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Abstract
Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
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2
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Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 2021; 184:4579-4592.e24. [PMID: 34297925 PMCID: PMC8382161 DOI: 10.1016/j.cell.2021.06.033] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sophie Lavalette
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
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3
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Kuldeep J, Sharma SK, Singh BN, Siddiqi MI. Computational exploration and anti-mycobacterial activity of potential inhibitors of Mycobacterium tuberculosis acetyl coenzyme A carboxylase as anti-tubercular agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:191-205. [PMID: 33612029 DOI: 10.1080/1062936x.2021.1882563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Acetyl Coenzyme A Carboxylase (AccD6) is a homodimeric protein which is involved in the carboxylation of acetyl coenzyme A to produce malonyl coenzyme A, which plays an important role in the biosynthesis of fatty acid chain. However, studies suggest that AccD6 in combination with AccA3 produces malonyl co-A. Certain herbicides are known to inhibit plant ACC. Among these herbicides, haloxyfop was found to inhibit AccD6 at IC50 of 21.1 ± 1 µM. In this study, we have performed molecular docking of the Maybridge database consisting of ~55,000 compounds in the active site of the protein with haloxyfop as a reference molecule, followed by molecular dynamics study and biological activity determination of prioritized compounds. Out of the nine compounds selected for biological evaluation, three compounds - CD07230, HTS08529 and KM08871 - were found to exhibit anti-mycobacterial activity.
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Affiliation(s)
- J Kuldeep
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - S K Sharma
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - B N Singh
- Microbiology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - M I Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
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Wang P, Li RQ, Wang L, Yang WT, Zou QH, Xiao D. Proteomic Analyses of Acinetobacter baumannii Clinical Isolates to Identify Drug Resistant Mechanism. Front Cell Infect Microbiol 2021; 11:625430. [PMID: 33718272 PMCID: PMC7943614 DOI: 10.3389/fcimb.2021.625430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022] Open
Abstract
Acinetobacter baumannii is one of the main causes of nosocomial infections. Increasing numbers of multidrug-resistant Acinetobacter baumannii cases have been reported in recent years, but its antibiotic resistance mechanism remains unclear. We studied 9 multidrug-resistant (MDR) and 10 drug-susceptible Acinetobacter baumannii clinical isolates using Label free, TMT labeling approach and glycoproteomics analysis to identify proteins related to drug resistance. Our results showed that 164 proteins exhibited different expressions between MDR and drug-susceptible isolates. These differential proteins can be classified into six groups: a. proteins related to antibiotic resistance, b. membrane proteins, membrane transporters and proteins related to membrane formation, c. Stress response-related proteins, d. proteins related to gene expression and protein translation, e. metabolism-related proteins, f. proteins with unknown function or other functions containing biofilm formation and virulence. In addition, we verified seven proteins at the transcription level in eight clinical isolates by using quantitative RT-PCR. Results showed that four of the selected proteins have positive correlations with the protein level. This study provided an insight into the mechanism of antibiotic resistance of multidrug-resistant Acinetobacter baumannii.
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Affiliation(s)
- Ping Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ren-Qing Li
- Institute for Control of Infectious Diseases and Endemic Diseases, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Lei Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen-Tao Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing-Hua Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Di Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Shahbaaz M, Potemkin V, Bisetty K, Hassan MI, Hussien MA. Classification and functional analyses of putative virulence factors of Mycobacterium tuberculosis: A combined sequence and structure based study. Comput Biol Chem 2020; 87:107270. [PMID: 32438116 DOI: 10.1016/j.compbiolchem.2020.107270] [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: 09/06/2019] [Revised: 04/16/2020] [Accepted: 04/26/2020] [Indexed: 11/17/2022]
Abstract
The emergence of the drug-resistant mechanisms in Mycobacterium tuberculosis poses the biggest challenges to the current therapeutic measures, which necessitates the identification of new drug targets. The Hypothetical Proteins (HPs), a class of functionally uncharacterized proteins, may provide a new class of undiscovered therapeutic targets. The genome of M. tuberculosis contains 1000 HPs with their sequences were analyzed using a variety of bioinformatics tools and the functional annotations were performed. The functions of 662 HPs were successfully predicted and further classified 483 HPs as enzymes, 141 HPs were predicted to be involved in the diverse cellular mechanisms and 38 HPs may function as transporters and carriers proteins. Furthermore, 28 HPs were predicted to be virulent in nature. Amongst them, the HP P95201, HP P9WM79, HP I6WZ30, HP I6 × 9T8, HP P9WKP3, and HP P9WK89 showed the highest virulence scores. Therefore, these proteins were subjected to extensive structure analyses and dynamics of their conformations were investigated using the principles of molecular dynamics simulations, each for a 150 ns time scale. This study provides a deeper understanding of the undiscovered drug targets and the generated outputs will facilitate the process of drug design and discovery against the infection of M. tuberculosis.
