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Malinowska M, Czerniecka M, Jastrzebska I, Ratkiewicz A, Tylicki A, Wawrusiewicz-Kurylonek N. In Vitro and In Silico Studies on Cytotoxic Properties of Oxythiamine and 2'-Methylthiamine. Int J Mol Sci 2024; 25:4359. [PMID: 38673944 PMCID: PMC11050282 DOI: 10.3390/ijms25084359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
It is important to search for cytostatic compounds in order to fight cancer. One of them could be 2'-methylthiamine, which is a thiamine antimetabolite with an additional methyl group at the C-2 carbon of thiazole. So far, the cytostatic potential of 2'-methylthiamine has not been studied. We have come forward with a simplified method of synthesis using commercially available substrates and presented a comparison of its effects, as boosted by oxythiamine, on normal skin fibroblasts and HeLa cancer cells, having adopted in vitro culture techniques. Oxythiamine has been found to inhibit the growth and metabolism of cancer cells significantly better than 2'-methylthiamine (GI50 36 and 107 µM, respectively), while 2'-methylthiamine is more selective for cancer cells than oxythiamine (SI = 180 and 153, respectively). Docking analyses have revealed that 2'-methylthiamine (ΔG -8.2 kcal/mol) demonstrates a better affinity with thiamine pyrophosphokinase than thiamine (ΔG -7.5 kcal/mol ) and oxythiamine (ΔG -7.0 kcal/mol), which includes 2'-methylthiamine as a potential cytostatic. Our results suggest that the limited effect of 2'-methylthiamine on HeLa arises from the related arduous transport as compared to oxythiamine. Given that 2'-methylthiamine may possibly inhibit thiamine pyrophosphokinase, it could once again be considered a potential cytostatic. Thus, research should be carried out in order to find the best way to improve the transport of 2'-methylthiamine into cells, which may trigger its cytostatic properties.
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Affiliation(s)
- Marta Malinowska
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland; (M.M.); (I.J.)
| | - Magdalena Czerniecka
- Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland;
- Laboratory of Tissue Culture, Department of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
| | - Izabella Jastrzebska
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland; (M.M.); (I.J.)
| | - Artur Ratkiewicz
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland; (M.M.); (I.J.)
| | - Adam Tylicki
- Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland;
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Diamanti E, Souza PCT, Setyawati I, Bousis S, Monjas L, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Commun Biol 2023; 6:1182. [PMID: 37985798 PMCID: PMC10662466 DOI: 10.1038/s42003-023-05555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes. Here, we report on the identification of a promising class of inhibitors of the ECF transporters. We used coarse-grained molecular dynamics simulations on Lactobacillus delbrueckii ECF-FolT2 and ECF-PanT to profile the binding mode and mechanism of inhibition of this novel chemotype. The results corroborate the postulated mechanism of transport and pave the way for further drug-discovery efforts.
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Affiliation(s)
- Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
- Laboratoire de Biologie et Modélisation de la Cellule (UMR 5239, Inserm, U1293) and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 and CNRS, 46 Allée d'Italie, 69007, Lyon, France
| | - Inda Setyawati
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
- Department of Biochemistry, Bogor Agricultural University, Dramaga, 16680, Bogor, Indonesia
| | - Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Leticia Monjas
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lotteke J Y M Swier
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Aleksei Tsarenko
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Weronika K Stanek
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Manuel Jäger
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Siewert J Marrink
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands.
