Structure and Function of L,D- and D,D-Transpeptidase Family Enzymes from Mycobacterium tuberculosis

Page: [3250 - 3267] Pages: 18

  • * (Excluding Mailing and Handling)

Abstract

Peptidoglycan, the exoskeleton of bacterial cell and an essential barrier that protects the cell, is synthesized by a pathway where the final steps are catalysed by transpeptidases. Knowledge of the structure and function of these vital enzymes that generate this macromolecule in M. tuberculosis could facilitate the development of potent lead compounds against tuberculosis. This review summarizes the experimental and computational studies to date on these aspects of transpeptidases in M. tuberculosis that have been identified and validated. The reported structures of L,D- and D,D-transpeptidases, as well as their functionalities, are reviewed and the proposed enzymatic mechanisms for L,D-transpeptidases are summarized. In addition, we provide bioactivities of known tuberculosis drugs against these enzymes based on both experimental and computational approaches. Advancing knowledge about these prominent targets supports the development of new drugs with novel inhibition mechanisms overcoming the current need for new drugs against tuberculosis.

Keywords: Mycobacterium tuberculosis (Mtb), Peptidoglycan (PG), L, D-transpeptidase, D, D-transpeptidase, drugs, enzymes.

[1]
Cole, S.; Brosch, R.; Parkhill, J.; Garnier, T.; Churcher, C.; Harris, D.; Gordon, S.; Eiglmeier, K.; Gas, S.; Barry, C.E., III; Tekaia, F.; Badcock, K.; Basham, D.; Brown, D.; Chillingworth, T.; Connor, R.; Davies, R.; Devlin, K.; Feltwell, T.; Gentles, S.; Hamlin, N.; Holroyd, S.; Hornsby, T.; Jagels, K.; Krogh, A.; McLean, J.; Moule, S.; Murphy, L.; Oliver, K.; Osborne, J.; Quail, M.A.; Rajandream, M.A.; Rogers, J.; Rutter, S.; Seeger, K.; Skelton, J.; Squares, R.; Squares, S.; Sulston, J.E.; Taylor, K.; Whitehead, S.; Barrell, B.G. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 1998, 393(6685), 537-544.
[http://dx.doi.org/10.1038/31159] [PMID: 9634230]
[2]
Petersen, P.E.; Bourgeois, D.; Ogawa, H.; Estupinan-Day, S.; Ndiaye, C. The global burden of oral diseases and risks to oral health. Bull. World Health Organ., 2005, 83(9), 661-669.https://dx.doi.org//S0042-96862005000900011
[PMID: 16211157]
[3]
World Health Organization. Global tuberculosis report, 2017.
[4]
Connolly, L.E.; Edelstein, P.H.; Ramakrishnan, L. Why is long-term therapy required to cure tuberculosis? PLoS Med., 2007, 4(3) e120
[http://dx.doi.org/10.1371/journal.pmed.0040120] [PMID: 17388672]
[5]
Kerantzas, C.A.; Jacobs, W.R., Jr Origins of combination therapy for tuberculosis: lessons for future antimicrobial development and application. MBio, 2017, 8(2), e01586-e01516.
[http://dx.doi.org/10.1128/mBio.01586-16] [PMID: 28292983]
[6]
Nachega, J.B.; Chaisson, R.E. Tuberculosis drug resistance: a global threat. Clin. Infect. Dis., 2003, 36(Suppl. 1), S24-S30.
[http://dx.doi.org/10.1086/344657] [PMID: 12516027]
[7]
Lamichhane, G.; Bishai, W. Defining the ‘survivasome’ of Mycobacterium tuberculosis. Nat. Med., 2007, 13(3), 280-282.
[http://dx.doi.org/10.1038/nm0307-280] [PMID: 17342137]
[8]
Sassetti, C.M.; Boyd, D.H.; Rubin, E.J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol., 2003, 48(1), 77-84.