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Affiliation(s)
- Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa; Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, 4000, South Africa
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia; Department of Chemistry, Faculty of Science, Port Said University, Port Said, 42521, Egypt
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Ding F, Li LX, Peng W, Peng YK, Liu BQ. Molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides and its environmental relevance: A combined experimental and computational study. CHEMOSPHERE 2019; 235:1030-1040. [PMID: 31561292 DOI: 10.1016/j.chemosphere.2019.07.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
Organic pesticides are one of the main environmental pollutants, and how to reduce their environmental risks is an important issue. In this contribution, we disclose the molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides using site-directed mutagenesis and molecular modeling and then construct an effective screening model. The results indicated that the target-site mutation (Trp-1999-Leu) in acetyl-coenzyme A carboxylase (ACCase) can affect the effectiveness of the pesticides (clodinafop, fenoxaprop, cyhalofop, and metamifop), and the plant resistance to fenoxaprop, clodinafop, cyhalofop, and metamifop was found to be 564, 19.5, 10, and 0.19 times, respectively. The established computational models (i.e. wild-type/mutant ACCase models) could be used for rational screening and evaluation of the resistance to pesticides. The resistance induced by target gene mutation can markedly reduce the bioreactivity of the ACCase-clodinafop/fenoxaprop adducts, and the magnitudes are 10 and 102, respectively. Such event will seriously aggravate environmental pollution. However, the biological issue has no distinct effect on cyhalofop (RI=10), and meanwhile it may markedly increase the bioefficacy of metamifop (RI=0.19). We could selectively adopt the two chemicals so as to decrease the residual pesticides in the environment. Significantly, research findings from the computational screening models were found to be negatively correlated with the resistance level derived from the bioassay testing, suggesting that the screening models can be used to guide the usage of pesticides. Obviously, this story may shed novel insight on the reduction of environmental risks of pesticides and other organic pollutants.
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Affiliation(s)
- Fei Ding
- School of Environmental Science and Engineering, Chang'an University, Xi'an, 710064, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, No. 126 Yanta Road, Yanta District, Xi'an, 710064, China
| | - Ling-Xu Li
- Department of Agricultural Chemistry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Peng
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China; Department of Chemistry, China Agricultural University, Beijing, 100193, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision, Inspection & Testing, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Bing-Qi Liu
- Department of Agricultural Chemistry, Qingdao Agricultural University, Qingdao, 266109, China
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Wang L, Zhang L, Feng RR, Dong X, Lu HZ, Zhang JJ. Unravelling the binding affinity between model transport protein and a prospective tuberculosis therapeutic agent: a spectroscopic and theoretical simulation exploration. J Biomol Struct Dyn 2019; 37:4507-4521. [DOI: 10.1080/07391102.2018.1552624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Leng Wang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Li Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Rui Rui Feng
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Xue Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Hui Zhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Jian Jun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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Thailandamide, a Fatty Acid Synthesis Antibiotic That Is Coexpressed with a Resistant Target Gene. Antimicrob Agents Chemother 2018; 62:AAC.00463-18. [PMID: 29914944 DOI: 10.1128/aac.00463-18] [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] [Received: 03/09/2018] [Accepted: 06/09/2018] [Indexed: 12/25/2022] Open
Abstract
Microbes encode many uncharacterized gene clusters that may produce antibiotics and other bioactive small molecules. Methods for activating these genes are needed to explore their biosynthetic potential. A transposon containing an inducible promoter was randomly inserted into the genome of the soil bacterium Burkholderia thailandensis to induce antibiotic expression. This screen identified the polyketide/nonribosomal peptide thailandamide as an antibiotic and discovered its regulator, AtsR. Mutants of Salmonella resistant to thailandamide had mutations in the accA gene for acetyl coenzyme A (acetyl-CoA) carboxylase, which is one of the first enzymes in the fatty acid synthesis pathway. A second copy of accA in the thailandamide synthesis gene cluster keeps B. thailandensis resistant to its own antibiotic. These genetic techniques will likely be powerful tools for discovering other unusual antibiotics.