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3
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Tahir Khan M, Dumont E, Chaudhry AR, Wei DQ. Free energy landscape and thermodynamics properties of novel mutations in PncA of pyrazinamide resistance isolates of Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-12. [PMID: 37837425 DOI: 10.1080/07391102.2023.2268216] [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: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Pyrazinamide (PZA) is one of the first-line antituberculosis therapy, active against non-replicating Mycobacterium tuberculosis (Mtb). The conversion of PZA into pyrazinoic acid (POA), the active form, required the activity of pncA gene product pyrazinamidase (PZase) activity. Mutations occurred in pncA are the primary cause behind the PZA resistance. However, the resistance mechanism is important to explore using high throughput computational approaches. Here we aimed to explore the mechanism of PZA resistance behind novel P62T, L120R, and V130M mutations in PZase using 200 ns molecular dynamics (MD) simulations. MD simulations were performed to observe the structural changes for these three mutants (MTs) compared to the wild types (WT). Root means square fluctuation, the radius of gyration, free energy landscape, root means square deviation, dynamic cross-correlation motion, and pocket volume were found in variation between WT and MTs, revealing the effects of P62T, L120R, and V130M. The free energy conformational landscape of MTs differs significantly from the WT system, lowering the binding of PZA. The geometric shape complementarity of the drug (PZA) and target protein (PZase) further confirmed that P62T, L120R, and V130M affect the protein structure. These effects on PZase may cause vulnerability to convert PZA into POA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, PR China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR7272, Nice, France
- Institut Universitaire de France, Paris, France
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Dong X, Liu W, Dong Y, Wang K, Li K, Bian L. Metallo-β-lactamase SMB-1 evolves into a more efficient hydrolase under the selective pressure of meropenem. J Inorg Biochem 2023; 247:112323. [PMID: 37478781 DOI: 10.1016/j.jinorgbio.2023.112323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Metallo-β-lactamases (MβLs) are the primary mechanism of resistance to carbapenem antibiotics. To elucidate how MβLs have evolved with the introduction and use of antibiotics, the mutation and evolution of SMB-1 from Serratia marcescens were investigated in microbial evolution plates containing discontinuous meropenem (MEM) concentration gradients. The results revealed 2-point mutations, A242G and S257R; 1 double-site mutation, C240G/E258G; and 3 frameshift mutations, M5, M12, and M13, which are all missense mutations situated at the C-terminus. Compared with that of the wild-type (WT), the minimum inhibitory concentrations (MICs) of MEM for A242G, C240G/E258G, M5, M12, and M13 increased at least 120-fold, and that of S257R increased 8-fold. The catalytic efficiency kcat/Km increased by 365% and 647%, respectively. Concerning the structural changes, the structure at the active site changed from an ordered structure to an unordered conformation. Simultaneously, the flexibility of loop 1 was enhanced. These changes increased the volume of the active site cavity; thus, this was more conducive to exposing the Zn2+ site, facilitating substrate binding and conversion to products. In A242G, structural changes in Gly-242 can be transmitted to the active region via a network of interactions between the side chains of Gly-242 and the amino acid side chains near the active pocket. Together, these results pointed to the process of persistent drug tolerance and resistance, the SMB-1 enzyme evolved into a more exquisite structure with increased flexibility and stability, and stronger hydrolysis activity via genetic mutations and structural changes.
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Affiliation(s)
- Xiaoting Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Wenli Liu
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Yuxuan Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kun Wang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kewei Li
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, China.
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Chan AHY, Ho TCS, Irfan R, Hamid RAA, Rudge ES, Iqbal A, Turner A, Hirsch AKH, Leeper FJ. Design of thiamine analogues for inhibition of thiamine diphosphate (ThDP)-dependent enzymes: Systematic investigation through Scaffold-Hopping and C2-Functionalisation. Bioorg Chem 2023; 138:106602. [PMID: 37201323 DOI: 10.1016/j.bioorg.2023.106602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
Thiamine diphosphate (ThDP), the bioactive form of vitamin B1, is an essential coenzyme needed for processes of cellular metabolism in all organisms. ThDP-dependent enzymes all require ThDP as a coenzyme for catalytic activity, although individual enzymes vary significantly in substrate preferences and biochemical reactions. A popular way to study the role of these enzymes through chemical inhibition is to use thiamine/ThDP analogues, which typically feature a neutral aromatic ring in place of the positively charged thiazolium ring of ThDP. While ThDP analogues have aided work in understanding the structural and mechanistic aspects of the enzyme family, at least two key questions regarding the ligand design strategy remain unresolved: 1) which is the best aromatic ring? and 2) how can we achieve selectivity towards a given ThDP-dependent enzyme? In this work, we synthesise derivatives of these analogues covering all central aromatic rings used in the past decade and make a head-to-head comparison of all the compounds as inhibitors of several ThDP-dependent enzymes. Thus, we establish the relationship between the nature of the central ring and the inhibitory profile of these ThDP-competitive enzyme inhibitors. We also demonstrate that introducing a C2-substituent onto the central ring to explore the unique substrate-binding pocket can further improve both potency and selectivity.
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Affiliation(s)
- Alex H Y Chan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Terence C S Ho
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rimsha Irfan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rawia A A Hamid
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Emma S Rudge
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Amjid Iqbal
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Biochemistry, Science Unit, Deanship of Educational Services, Qassim University, Saudi Arabia
| | - Alex Turner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Khan MT, Chinnasamy S, Cui Z, Irfan M, Wei DQ. Mechanistic analysis of A46V, H57Y, and D129N in pyrazinamidase associated with pyrazinamide resistance. Saudi J Biol Sci 2020; 27:3150-3156. [PMID: 33100877 PMCID: PMC7569123 DOI: 10.1016/j.sjbs.2020.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
Pyrazinamide (PZA) is a component of first-line drugs, active against latent Mycobacterium tuberculosis (MTB) isolates. The prodrug is activated into the active form, pyrazinoic acid (POA) via pncA gene-encoded pyrazinamidase (PZase). Mutations in pncA have been reported, most commonly responsible for PZA-resistance in more than 70% of the resistant cases. In our previous study, we detected many mutations in PZase among PZA-resistance MTB isolates including A46V, H71Y, and D129N. The current study was aimed to investigate the molecular mechanism of PZA-resistance behind mutants (MTs) A46V, H71Y, and D129N in comparison with the wild type (WT) through molecular dynamic (MD) simulation. MTB positive samples were subjected to PZA drug susceptibility testing (DST) against critical concentration (100ug/ml). The resistant samples were subjected to pncA sequencing. Thirty-six various mutations have been observed in the coding region of pncA of PZA-resistant isolates (GenBank accession No. MH461111) including A46V, H71Y, and D129N. The post-simulation analysis revealed a significant variation in MTs structural dynamics as compared to the WT. Root means square deviations (RMSD) and Root means square fluctuation (RMSF) has been found in variation between WT and MTs. Folding effect and pocket volume were altered in MTs when compared with WT. Geometric matching supports the effect of mutation A46V, H71Y, and D129N on PZase structure that may have an insight effect on PZase dynamics, making them vulnerable to convert pro-PZA into active form, POA. In conclusion, the current analyses will provide useful information behind PZA-resistance for better management of drug-resistant TB.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhilei Cui
- Department of Respiratory Medicine, XinHua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Muhammad Irfan
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
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Ali A, Khan MT, Khan A, Ali S, Chinnasamy S, Akhtar K, Shafiq A, Wei DQ. Pyrazinamide resistance of novel mutations in pncA and their dynamic behavior. RSC Adv 2020; 10:35565-35573. [PMID: 35515677 PMCID: PMC9056903 DOI: 10.1039/d0ra06072k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
Pyrazinamide (PZA) is one of the essential anti-mycobacterium drugs, active against non-replicating Mycobacterium tuberculosis (MTB) isolates. PZA is converted into its active state, called pyrazinoic acid (POA), by action of pncA encoding pyrazinamidase (PZase). In the majority of PZA-resistance isolates, pncA harbored mutations in the coding region. In our recent report, we detected a number of novel variants in PZA-resistance (PZAR) MTB isolates, whose resistance mechanisms were yet to be determined. Here we performed several analyses to unveil the PZAR mechanism of R123P, T76P, G150A, and H71R mutants (MTs) through molecular dynamics (MD) simulations. In brief, culture positive MTB isolates were subjected to PZA susceptibility tests using the WHO recommended concentration of PZA (100 μg ml−1). The PZAR samples were screened for mutations in pncA along sensitive isolates through polymerase chain reactions and sequencing. A large number of variants (GeneBank accession no. MH461111), including R123P, T76P, G150A, and H71R, have been spotted in more than 70% of isolates. However, the mechanism of PZAR for mutants (MTs) R123P, T76P, G150A, and H71R was unknown. For the MTs and native PZase structures (WT), thermodynamic properties were compared using molecular dynamics simulations for 100 ns. The MTs structural activity was compared to the WT. Folding effect and pocket volume variations have been detected when comparing between WT and MTs. Geometric matching further confirmed the effect of R123P, T76P, G150A, and H71R mutations on PZase dynamics, making them vulnerable for activating the pro-drug into POA. This study offers a better understanding for management of PZAR TB. The results may be used as alternative diagnostic tools to infer PZA resistance at a structural dynamics level. We performed several analyses to unveil the pyrazinamide-resistance mechanism of R123P, T76P, G150A, and H71R mutants through molecular dynamics simulations.![]()
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Affiliation(s)
- Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology Pakistan
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Sajid Ali
- Quaid-i-Azam University Islamabad, Provincial Tuberculosis Reference Laboratory Hayatabad Medical Complex Peshawar Pakistan
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Khalid Akhtar
- National University of Science and Technology Pakistan
| | - Athar Shafiq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573.,Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District Shenzhen Guangdong 518055 China
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Zang H, Wang H, Miao L, Cheng Y, Zhang Y, Liu Y, Sun S, Wang Y, Li C. Carboxylesterase, a de-esterification enzyme, catalyzes the degradation of chlorimuron-ethyl in Rhodococcus erythropolis D310-1. JOURNAL OF HAZARDOUS MATERIALS 2020; 387:121684. [PMID: 31784128 DOI: 10.1016/j.jhazmat.2019.121684] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Microbial degradation is considered to be the most acceptable method for degradation of chlorimuron-ethyl, a typical long-term residual sulfonylurea herbicide, but the underlying mechanism at the genetic and biochemical levels is unclear. In this work, the genome sequence of the chlorimuron-ethyl-degrading bacterium Rhodococcus erythropolis D310-1 was completed, and the gene clusters responsible for the degradation of chlorimuron-ethyl in D310-1 were predicted. A carboxylesterase gene, carE, suggested to be responsible for carboxylesterase de-esterification, was cloned from D310-1. CarE was expressed in Escherichia coli BL21 and purified to homogeneity. The active site of the chlorimuron-ethyl-degrading enzyme CarE and the biochemical activities of CarE were elucidated. The results demonstrated that CarE is involved in catalyzing the de-esterification of chlorimuron-ethyl. A carE deletion mutant strain, D310-1ΔcarE, was constructed, and the chlorimuron-ethyl degradation rate in the presence of 100 mg L-1 chlorimuron-ethyl within 120 h decreased from 86.5 % (wild-type strain D310-1) to 58.2 % (mutant strain D310-1ΔcarE). Introduction of the plasmid pNit-carE restored the ability of the mutant strain to utilize chlorimuron-ethyl. This study is the first to demonstrate that carboxylesterase can catalyze the de-esterification reaction of chlorimuron-ethyl and provides new insights into the mechanism underlying the degradation of sulfonylurea herbicides and a theoretical basis for the utilization of enzyme resources.
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Affiliation(s)
- Hailian Zang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Hailan Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Lei Miao
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yi Cheng
- College of Science, China Agricultural University, Beijing, 100083, PR China
| | - Yuting Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yi Liu
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Shanshan Sun
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Yue Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin, 150030, Heilongjiang, PR China.