[http://dx.doi.org/10.1046/j.1365-2958.2003.03425.x] [PMID: 12657046]
[9]
Correale, S.; Ruggiero, A.; Capparelli, R.; Pedone, E.; Berisio, R. Structures of free and inhibited forms of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis. Acta Crystallogr. D Biol. Crystallogr., 2013, 69(Pt 9), 1697-1706.
[http://dx.doi.org/10.1107/S0907444913013085] [PMID: 23999293]
[10]
World Health Organization. World Malaria Report, 2016.
[11]
Fedarovich, A.; Nicholas, R.A.; Davies, C. Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis. J. Mol. Biol., 2010, 398(1), 54-65.
[http://dx.doi.org/10.1016/j.jmb.2010.02.046] [PMID: 20206184]
[12]
Fedarovich, A.; Nicholas, R.A.; Davies, C. The role of the β5-α11 loop in the active-site dynamics of acylated penicillin-binding protein A from Mycobacterium tuberculosis. J. Mol. Biol., 2012, 418(5), 316-330.
[http://dx.doi.org/10.1016/j.jmb.2012.02.021] [PMID: 22365933]
[13]
Bhakta, S.; Basu, J. Overexpression, purification and biochemical characterization of a class A high-molecular-mass penicillin-binding protein (PBP), PBP1* and its soluble derivative from Mycobacterium tuberculosis. Biochem. J., 2002, 361(Pt 3), 635-639.
[http://dx.doi.org/10.1042/0264-6021:3610635] [PMID: 11802794]
[14]
Correale, S.; Ruggiero, A.; Pedone, E.; Berisio, R. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 2013, 69(Pt 3), 253-256.
[http://dx.doi.org/10.1107/S1744309112052141] [PMID: 23519798]
[15]
Cordillot, M.; Dubée, V.; Triboulet, S.; Dubost, L.; Marie, A.; Hugonnet, J.sE.; Arthur, M.; Mainardi, J.L. In vitro cross-linking of Mycobacterium tuberculosis peptidoglycan by L,D-transpeptidases and inactivation of these enzymes by carbapenems. Antimicrob. Agents Chemother., 2013, 57(12), 5940-5945.
[http://dx.doi.org/10.1128/AAC.01663-13] [PMID: 24041897]
[16]
Böth, D.; Steiner, E.M.; Stadler, D.; Lindqvist, Y.; Schnell, R.; Schneider, G. Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis. Acta Crystallogr. D Biol. Crystallogr., 2013, 69(Pt 3), 432-441.
[http://dx.doi.org/10.1107/S0907444912049268] [PMID: 23519418]
[17]
Erdemli, S.B.; Gupta, R.; Bishai, W.R.; Lamichhane, G.; Amzel, L.M.; Bianchet, M.A. Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2. Structure, 2012, 20(12), 2103-2115.
[http://dx.doi.org/10.1016/j.str.2012.09.016] [PMID: 23103390]
[18]
Mattoo, R.; Lloyd, E.P.; Kaushik, A.; Kumar, P.; Brunelle, J.L.; Townsend, C.A.; Lamichhane, G. LdtMav2, a nonclassical transpeptidase and susceptibility of Mycobacterium avium to carbapenems. Future Microbiol., 2017, 12(7), 595-607.
[http://dx.doi.org/10.2217/fmb-2016-0208] [PMID: 28555497]
[19]
Mainardi, J.L.; Fourgeaud, M.; Hugonnet, J.E.; Dubost, L.; Brouard, J.P.; Ouazzani, J.; Rice, L.B.; Gutmann, L.; Arthur, M. A novel peptidoglycan cross-linking enzyme for a beta-lactam-resistant transpeptidation pathway. J. Biol. Chem., 2005, 280(46), 38146-38152.