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Striking Diversity in Holoenzyme Architecture and Extensive Conformational Variability in Biotin-Dependent Carboxylases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:161-194. [PMID: 28683917 DOI: 10.1016/bs.apcsb.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biotin-dependent carboxylases are widely distributed in nature and have central roles in the metabolism of fatty acids, amino acids, carbohydrates, and other compounds. The last decade has seen the accumulation of structural information on most of these large holoenzymes, including the 500-kDa dimeric yeast acetyl-CoA carboxylase, the 750-kDa α6β6 dodecameric bacterial propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, and geranyl-CoA carboxylase, the 720-kDa hexameric bacterial long-chain acyl-CoA carboxylase, the 500-kDa tetrameric bacterial single-chain pyruvate carboxylase, the 370-kDa α2β4 bacterial two-subunit pyruvate carboxylase, and the 130-kDa monomeric eukaryotic urea carboxylase. A common theme that has emerged from these studies is the dramatic structural flexibility of these holoenzymes despite their strong overall sequence conservation, evidenced both by the extensive diversity in the architectures of the holoenzymes and by the extensive conformational variability of their domains and subunits. This structural flexibility is crucial for the function and regulation of these enzymes and identifying compounds that can interfere with it represents an attractive approach for developing novel modulators and drugs. The extensive diversity observed in the structures so far and its biochemical and functional implications will be the focus of this review.
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Bennett M, Högbom M. Crystal structure of the essential biotin-dependent carboxylase AccA3 from Mycobacterium tuberculosis. FEBS Open Bio 2017; 7:620-626. [PMID: 28469974 PMCID: PMC5407890 DOI: 10.1002/2211-5463.12212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
Biotin‐dependent acetyl‐CoA carboxylases catalyze the committed step in type II fatty acid biosynthesis, the main route for production of membrane phospholipids in bacteria, and are considered a key target for antibacterial drug discovery. Here we describe the first structure of AccA3, an essential component of the acetyl‐CoA carboxylase system in Mycobacterium tuberculosis (MTb). The structure, sequence comparisons, and modeling of ligand‐bound states reveal that the ATP cosubstrate‐binding site shows distinct differences compared to other bacterial and eukaryotic biotin carboxylases, including all human homologs. This suggests the possibility to design MTb AccA3 subtype‐specific inhibitors. Database Coordinates and structure factors have been deposited in the Protein Data Bank with the accession number 5MLK.
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Affiliation(s)
- Matthew Bennett
- Department of Biochemistry and Biophysics; Arrhenius Laboratories for Natural Sciences; Stockholm University; Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics; Arrhenius Laboratories for Natural Sciences; Stockholm University; Sweden
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11
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Anti-tubercular drug discovery: in silico implications and challenges. Eur J Pharm Sci 2017; 104:1-15. [PMID: 28341614 DOI: 10.1016/j.ejps.2017.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them. To overcome this drug-resistance, efforts are continuously being made to develop new therapeutics. New drug-targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target-based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed.
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Xia X, Tang W, He S, Kang J, Ma H, Li J. Mechanism of metamifop inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in Echinochloa crus-galli. Sci Rep 2016; 6:34066. [PMID: 27666674 PMCID: PMC5036181 DOI: 10.1038/srep34066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/06/2016] [Indexed: 11/09/2022] Open
Abstract
Acetyl-coenzyme A carboxylase (ACCase) plays crucial roles in fatty acid metabolism and is an attractive target for herbicide discovery. Metamifop is a novel ACCase-inhibiting herbicide that can be applied to control sensitive weeds in paddy fields. In this study, the effects of metamifop on the chloroplasts, ACCase activity and carboxyltransferase (CT) domain gene expression in Echinochloa crus-galli were investigated. The results showed that metamifop interacted with the CT domain of ACCase in E. crus-galli. The three-dimensional structure of the CT domain of E. crus-galli ACCase in complex with metamifop was examined by homology modelling, molecular docking and molecular dynamics (MD) simulations. Metamifop has a different mechanism of inhibiting the CT domain compared with other ACCase inhibitors as it interacted with a different region in the active site of the CT domain. The protonation of nitrogen in the oxazole ring of metamifop plays a crucial role in the interaction between metamifop and the CT domain. The binding mode of metamifop provides a foundation for elucidating the molecular mechanism of target resistance and cross-resistance among ACCase herbicides, and for designing and optimizing ACCase inhibitors.