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9
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Khan MT, Malik SI. Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance. J Biomol Struct Dyn 2019; 38:3003-3017. [PMID: 31357912 DOI: 10.1080/07391102.2019.1650113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase). The major cause of PZA-resistance has been associated with mutations in the pncA gene. We have detected several novel mutations including V131F, Q141P, R154T, A170P, and V180F (GeneBank Accession No. MH461111) in the pncA gene of PZA-resistant isolates during PZA drug susceptibility testing followed by pncA gene sequencing. Here, we investigated molecular mechanism of PZA-resistance by comparing the results of experimental and molecular dynamics. The mutants (MTs) and wild type (WT) PZase structures in apo and complex with PZA were subjected to molecular dynamic simulations (MD) at the 40 ns. Multiple factors, including root mean square deviations (RMSD), binding pocket, total energy, dynamic cross correlation, and root mean square fluctuations (RMSF) of MTs and WT were compared. The MTs attained a high deviation and fluctuation compared to WT. Binding pocket volumes of the MTs, were found, lower than the WT, and the docking scores were high than WT while shape complementarity scores were lower than that of the WT. Residual motion in MTs are seemed to be dominant in anti-correlated motion. Mutations at locations, V131F, Q141P, R154T, A170P, and V180F, might be involved in the structural changes, possibly affecting the catalytic property of PZase to convert PZA into POA. Our study provides useful information that will enhance the understanding for better management of TB. AbbreviationsDSTdrug susceptibility testingΔelecelectrostatic energyLJLowenstein-Jensen mediumMGITmycobacterium growth indicator tubesMTsmutantsMDmolecular dynamic simulationsMTBMycobacterium tuberculosisNALC-NaOHN-acetyl-l-cysteine-sodium hydroxideNIHNational Institutes of HealthNPTamount of substance (N), pressure (P) temperature (T)NVTmoles (N), volume (V) temperature (T)PZasepyrazinamidaseΔpspolar solvation energyPTRLProvincial Tuberculosis Reference LaboratoryRMSDroot mean square deviationsRMSFroot mean square fluctuationsΔSASAsolvent accessible surface area energyTBtuberculosisGTotaltotal binding free energyΔvdWVan der Waals energyWTwild typeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
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Khan MT, Khan A, Rehman AU, Wang Y, Akhtar K, Malik SI, Wei DQ. Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. Sci Rep 2019; 9:7482. [PMID: 31097767 PMCID: PMC6522564 DOI: 10.1038/s41598-019-44013-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/29/2019] [Indexed: 02/04/2023] Open
Abstract
Resistance to key first-line drugs is a major hurdle to achieve the global end tuberculosis (TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB, recommended in drug resistance and susceptible Mycobacterium tuberculosis (MTB) isolates. The prodrug conversion into active form, pyrazinoic acid (POA), required the activity of pncA gene encoded pyrazinamidase (PZase). Although pncA mutations have been commonly associated with PZA resistance but a small number of resistance cases have been associated with mutationss in RpsA protein. Here in this study a total of 69 PZA resistance isolates have been sequenced for pncA mutations. However, samples that were found PZA resistant but pncA wild type (pncAWT), have been sequenced for rpsA and panD genes mutation. We repeated a drug susceptibility testing according to the WHO guidelines on 18 pncAWT MTB isolates. The rpsA and panD genes were sequenced. Out of total 69 PZA resistant isolates, 51 harbored 36 mutations in pncA gene (GeneBank Accession No. MH46111) while, fifteen different mutations including seven novel, were detected in the fourth S1 domain of RpsA known as C-terminal (MtRpsACTD) end. We did not detect any mutations in panD gene. Among the rpsA mutations, we investigated the molecular mechanism of resistance behind mutations, D342N, D343N, A344P, and I351F, present in the MtRpsACTD through molecular dynamic simulations (MD). WT showed a good drug binding affinity as compared to mutants (MTs), D342N, D343N, A344P, and I351F. Binding pocket volume, stability, and fluctuations have been altered whereas the total energy, protein folding, and geometric shape analysis further explored a significant variation between WT and MTs. In conclusion, mutations in MtRpsACTD might be involved to alter the RpsA activity, resulting in drug resistance. Such molecular mechanism behind resistance may provide a better insight into the resistance mechanism to achieve the global TB control targets.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Abbas Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ashfaq Ur Rehman
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Wang
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Khalid Akhtar
- National University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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Khan MT, Junaid M, Mao X, Wang Y, Hussain A, Malik SI, Wei DQ. Pyrazinamide resistance and mutations L19R, R140H, and E144K in Pyrazinamidase of Mycobacterium tuberculosis. J Cell Biochem 2019; 120:7154-7166. [PMID: 30485476 DOI: 10.1002/jcb.27989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
