amino acids. The gene coding for the AHAS catalytic subunit from Haemophilus influenzae (Hi) was cloned, overexpressed in Escherichia coli, and purified. To identify new inhibitory scaffolds, we used a high-throughput screen to test 221 small diverse chemical compounds against Hi-AHAS. Compounds were selected for their ability to inhibit AHAS in vitro. The screen identified 3 compounds, each representing a structural class, as Hi-AHAS inhibitors with an IC(50) in the low micromolar range (4.4-14.6 μM). The chemical scaffolds of the three compounds were oxa-1-thia-4-aza-cyclopenta[b]naphthalene (KHG25229), phenyl-2,3-dihydro-isothiazole (KHG25386), and phenyl-pyrrolidine-3-carboxylic acid phenylamide (KHG25056). Further, molecular docking of the two most potent chemicals, KHG25229 and KHG25386, in Hi-AHAS yielded binding energies of -10.41 and -9.21 kcal/mol, respectively. The binding modes were consistent with inhibition mechanisms, as both chemicals oriented outside the active site. As the need for novel antibiotic classes to combat drug resistant bacteria increases, screening compounds that act against Hi-AHAS may assist in the identification of potential new anti-Hi drugs.
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Affiliation(s)
- Vinayakumar Gedi
- Department of Chemistry and Research institute of Natural sciences, Hanyang University, Seoul 133-791, South Korea
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47
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Du Q, Wang H, Xie J. Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int J Biol Sci 2011; 7:41-52. [PMID: 21234302 PMCID: PMC3020362 DOI: 10.7150/ijbs.7.41] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 01/05/2011] [Indexed: 12/24/2022] Open
Abstract
Drug resistance of pathogens has necessitated the identification of novel targets for antibiotics. Thiamin (vitamin B1) is an essential cofactor for all organisms in its active form thiamin diphosphate (ThDP). Therefore, its metabolic pathways might be one largely untapped source of antibiotics targets. This review describes bacterial thiamin biosynthetic, salvage, and transport pathways. Essential thiamin synthetic enzymes such as Dxs and ThiE are proposed as promising drug targets. The regulation mechanism of thiamin biosynthesis by ThDP riboswitch is also discussed. As drug targets of existing antimicrobial compound pyrithiamin, the ThDP riboswitch might serves as alternative targets for more antibiotics.
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Affiliation(s)
- Qinglin Du
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of Three Gorges Area, School of Life Sciences, Southwest University, Beibei Chongqing, 400715, China
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48
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Singh V, Chandra D, Srivastava BS, Srivastava R. Biochemical and transcription analysis of acetohydroxyacid synthase isoforms in Mycobacterium tuberculosis identifies these enzymes as potential targets for drug development. Microbiology (Reading) 2011; 157:29-37. [DOI: 10.1099/mic.0.041343-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is a biosynthetic enzyme essential for de novo synthesis of branched-chain amino acids. The genome sequence of Mycobacterium tuberculosis revealed genes encoding four catalytic subunits, ilvB1 (Rv3003c), ilvB2 (Rv3470c), ilvG (Rv1820) and ilvX (Rv3509c), and one regulatory subunit, ilvN (Rv3002c), of AHAS. All these genes were found to be expressed in M. tuberculosis growing in vitro. Each AHAS subunit gene was cloned and expressed in Escherichia coli. AHAS activity of IlvB1 and IlvG was found in cell-free lysates and with recombinant purified proteins. Kinetic studies with purified IlvG revealed positive cooperativity towards substrate and cofactors. To understand the role of the catalytic subunits in the biology of M. tuberculosis, expression of AHAS genes was analysed in different physiological conditions. ilvB1, ilvB2 and ilvG were differentially expressed. The role of ilvB1 in persistence is known, but the upregulation of ilvB2 and ilvG in extended stationary phase, ex vivo, and in acid stress and hypoxic environments, suggests the relevance of AHAS enzymes in the metabolism and survival of M. tuberculosis by functioning as catabolic AHAS. These enzymes are therefore potential targets for drug development.
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Affiliation(s)
- Vinayak Singh
- Microbiology Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Deepak Chandra
- Department of Biochemistry, University of Lucknow, Lucknow 226001, India
| | - Brahm S. Srivastava
- Microbiology Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
| | - Ranjana Srivastava
- Microbiology Division, Central Drug Research Institute, CSIR, Lucknow 226001, India
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49
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Characterization of acetohydroxyacid synthase I from Escherichia coli K-12 and identification of its inhibitors. Biosci Biotechnol Biochem 2010; 74:2281-6. [PMID: 21071847 DOI: 10.1271/bbb.100496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The first step in branched-chain amino acid biosynthesis is catalyzed by acetohydroxyacid synthase (EC 2.2.1.6). This reaction involves decarboxylation of pyruvate followed by condensation with either an additional pyruvate molecule or with 2-oxobutyrate. The enzyme requires three cofactors, thiamine diphosphate (ThDP), a divalent ion, and flavin adenine dinucleotide (FAD). Escherichia coli contains three active isoenzymes, and acetohydroxyacid synthase I (AHAS I) large subunit is encoded by the ilvB gene. In this study, the ilvB gene from E. coli K-12 was cloned into expression vector pETDuet-1, and was expressed in E. coli BL21 (DH3). The purified protein was identified on a 12% SDS-PAGE gel as a single band with a mass of 65 kDa. The optimum temperature, buffer, and pH for E. coli K-12 AHAS I were 37 °C, potassium phosphate buffer, and 7.5. Km values for E. coli K-12 AHAS I binding to pyruvate, Mg(+2), ThDP, and FAD were 4.15, 1.26, 0.2 mM, and 0.61 µM respectively. Inhibition of purified AHAS I protein was determined with herbicides and new compounds.
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Choi JD, Gedi V, Pham CN, Ryu KH, Lee HS, Kim GH, Yoon MY. Site-directed mutagenesis of catalytic and regulatory subunits of Mycobacterium tuberculosis acetohydroxyacid synthase. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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