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Affiliation(s)
- Xiangdong Xia
- Department of Plant Protection, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wenjie Tang
- Department of Applied Chemistry, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shun He
- Department of Plant Protection, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jing Kang
- Department of Applied Chemistry, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Hongju Ma
- Department of Plant Protection, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianhong Li
- Department of Plant Protection, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
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13
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Hagmann A, Hunkeler M, Stuttfeld E, Maier T. Hybrid Structure of a Dynamic Single-Chain Carboxylase from Deinococcus radiodurans. Structure 2016; 24:1227-1236. [DOI: 10.1016/j.str.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/04/2016] [Accepted: 06/02/2016] [Indexed: 11/28/2022]
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14
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Ehebauer MT, Zimmermann M, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Lanéelle MA, Daffé M, Sachse C, Dziembowski A, Sauer U, Wilmanns M. Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism. PLoS Pathog 2015; 11:e1004623. [PMID: 25695631 PMCID: PMC4347857 DOI: 10.1371/journal.ppat.1004623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/11/2014] [Indexed: 01/22/2023] Open
Abstract
Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key
step in lipid biosynthesis that is carried out by multienzyme complexes to extend
fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high
redundancy of carboxyltransferase genes and biotin carboxylase genes, creating
multiple combinations of protein/protein complexes of unknown overall composition and
functional readout. By combining pull-down assays with mass spectrometry, we
identified nine binary protein/protein interactions and four validated holo
acyl-coenzyme A carboxylase complexes. We investigated one of these - the AccD1-AccA1
complex from Mycobacterium tuberculosis with hitherto unknown
physiological function. Using genetics, metabolomics and biochemistry we found that
this complex is involved in branched amino-acid catabolism with methylcrotonyl
coenzyme A as the substrate. We then determined its overall architecture by electron
microscopy and found it to be a four-layered dodecameric arrangement that matches the
overall dimensions of a distantly related methylcrotonyl coenzyme A holo complex. Our
data argue in favor of distinct structural requirements for biotin-mediated
γ-carboxylation of α−β unsaturated acid esters and will
advance the categorization of acyl-coenzyme A carboxylase complexes. Knowledge about
the underlying structural/functional relationships will be crucial to make the target
category amenable for future biomedical applications. Tuberculosis is deadly human disease caused by infection with the bacterium
Mycobacterium tuberculosis. This pathogen has a complex
metabolism with many genes required for the synthesis of components of its unique
cell envelope. We have investigated a family of closely related genes coding for
different acyl CoA carboxylase enzyme complexes with previously unexplained genetic
redundancy that have been thought to have an involvement in the synthesis of these
cell envelope components. We identified five functional multienzyme complexes. Of the
two complexes with hitherto unknown function we chose to investigate, one
specifically and to our surprise it is required for the degradation of the amino acid
leucine. To our knowledge this is the first demonstration that mycobacteria have a
specific pathway for leucine degradation and thus broaden the functional diversity
associated with acyl CoA carboxylase coding genes.
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Affiliation(s)
| | | | - Arjen J. Jakobi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Elke E. Noens
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
| | - Daniel Laubitz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Bogdan Cichocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Hedia Marrakchi
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Marie-Antoinette Lanéelle
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Mamadou Daffé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de
Biologie Structurale, Tuberculosis & Infection Biology Department, Toulouse,
France; Université Paul Sabatier, Toulouse, France
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural Biology and Computational
Biology Programme, Heidelberg, Germany
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw,
Poland
- Department of Genetics & Biotechnology, Warsaw University, Warsaw,
Poland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich,
Switzerland
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg,
Germany
- Center for Structural Systems Biology, Hamburg, Germany
- * E-mail:
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