[http://dx.doi.org/10.1074/jbc.M507384200] [PMID: 16144833]
[20]
Lavollay, M.; Arthur, M.; Fourgeaud, M.; Dubost, L.; Marie, A.; Veziris, N.; Blanot, D.; Gutmann, L.; Mainardi, J.L. The peptidoglycan of stationary-phase Mycobacterium tuberculosis predominantly contains cross-links generated by L,D-transpeptidation. J. Bacteriol., 2008, 190(12), 4360-4366.
[http://dx.doi.org/10.1128/JB.00239-08] [PMID: 18408028]
[21]
Story-Roller, E.; Lamichhane, G. Have we realized the full potential of β-lactams for treating drug-resistant TB? IUBMB Life, 2008, 70(9), 881-888.
[http://dx.doi.org/10.1002/iub.1875] [PMID: 29934998]
[22]
Hatfull, G.F.; Jacobs, W.R., Jr Molecular Genetics of Mycobacteria; American Society of Microbiology, 2nd ed.. , 2014.
[23]
Wietzerbin, J.; Das, B.C.; Petit, J.F.; Lederer, E. Leyh- Bouille, M.; Ghuysen, J.M. Occurrence of D-alanyl-(D)- meso-diaminopimelic acid and meso-diaminopimelyl-mesodiaminopimelic acid interpeptide linkages in the peptidoglycan of Mycobacteria. Biochemistry, 1974, 13(17), 3471-3476.
[http://dx.doi.org/10.1021/bi00714a008] [PMID: 4210702]
[24]
Sanders, A.N.; Wright, L.F.; Pavelka, M.S. Genetic characterization of mycobacterial L,D-transpeptidases. Microbiology, 2014, 160(Pt 8), 1795-1806.
[http://dx.doi.org/10.1099/mic.0.078980-0] [PMID: 24855140]
[25]
Behera, B.; Mathur, P.; Das, A.; Kapil, A. Ertapenem susceptibility of extended spectrum beta-lactamase-producing Enterobacteriaceae at a tertiary care centre in India. Singapore Med. J., 2009, 50(6), 628-632.
[PMID: 19551319]
[26]
Steiner, E.M.; Schneider, G.; Schnell, R. Binding and processing of β-lactam antibiotics by the transpeptidase LdtMt2 from Mycobacterium tuberculosis. FEBS J., 2017, 284(5), 725-741.
[http://dx.doi.org/10.1111/febs.14010] [PMID: 28075068]
[27]
Triboulet, S.; Arthur, M.; Mainardi, J.L.; Veckerlé, C.; Dubée, V.; Nguekam-Moumi, A.; Gutmann, L.; Rice, L.B.; Hugonnet, J.E. Inactivation kinetics of a new target of beta-lactam antibiotics. J. Biol. Chem., 2011, 286(26), 22777-22784.
[http://dx.doi.org/10.1074/jbc.M111.239988] [PMID: 21543331]
[28]
Triboulet, S.; Dubée, V.; Lecoq, L.; Bougault, C.; Mainardi, J.L.; Rice, L.B.; Ethève-Quelquejeu, M.; Gutmann, L.; Marie, A.; Dubost, L.; Hugonnet, J.E.; Simorre, J.P.; Arthur, M. Kinetic features of L,D-transpeptidase inactivation critical for β-lactam antibacterial activity. PLoS One, 2013, 8(7) e67831
[http://dx.doi.org/10.1371/journal.pone.0067831] [PMID: 23861815]
[29]
Kumar, P.; Kaushik, A.; Lloyd, E.P.; Li, S.G.; Mattoo, R.; Ammerman, N.C.; Bell, D.T.; Perryman, A.L.; Zandi, T.A.; Ekins, S.; Ginell, S.L.; Townsend, C.A.; Freundlich, J.S.; Lamichhane, G. Non-classical transpeptidases yield insight into new antibacterials. Nat. Chem. Biol., 2017, 13(1), 54-61.
[http://dx.doi.org/10.1038/nchembio.2237] [PMID: 27820797]
[30]
Goffin, C.; Ghuysen, J.M. Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent. Microbiol. Mol. Biol. Rev., 2002, 66(4), 702-738.
[http://dx.doi.org/10.1128/MMBR.66.4.702-738.2002] [PMID: 12456788]
[31]
Sauvage, E.; Kerff, F.; Terrak, M.; Ayala, J.A.; Charlier, P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol. Rev., 2008, 32(2), 234-258.
[http://dx.doi.org/10.1111/j.1574-6976.2008.00105.x] [PMID: 18266856]
[32]
Goffin, C.; Ghuysen, J.M. Multimodular penicillin-binding proteins: an enigmatic family of orthologs and paralogs. Microbiol. Mol. Biol. Rev., 1998, 62(4), 1079-1093.
[http://dx.doi.org/10.1128/MMBR.62.4.1079-1093.1998] [PMID: 9841666]
[33]
Gupta, R.; Lavollay, M.; Mainardi, J.L.; Arthur, M.; Bishai, W.R.; Lamichhane, G. The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin. Nat. Med., 2010, 16(4), 466-469.
[http://dx.doi.org/10.1038/nm.2120] [PMID: 20305661]
[34]
Filippova, E.V.; Kieser, K.J.; Luan, C.H.; Wawrzak, Z.; Kiryukhina, O.; Rubin, E.J.; Anderson, W.F. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J., 2016, 283(12), 2206-2218.
[http://dx.doi.org/10.1111/febs.13738] [PMID: 27101811]
[35]
Calvanese, L.; Falcigno, L.; Maglione, C.; Marasco, D.; Ruggiero, A.; Squeglia, F.; Berisio, R.; D’Auria, G. Structural and binding properties of the PASTA domain of PonA2, a key penicillin binding protein from Mycobacterium tuberculosis. Biopolymers, 2014, 101(7), 712-719.
[http://dx.doi.org/10.1002/bip.22447] [PMID: 24281824]
[36]
Kim, H.S.; Kim, J.; Im, H.N.; Yoon, J.Y.; An, D.R.; Yoon, H.J.; Kim, J.Y.; Min, H.K.; Kim, S.J.; Lee, J.Y.; Han, B.W.; Suh, S.W. Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains. Acta Crystallogr. D Biol. Crystallogr., 2013, 69(Pt 3), 420-431.
[http://dx.doi.org/10.1107/S0907444912048998] [PMID: 23519417]
[37]
Bianchet, M.A.; Pan, Y.H.; Basta, L.A.B.; Saavedra, H.; Lloyd, E.P.; Kumar, P.; Mattoo, R.; Townsend, C.A.; Lamichhane, G. Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem. BMC Biochem., 2017, 18(1), 8.
[http://dx.doi.org/10.1186/s12858-017-0082-4] [PMID: 28545389]
[38]
Gokulan, K.; Khare, S.; Cerniglia, C.E.; Foley, S.L.; Varughese, K.I. Structure and inhibitor specificity of L,D-transpeptidase (LdtMt2) from Mycobacterium tuberculosis and antibiotic resistance: calcium binding promotes dimer formation. AAPS J., 2018, 20(2), 44.
[http://dx.doi.org/10.1208/s12248-018-0193-x] [PMID: 29524047]
[39]
Brammer Basta, L.A.; Ghosh, A.; Pan, Y.; Jakoncic, J.; Lloyd, E.P.; Townsend, C.A.; Lamichhane, G.; Bianchet, M.A. Loss of a functionally and structurally distinct ld-transpeptidase, LdtMt5, compromises cell wall integrity in Mycobacterium tuberculosis. J. Biol. Chem., 2015, 290(42), 25670-25685.
[http://dx.doi.org/10.1074/jbc.M115.660753] [PMID: 26304120]
[40]
Hett, E.C.; Chao, M.C.; Deng, L.L.; Rubin, E.J. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog., 2008, 4(2) e1000001
[http://dx.doi.org/10.1371/journal.ppat.1000001] [PMID: 18463693]
[41]
Shah, I.M.; Laaberki, M-H.; Popham, D.L.; Dworkin, J. A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments. Cell, 2008, 135(3), 486-496.
[http://dx.doi.org/10.1016/j.cell.2008.08.039] [PMID: 18984160]
[42]
Squeglia, F.; Marchetti, R.; Ruggiero, A.; Lanzetta, R.; Marasco, D.; Dworkin, J.; Petoukhov, M.; Molinaro, A.; Berisio, R.; Silipo, A. Chemical basis of peptidoglycan discrimination by PrkC, a key kinase involved in bacterial resuscitation from dormancy. J. Am. Chem. Soc., 2011, 133(51), 20676-20679.
[http://dx.doi.org/10.1021/ja208080r] [PMID: 22111897]
[43]
Tipper, D.J.; Strominger, J.L. Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine. Proc. Natl. Acad. Sci. USA, 1965, 54(4), 1133-1141.
[http://dx.doi.org/10.1073/pnas.54.4.1133] [PMID: 5219821]
[44]
Kastrinsky, D.B.; Barry, C.E., III Synthesis of labeled meropenem for the analysis of M. tuberculosis transpeptidases. Tetrahedron Lett., 2010, 51(1), 197-200.
[http://dx.doi.org/10.1016/j.tetlet.2009.10.124] [PMID: 20161438]
[45]
Finn, R.D.; Mistry, J.; Schuster-Böckler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S.R.; Sonnhammer, E.L.; Bateman, A. Pfam: clans, web tools and services. Nucleic Acids Res., 2006, 34(Database issue), D247-D251.
[http://dx.doi.org/10.1093/nar/gkj149] [PMID: 16381856]
[46]
Biarrotte-Sorin, S.; Hugonnet, J.E.; Delfosse, V.; Mainardi, J.L.; Gutmann, L.; Arthur, M.; Mayer, C. Crystal structure of a novel beta-lactam-insensitive peptidoglycan transpeptidase. J. Mol. Biol., 2006, 359(3), 533-538.
[http://dx.doi.org/10.1016/j.jmb.2006.03.014] [PMID: 16647082]
[47]
Magnet, S.; Arbeloa, A.; Mainardi, J.L.; Hugonnet, J.E.; Fourgeaud, M.; Dubost, L.; Marie, A.; Delfosse, V.; Mayer, C.; Rice, L.B.; Arthur, M. Specificity of L,D-transpeptidases from gram-positive bacteria producing different peptidoglycan chemotypes. J. Biol. Chem., 2007, 282(18), 13151-13159.
[http://dx.doi.org/10.1074/jbc.M610911200] [PMID: 17311917]
[48]
Betts, J.C.; Lukey, P.T.; Robb, L.C.; McAdam, R.A.; Duncan, K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol., 2002, 43(3), 717-731.
[http://dx.doi.org/10.1046/j.1365-2958.2002.02779.x] [PMID: 11929527]
[49]
Bielnicki, J.; Devedjiev, Y.; Derewenda, U.; Dauter, Z.; Joachimiak, A.; Derewenda, Z.S.B. B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes. Proteins, 2006, 62(1), 144-151.
[http://dx.doi.org/10.1002/prot.20702] [PMID: 16287140]
[50]
Li, W.J.; Li, D.F.; Hu, Y.L.; Zhang, X.E.; Bi, L.J.; Wang, D.C. Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis. Cell Res., 2013, 23(5), 728-731.
[http://dx.doi.org/10.1038/cr.2013.53] [PMID: 23588382]
[51]
Lecoq, L.; Dubée, V.; Triboulet, S.; Bougault, C.; Hugonnet, J.E.; Arthur, M.; Simorre, J.P. Structure of Enterococcus faeciuml,d-transpeptidase acylated by ertapenem provides insight into the inactivation mechanism. ACS Chem. Biol., 2013, 8(6), 1140-1146.
[http://dx.doi.org/10.1021/cb4001603] [PMID: 23574509]
[52]
Brennan, P.J. Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis (Edinb.), 2003, 83(1-3), 91-97.
[http://dx.doi.org/10.1016/S1472-9792(02)00089-6] [PMID: 12758196]
[53]
Moraes, G.L.; Gomes, G.C.; Monteiro de Sousa, P.R.; Alves, C.N.; Govender, T.; Kruger, H.G.; Maguire, G.E.M.; Lamichhane, G.; Lameira, J. Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. Tuberculosis (Edinb.), 2015, 95(2), 95-111.
[http://dx.doi.org/10.1016/j.tube.2015.01.006] [PMID: 25701501]
[54]
Fakhar, Z.; Naiker, S.; Alves, C.N.; Govender, T.; Maguire, G.E.M.; Lameira, J.; Lamichhane, G.; Kruger, H.G.; Honarparvar, B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J. Biomol. Struct. Dyn., 2016, 34(11), 2399-2417.
[http://dx.doi.org/10.1080/07391102.2015.1117397] [PMID: 26612108]
[55]
Mainardi, J.L.; Hugonnet, J.E.; Rusconi, F.; Fourgeaud, M.; Dubost, L.; Moumi, A.N.; Delfosse, V.; Mayer, C.; Gutmann, L.; Rice, L.B.; Arthur, M. Unexpected inhibition of peptidoglycan LD-transpeptidase from Enterococcus faecium by the beta-lactam imipenem. J. Biol. Chem., 2007, 282(42), 30414-30422.
[http://dx.doi.org/10.1074/jbc.M704286200] [PMID: 17646161]
[56]
Dodson, G.; Wlodawer, A. Catalytic triads and their relatives. Trends Biochem. Sci., 1998, 23(9), 347-352.
[http://dx.doi.org/10.1016/S0968-0004(98)01254-7] [PMID: 9787641]
[57]
Silva, J.R.A.; Govender, T.; Maguire, G.E.M.; Kruger, H.G.; Lameira, J.; Roitberg, A.E.; Alves, C.N. Simulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems. Chem. Commun. (Camb.), 2015, 51(63), 12560-12562.
[http://dx.doi.org/10.1039/C5CC03202D] [PMID: 26153571]
[58]
Silva, J.R.; Roitberg, A.E.; Alves, C.N. Catalytic mechanism of L,D-transpeptidase 2 from Mycobacterium tuberculosis described by a computational approach: insights for the design of new antibiotics drugs. J. Chem. Inf. Model., 2014, 54(9), 2402-2410.
[http://dx.doi.org/10.1021/ci5003069] [PMID: 25149147]
[59]
Waksman, S.A. Streptomycin: Nature and practical applications, 1949.
[60]
Lehmann, J. Twenty years afterward. Historical notes on the discovery of the antituberculosis effect of para-aminosalicylic acid (PAS) and the first clinical trials (Editorial). Am. Rev. Respir. Dis., 1964, 90, 953-956.
[http://dx.doi.org/10.1164/arrd.1964.90.6.953] [PMID: 14233801]
[61]
Verma, A.K.; Kalra, O.P. Discovery of new drugs against Tuberculosis: History Guides. Arch. Clin. Infect. Dis., 2012, 7(4), 109-112.
[http://dx.doi.org/10.5812/archcid.15088]
[62]
Waksman, S.A. Streptomycin and neomycin: an antibiotic approach to tuberculosis. BMJ, 1950, 2(4679), 595-600.
[http://dx.doi.org/10.1136/bmj.2.4679.595] [PMID: 14772423]
[63]
World Health Organization. Treatment of tuberculosis: guidelines, 4th ed; , 2010.
[64]
Kaplan, J.E.; Benson, C.; Holmes, K.K.; Brooks, J.T.; Pau, A.; Masur, H. Centers for Disease Control and Prevention (CDC); National Institutes of Health; HIV Medicine Association of the Infectious Diseases Society of America. Guidelines for prevention and treatment opportunistic infections in HIV-infected adults and adolescents: recommendations from CDC, the National Institutes of Health, and the HIV Medicine Association/Infectious Diseases Society of America. MMWR Recomm. Rep., 2009, 58(RR-4), 1-207.
[PMID: 19357635]
[65]
Chetty, S.; Ramesh, M.; Singh-Pillay, A.; Soliman, M.E. Recent advancements in the development of anti-tuberculosis drugs. Bioorg. Med. Chem. Lett., 2017, 27(3), 370-386.
[http://dx.doi.org/10.1016/j.bmcl.2016.11.084] [PMID: 28017531]
[66]
Ma, Z.; Lienhardt, C.; McIlleron, H.; Nunn, A.J.; Wang, X. Global tuberculosis drug development pipeline: the need and the reality. Lancet, 2010, 375(9731), 2100-2109.
[http://dx.doi.org/10.1016/S0140-6736(10)60359-9] [PMID: 20488518]
[67]
Papp-Wallace, K.M.; Endimiani, A.; Taracila, M.A.; Bonomo, R.A. Carbapenems: past, present, and future. Antimicrob. Agents Chemother., 2011, 55(11), 4943-4960.
[http://dx.doi.org/10.1128/AAC.00296-11] [PMID: 21859938]
[68]
Shaikh, S.; Fatima, J.; Shakil, S.; Rizvi, S.M.D.; Kamal, M.A. Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J. Biol. Sci., 2015, 22(1), 90-101.
[http://dx.doi.org/10.1016/j.sjbs.2014.08.002] [PMID: 25561890]
[69]
Birnbaum, J.; Kahan, F.M.; Kropp, H.; MacDonald, J.S. Carbapenems, a new class of beta-lactam antibiotics. Discovery and development of imipenem/cilastatin. Am. J. Med., 1985, 78(6A), 3-21.
[http://dx.doi.org/10.1016/0002-9343(85)90097-X] [PMID: 3859213]
[70]
Baughman, R.P. The use of carbapenems in the treatment of serious infections. J. Intensive Care Med., 2009, 24(4), 230-241.
[http://dx.doi.org/10.1177/0885066609335660] [PMID: 19617229]
[71]
Livermore, D.M. Of Pseudomonas, porins, pumps and carbapenems. J. Antimicrob. Chemother., 2001, 47(3), 247-250.
[http://dx.doi.org/10.1093/jac/47.3.247] [PMID: 11222556]
[72]
Jaganath, D.; Lamichhane, G.; Shah, M. Carbapenems against Mycobacterium tuberculosis: a review of the evidence. Int. J. Tuberc. Lung Dis., 2016, 20(11), 1436-1447.
[http://dx.doi.org/10.5588/ijtld.16.0498] [PMID: 27776583]
[73]
England, K.; Boshoff, H.I.; Arora, K.; Weiner, D.; Dayao, E.; Schimel, D.; Via, L.E.; Barry, C.E., III Meropenem-clavulanic acid shows activity against Mycobacterium tuberculosis in vivo. Antimicrob. Agents Chemother., 2012, 56(6), 3384-3387.
[http://dx.doi.org/10.1128/AAC.05690-11] [PMID: 22450968]
[74]
Tremblay, L.W.; Fan, F.; Blanchard, J.S. Biochemical and structural characterization of Mycobacterium tuberculosis beta-lactamase with the carbapenems ertapenem and doripenem. Biochemistry, 2010, 49(17), 3766-3773.
[http://dx.doi.org/10.1021/bi100232q] [PMID: 20353175]
[75]
Schurek, K.N.; Wiebe, R.; Karlowsky, J.A.; Rubinstein, E.; Hoban, D.J.; Zhanel, G.G. Faropenem: review of a new oral penem. Expert Rev. Anti Infect. Ther., 2007, 5(2), 185-198.
[http://dx.doi.org/10.1586/14787210.5.2.185] [PMID: 17402834]
[76]
Dubée, V.; Triboulet, S.; Mainardi, J.L. Ethève- Quelquejeu, M.; Gutmann, L.; Marie, A.; Dubost, L.; Hugonnet, J.E.; Arthur, M. Inactivation of Mycobacterium tuberculosis l,d-transpeptidase LdtMt1 by carbapenems and cephalosporins. Antimicrob. Agents Chemother., 2012, 56(8), 4189-4195.
[http://dx.doi.org/10.1128/AAC.00665-12] [PMID: 22615283]
[77]
Schoonmaker, M.K.; Bishai, W.R.; Lamichhane, G. Nonclassical transpeptidases of Mycobacterium tuberculosis alter cell size, morphology, the cytosolic matrix, protein localization, virulence, and resistance to β-lactams. J. Bacteriol., 2014, 196(7), 1394-1402.
[http://dx.doi.org/10.1128/JB.01396-13] [PMID: 24464457]
[78]
Kaushik, A.; Makkar, N.; Pandey, P.; Parrish, N.; Singh, U.; Lamichhane, G. Carbapenems and rifampin exhibit synergy against Mycobacterium tuberculosis and Mycobacterium abscessus. Antimicrob. Agents Chemother., 2015, 59(10), 6561-6567.
[http://dx.doi.org/10.1128/AAC.01158-15] [PMID: 26259792]
[79]
Dhar, N.; Dubée, V.; Ballell, L.; Cuinet, G.; Hugonnet, J.E.; Signorino-Gelo, F.; Barros, D.; Arthur, M.; McKinney, J.D. Rapid cytolysis of Mycobacterium tuberculosis by faropenem, an orally bioavailable β-lactam antibiotic. Antimicrob. Agents Chemother., 2015, 59(2), 1308-1319.
[http://dx.doi.org/10.1128/AAC.03461-14] [PMID: 25421469]
[80]
Cynamon, M.H.; Speirs, R.J.; Welch, J.T. In vitro antimycobacterial activity of 5-chloropyrazinamide. Antimicrob. Agents Chemother., 1998, 42(2), 462-463.
[PMID: 9527809]
[81]
Acevedo, O.; Jorgensen, W.L. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc. Chem. Res., 2010, 43(1), 142-151.
[http://dx.doi.org/10.1021/ar900171c] [PMID: 19728702]
[82]
Silva, J.R.A.; Bishai, W.R.; Govender, T.; Lamichhane, G.; Maguire, G.E.M.; Kruger, H.G.; Lameira, J.; Alves, C.N. Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2. J. Biomol. Struct. Dyn., 2016, 34(2), 304-317.
[http://dx.doi.org/10.1080/07391102.2015.1029000] [PMID: 25762064]
[83]
Miller, B.R., III; McGee, T.D., Jr; Swails, J.M.; Homeyer, N.; Gohlke, H.; Roitberg, A.E. MMPBSA. py: an efficient program for end-state free energy calculations. J. Chem. Theory Comput., 2012, 8(9), 3314-3321.
[http://dx.doi.org/10.1021/ct300418h] [PMID: 26605738]
[84]
Naïm, M.; Bhat, S.; Rankin, K.N.; Dennis, S.; Chowdhury, S.F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C.I.; Jakalian, A.; Purisima, E.O. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. J. Chem. Inf. Model., 2007, 47(1), 122-133.
[http://dx.doi.org/10.1021/ci600406v] [PMID: 17238257]
[85]
Fakhar, Z.; Govender, T.; Lamichhane, G.; Maguire, G.E.M.; Kruger, H.G.; Honarparvar, B. Computational model for the acylation step of the β-lactam ring: Potential application for l, d-transpeptidase 2 in Mycobacterium tuberculosis. J. Mol. Struct., 2017, 1128, 94-102.
[http://dx.doi.org/10.1016/j.molstruc.2016.08.049]
[86]
Fakhar, Z.; Govender, T.; Maguire, G.E.M.; Lamichhane, G.; Walker, R.C.; Kruger, H.G.; