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Li Y, Kong X, Li Y, Tao N, Wang T, Li Y, Hou Y, Zhu X, Han Q, Zhang Y, An Q, Liu Y, Li H. Association between fatty acid metabolism gene mutations and Mycobacterium tuberculosis transmission revealed by whole genome sequencing. BMC Microbiol 2023; 23:379. [PMID: 38041005 PMCID: PMC10691062 DOI: 10.1186/s12866-023-03072-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Fatty acid metabolism greatly promotes the virulence and pathogenicity of Mycobacterium tuberculosis (M.tb). However, the regulatory mechanism of fatty acid metabolism in M.tb remains to be elucidated, and limited evidence about the effects of gene mutations in fatty acid metabolism on the transmission of M.tb was reported. RESULTS Overall, a total of 3193 M.tb isolates were included in the study, of which 1596 (50%) were genomic clustered isolates. Most of the tuberculosis isolates belonged to lineage2(n = 2744,85.93%), followed by lineage4(n = 439,13.75%) and lineage3(n = 10,0.31%).Regression results showed that the mutations of gca (136,605, 317G > C, Arg106Pro; OR, 22.144; 95% CI, 2.591-189.272), ogt(1,477,346, 286G > C ,Gly96Arg; OR, 3.893; 95%CI, 1.432-10.583), and rpsA (1,834,776, 1235 C > T, Ala412Val; OR, 3.674; 95% CI, 1.217-11.091) were significantly associated with clustering; mutations in gca and rpsA were also significantly associated with clustering of lineage2. Mutation in arsA(3,001,498, 885 C > G, Thr295Thr; OR, 6.278; 95% CI, 2.508-15.711) was significantly associated with cross-regional clusters. We also found that 20 mutation sites were positively correlated with cluster size, while 11 fatty acid mutation sites were negatively correlated with cluster size. CONCLUSION Our research results suggested that mutations in genes related to fatty acid metabolism were related to the transmission of M.tb. This research could help in the future control of the transmission of M.tb.
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Affiliation(s)
- Yameng Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250011, Shandong, People's Republic of China
| | - Yifan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, 250031, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Tingting Wang
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yingying Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Yawei Hou
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China
| | - Xuehan Zhu
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Qiqi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
| | - Huaichen Li
- Deartment of Chinese Medicine Integrated with Western Medicine, College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, 250355, Shandong, People's Republic of China.
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jingwuweiqi Road, Huaiyin District, Jinan, 250021, Shandong, People's Republic of China.
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Kumar G, Narayan R, Kapoor S. Chemical Tools for Illumination of Tuberculosis Biology, Virulence Mechanisms, and Diagnosis. J Med Chem 2020; 63:15308-15332. [PMID: 33307693 DOI: 10.1021/acs.jmedchem.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases and begs the scientific community to up the ante for research and exploration of completely novel therapeutic avenues. Chemical biology-inspired design of tunable chemical tools has aided in clinical diagnosis, facilitated discovery of therapeutics, and begun to enable investigation of virulence mechanisms at the host-pathogen interface of Mycobacterium tuberculosis. This Perspective highlights chemical tools specific to mycobacterial proteins and the cell lipid envelope that have furnished rapid and selective diagnostic strategies and provided unprecedented insights into the function of the mycobacterial proteome and lipidome. We discuss chemical tools that have enabled elucidating otherwise intractable biological processes by leveraging the unique lipid and metabolite repertoire of mycobacterial species. Some of these probes represent exciting starting points with the potential to illuminate poorly understood aspects of mycobacterial pathogenesis, particularly the host membrane-pathogen interactions.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda 403 401, Goa, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
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Baran M, Grimes KD, Sibbald PA, Fu P, Boshoff HIM, Wilson DJ, Aldrich CC. Development of small-molecule inhibitors of fatty acyl-AMP and fatty acyl-CoA ligases in Mycobacterium tuberculosis. Eur J Med Chem 2020; 201:112408. [PMID: 32574901 PMCID: PMC7415619 DOI: 10.1016/j.ejmech.2020.112408] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/07/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
Lipid metabolism in Mycobacterium tuberculosis (Mtb) relies on 34 fatty acid adenylating enzymes (FadDs) that can be grouped into two classes: fatty acyl-CoA ligases (FACLs) involved in lipid and cholesterol catabolism and long chain fatty acyl-AMP ligases (FAALs) involved in biosynthesis of the numerous essential and virulence-conferring lipids found in Mtb. The precise biochemical roles of many FACLs remain poorly characterized while the functionally non-redundant FAALs are much better understood. Here we describe the systematic investigation of 5'-O-[N-(alkanoyl)sulfamoyl]adenosine (alkanoyl adenosine monosulfamate, alkanoyl-AMS) analogs as potential multitarget FadD inhibitors for their antitubercular activity and biochemical selectivity towards representative FAAL and FACL enzymes. We identified several potent compounds including 12-azidododecanoyl-AMS 28, 11-phenoxyundecanoyl-AMS 32, and nonyloxyacetyl-AMS 36 with minimum inhibitory concentrations (MICs) against M. tuberculosis ranging from 0.098 to 3.13 μM. Compound 32 was notable for its impressive biochemical selectivity against FAAL28 (apparent Ki = 0.7 μM) versus FACL19 (Ki > 100 μM), and uniform activity against a panel of multidrug and extensively drug-resistant TB strains with MICs ranging from 3.13 to 12.5 μM in minimal (GAST) and rich (7H9) media. The SAR analysis provided valuable insights for further optimization of 32 and also identified limitations to overcome.
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Affiliation(s)
- Marzena Baran
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States
| | - Kimberly D Grimes
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Paul A Sibbald
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Peng Fu
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Helena I M Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States.
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Mujumdar P, Bua S, Supuran CT, Peat TS, Poulsen SA. Synthesis, structure and bioactivity of primary sulfamate-containing natural products. Bioorg Med Chem Lett 2018; 28:3009-3013. [PMID: 29685656 DOI: 10.1016/j.bmcl.2018.04.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 01/17/2023]
Abstract
Here we report the synthesis of natural products (NPs) 5'-O-sulfamoyl adenosine 1 and 5'-O-sulfamoyl-2-chloroadenosine 2. As primary sulfamates these compounds represent an uncommon class of NPs, furthermore there are few NPs known that contain a NS bond. Compounds 1 and 2 were evaluated for inhibition of carbonic anhydrases (CA), a metalloenzyme family where the primary sulfamate is known to coordinate to the active site zinc and form key hydrogen bonds with adjacent CA active site residues. Both NPs were good to moderate CA inhibitors, with compound 2 a 20-50-fold stronger CA inhibitor (Ki values 65-234 nM) than compound 1. The protein X-ray crystal structures of 1 and 2 in complex with CA II show that it is not the halogen-hydrophobic interactions that give compound 2 a greater binding energy but a slight movement in orientation of the ribose ring that allows better hydrogen bonds to CA residues. Compounds 1 and 2 were further investigated for antimicrobial activity against a panel of microbes relevant to human health, including Gram-negative bacteria (4 strains), Gram-positive bacteria (1 strain) and yeast (2 strains). Antimicrobial activity and selectivity was observed. The minimum inhibitory concentration (MIC) of NP 1 was 10 µM against Gram-positive Staphylococcus aureus and NP 2 was 5 µM against Gram-negative Escherichia coli. This is the first time that NP primary sulfamates have been assessed for inhibition and binding to CAs, with systematic antimicrobial activity studies also reported.
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Affiliation(s)
- Prashant Mujumdar
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia
| | - Silvia Bua
- NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Thomas S Peat
- CSIRO, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia.
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Development of a one-pot assay for screening and identification of Mur pathway inhibitors in Mycobacterium tuberculosis. Sci Rep 2016; 6:35134. [PMID: 27734910 PMCID: PMC5062083 DOI: 10.1038/srep35134] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/23/2016] [Indexed: 01/21/2023] Open
Abstract
The cell wall of Mycobacterium tuberculosis (Mtb) consists of peptidoglycan, arabinogalactan and mycolic acids. The cytoplasmic steps in the peptidoglycan biosynthetic pathway, catalyzed by the Mur (A-F) enzymes, involve the synthesis of UDP-n-acetylmuramyl pentapeptide, a key precursor molecule required for the formation of the peptidoglycan monomeric building blocks. Mur enzymes are indispensable for cell integrity and their lack of counterparts in eukaryotes suggests them to be promising Mtb drug targets. However, the caveat is that most of the current assays utilize a single Mur enzyme, thereby identifying inhibitors against only one of the enzymes. Here, we report development of a one-pot assay that reconstructs the entire Mtb Mur pathway in vitro and has the advantage of eliminating the requirement for nucleotide intermediates in the pathway as substrates. The MurA-MurF enzymes were purified and a one-pot assay was developed through optimization of successive coupled enzyme assays using UDP-n-acetylglucosamine as the initial sugar substrate. The assay is biochemically characterized and optimized for high-throughput screening of molecules that could disrupt multiple targets within the pathway. Furthermore, we have validated the assay by performing it to identify D-Cycloserine and furan-based benzene-derived compounds with known Mur ligase inhibition as inhibitors of Mtb MurE and MurF.
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6
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Mujumdar P, Poulsen SA. Natural Product Primary Sulfonamides and Primary Sulfamates. JOURNAL OF NATURAL PRODUCTS 2015; 78:1470-1477. [PMID: 26035239 DOI: 10.1021/np501015m] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Primary sulfonamide and primary sulfamate functional groups feature prominently in the structures of U.S. FDA-approved drugs. However, the natural product chemical space contains few examples of these well-known zinc-binding chemotypes, with just two primary sulfonamide and five primary sulfamate natural products isolated and characterized to date. One of these natural products was isolated from a marine sponge, with the remainder isolated from Streptomyces species. In this review are outlined for the first time the discovery, isolation, striking breadth of bioactivity, and total synthesis (where available) for this rare group of natural products.
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Affiliation(s)
- Prashant Mujumdar
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
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Quadri LEN. Biosynthesis of mycobacterial lipids by polyketide synthases and beyond. Crit Rev Biochem Mol Biol 2014; 49:179-211. [DOI: 10.3109/10409238.2014.896859] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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Watkins D, Norris FA, Kumar S, Arya DP. A fluorescence-based screen for ribosome binding antibiotics. Anal Biochem 2012; 434:300-7. [PMID: 23262284 DOI: 10.1016/j.ab.2012.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/30/2012] [Accepted: 12/03/2012] [Indexed: 12/12/2022]
Abstract
The development of new antibacterial agents has become necessary to treat the large number of emerging bacterial strains resistant to current antibiotics. Despite the different methods of resistance developed by these new strains, the A-site of the bacterial ribosome remains an attractive target for new antibiotics. To develop new drugs that target the ribosomal A-site, a high-throughput screen is necessary to identify compounds that bind to the target with high affinity. To this end, we present an assay that uses a novel fluorescein-conjugated neomycin (F-neo) molecule as a binding probe to determine the relative binding affinity of a drug library. We show here that the binding of F-neo to a model Escherichia coli ribosomal A-site results in a large decrease in the fluorescence of the molecule. Furthermore, we have determined that the change in fluorescence is due to the relative change in the pK(a) of the probe resulting from the change in the electrostatic environment that occurs when the probe is taken from the solvent and localized into the negative potential of the A-site major groove. Finally, we demonstrate that F-neo can be used in a robust, highly reproducible assay, determined by a Z'-factor greater than 0.80 for 3 consecutive days. The assay is capable of rapidly determining the relative binding affinity of a compound library in a 96-well plate format using a single channel electronic pipette. The current assay format will be easily adaptable to a high-throughput format with the use of a liquid handling robot for large drug libraries currently available and under development.