Pyrazinamide (PZA) is an important component of first-line antituberculosis drugs activated by Mycobacterium tuberculosis pyrazinamidase (PZase) into its active form pyrazinoic acid. Mutations in the pncA gene have been recognized as the major cause of PZA resistance. We detected some novel mutations, Leucine19Arginine (L19R), Arginine140Histidine (R140H), and Glutamic acid144 Lysine (E144K), in the pncA gene of PZA-resistant isolates in our wet lab PZA drug susceptibility testing and sequencing. As the molecular mechanism of resistance of these variants has not been reported earlier, we have performed multiple analyses to unveil different mechanisms of resistance because of PZase mutations L19R, R140H, and E144K. The mutants and native PZase structures were subjected to comprehensive computational molecular dynamics (MD) simulations at 100 nanoseconds in apo and drug-bound form. Mutants and native PZase binding pocket were compared to observe the consequence of mutations on the binding pocket size. Hydrogen bonding, Gibbs free energy, and natural ligand Fe +2 effect were also analyzed between native and mutants. A significant variation between native and mutant PZase structure activity was observed. The native PZase protein docking score was found to be the maximum, showing strong binding affinity in comparison with mutants. MD simulations explored the effect of the variants on the biological function of PZase. Hydrogen bonding, metal ion Fe +2 deviation, and fluctuation also seemed to be affected because of the mutations L19R, R140H, and E144K. The variants L19R, R140H, and E144K play a significant role in PZA resistance, altering the overall activity of native PZase, including metal ion Fe +2 displacement and free energy. This study offers valuable evidence for better management of drug-resistant tuberculosis.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.,Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Mao
- Department of Bioinformatics and Biostatistics, Qianweichang College, Shanghai University, Shanghai, China
| | - Yanjie Wang
- Department of Computer Science, College of Computer Science and Information Tech, Henan Normal University, Xixiang, China
| | - Abid Hussain
- Department of Pharmaceutics, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Rehman AU, Khan MT, Liu H, Wadood A, Malik SI, Chen HF. Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 of Mycobacterium tuberculosis. J Chem Inf Model 2019; 59:1584-1597. [DOI: 10.1021/acs.jcim.8b00956] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Abdul Wadood
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
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Bousis S, Setyawati I, Diamanti E, Slotboom DJ, Hirsch AKH. Energy-Coupling Factor Transporters as Novel Antimicrobial Targets. ADVANCED THERAPEUTICS 2019. [DOI: 10.1002/adtp.201800066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
| | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
| | - Dirk J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Biochemistry; Bogor Agricultural University; Dramaga 16680 Bogor Indonesia
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI); Department of Drug Design and Optimization; Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 7 9747AG Groningen The Netherlands
- Department of Pharmacy; Saarland University; Saarbrücken, Campus Building E8.1 66123 Saarbrücken Germany
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Junaid M, Khan MT, Malik SI, Wei DQ. Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N. J Chem Inf Model 2018; 59:498-508. [PMID: 30481017 DOI: 10.1021/acs.jcim.8b00525] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In an effort to discover the mechanism of resistance offered by Mycobacterium tuberculosis (Mtb) toward the pyrazinamide (PZA) drug, an extensive molecular dynamics strategy was employed. PZA is a first-line prodrug that effectively cuts therapy time by 33% (from 9 to 6 months). Pyrazinamidase enzyme (PZase), encoded by the pncA gene, is responsible for the activation of prodrug PZA into pyrazinoic acid (POA). POA is toxic and potently inhibits the growth of latent Mtb even at low pH values. PZA resistance is caused by three genes pncA, rpsA, and panD. Among them, the pncA gene contributes 72-99% to the resistance. Hence, the present study focused on the novel mutations N11K, P69T, and D126N in the pncA gene. In the present study, the possible mechanism of these three mutations was studied through molecular dynamics simulation and docking techniques. Our in-depth analysis and results are in strong agreement with our experimental observation. The binding pocket analysis showed that mutations decrease the volume of the active site and hinder the correct orientation of PZA drug in the active site. Moreover, the Patchdock score was found to be low as compared to WT showing the disturbance of shape complementarity between PZase and PZA drug. These mutations were found to disturb the position of the Fe2+ ion. Among the mutations, D126N allosterically disturbed the position of the Fe2+ ion. MMGBSA analyses showed that these mutations decrease the binding affinity toward the PZA drug. In conclusion, mutations N11K, P69T, and D126N result in weak binding affinity with PZA and also cause significant structural deformations that lead to PZA resistance. This study provides useful information that mutations in other than active parts may also cause protein folding and ligand displacement effects, altering the biological functions.
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Affiliation(s)
- Muhammad Junaid
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240
| | - Muhammad Tahir Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240.,Department of Bioinformatics and Biosciences , Capital University of Science and Technology , Islamabad , Pakistan 44000
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences , Capital University of Science and Technology , Islamabad , Pakistan 44000
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240
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Khan MT, Rehaman AU, Junaid M, Malik SI, Wei DQ. Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance. Comput Struct Biotechnol J 2018; 16:379-387. [PMID: 30402208 PMCID: PMC6205349 DOI: 10.1016/j.csbj.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis drugs which is converted into active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoded, pyrazinamidase (PZase). Mutations in pncA are detected in >70% of PZA resistant isolates but, noticeably, not in all. In this study, we selected 18 PZA-resistant but wild type pncA (pncAWT) MTB isolates. Drug susceptibility testing (DST) of all the isolates were repeated at the critical concentration of PZA drug. All these PZA-resistance but pncAWT isolates were subjected to RpsA sequencing. Fifteen different mutations were identified in eleven isolates, where seven were present in a conserved region including, Ser324Phe, Glu325Lys, Gly341Arg. As the molecular mechanism of resistance behind these variants has not been reported earlier, we have performed multiple analysis to unveil the mechanisms of resistance behind mutations S324F, E325K, and G341R. The mutant and wild type RpsA structures were subjected to comprehensive computational molecular dynamic simulations at 50 ns. Root mean square deviation (RMSD), Root mean square fluctuation (RMSF), and Gibbs free energy of mutants were analyzed in comparison with wild type. Docking score of wild type-RpsA has been found to be maximum, showing a strong binding affinity in comparison with mutants. Pocket volume, RMSD and RMSF have also been found to be altered, whereas total energy, folding effect (radius of gyration) and shape complimentarily analysis showed that variants S324F, E325K, and G341R have been playing a significant role behind PZA-resistance. The study offers valuable information for better management of drug resistance tuberculosis.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Ashfaq Ur Rehaman
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Muhammad Junaid
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
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Monjas L, Swier LJYM, Setyawati I, Slotboom DJ, Hirsch AKH. Dynamic Combinatorial Chemistry to Identify Binders of ThiT, an S-Component of the Energy-Coupling Factor Transporter for Thiamine. ChemMedChem 2017; 12:1693-1696. [PMID: 28960943 PMCID: PMC5698757 DOI: 10.1002/cmdc.201700440] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/13/2017] [Indexed: 02/05/2023]
Abstract
We applied dynamic combinatorial chemistry (DCC) to identify ligands of ThiT, the S-component of the energy-coupling factor (ECF) transporter for thiamine in Lactococcus lactis. We used a pre-equilibrated dynamic combinatorial library (DCL) and saturation-transfer difference (STD) NMR spectroscopy to identify ligands of ThiT. This is the first report in which DCC is used for fragment growing to an ill-defined pocket, and one of the first reports for its application with an integral membrane protein as target.
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Affiliation(s)
- Leticia Monjas
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Lotteke J. Y. M. Swier
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- Biochemistry DepartmentBogor Agricultural UniversityBogorIndonesia
| | - Dirk J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
- Current address: Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)Department of Drug Design and Optimization66123SaarbrückenGermany
- Department of Pharmacy, Medicinal ChemistrySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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