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Akeroyd M, Olsthoorn M, Gerritsma J, Gutker-Vermaas D, Ekkelkamp L, van Rij T, Klaassen P, Plugge W, Smit E, Strupat K, Wenzel T, van Tilborg M, van der Hoeven R. Searching for microbial protein over-expression in a complex matrix using automated high throughput MS-based proteomics tools. J Biotechnol 2012; 164:112-20. [PMID: 23220267 DOI: 10.1016/j.jbiotec.2012.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 11/26/2012] [Accepted: 11/26/2012] [Indexed: 01/10/2023]
Abstract
In the discovery of new enzymes genomic and cDNA expression libraries containing thousands of differential clones are generated to obtain biodiversity. These libraries need to be screened for the activity of interest. Removing so-called empty and redundant clones significantly reduces the size of these expression libraries and therefore speeds up new enzyme discovery. Here, we present a sensitive, generic workflow for high throughput screening of successful microbial protein over-expression in microtiter plates containing a complex matrix based on mass spectrometry techniques. MALDI-LTQ-Orbitrap screening followed by principal component analysis and peptide mass fingerprinting was developed to obtain a throughput of ∼12,000 samples per week. Alternatively, a UHPLC-MS(2) approach including MS(2) protein identification was developed for microorganisms with a complex protein secretome with a throughput of ∼2000 samples per week. TCA-induced protein precipitation enhanced by addition of bovine serum albumin is used for protein purification prior to MS detection. We show that this generic workflow can effectively reduce large expression libraries from fungi and bacteria to their minimal size by detection of successful protein over-expression using MS.
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Affiliation(s)
- Michiel Akeroyd
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613AX Delft, The Netherlands.
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Duckworth BP, Nelson KM, Aldrich CC. Adenylating enzymes in Mycobacterium tuberculosis as drug targets. Curr Top Med Chem 2012; 12:766-96. [PMID: 22283817 DOI: 10.2174/156802612799984571] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/08/2011] [Indexed: 11/22/2022]
Abstract
Adenylation or adenylate-forming enzymes (AEs) are widely found in nature and are responsible for the activation of carboxylic acids to intermediate acyladenylates, which are mixed anhydrides of AMP. In a second reaction, AEs catalyze the transfer of the acyl group of the acyladenylate onto a nucleophilic amino, alcohol, or thiol group of an acceptor molecule leading to amide, ester, and thioester products, respectively. Mycobacterium tuberculosis encodes for more than 60 adenylating enzymes, many of which represent potential drug targets due to their confirmed essentiality or requirement for virulence. Several strategies have been used to develop potent and selective AE inhibitors including highthroughput screening, fragment-based screening, and the rationale design of bisubstrate inhibitors that mimic the acyladenylate. In this review, a comprehensive analysis of the mycobacterial adenylating enzymes will be presented with a focus on the identification of small molecule inhibitors. Specifically, this review will cover the aminoacyl tRNAsynthetases (aaRSs), MenE required for menaquinone synthesis, the FadD family of enzymes including the fatty acyl- AMP ligases (FAAL) and the fatty acyl-CoA ligases (FACLs) involved in lipid metabolism, and the nonribosomal peptide synthetase adenylation enzyme MbtA that is necessary for mycobactin synthesis. Additionally, the enzymes NadE, GuaA, PanC, and MshC involved in the respective synthesis of NAD, guanine, pantothenate, and mycothiol will be discussed as well as BirA that is responsible for biotinylation of the acyl CoA-carboxylases.
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Singh R, Vince R. 2-Azabicyclo[2.2.1]hept-5-en-3-one: Chemical Profile of a Versatile Synthetic Building Block and its Impact on the Development of Therapeutics. Chem Rev 2012; 112:4642-86. [DOI: 10.1021/cr2004822] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Rohit Singh
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street Southeast,
Minneapolis, MN 55455, United States
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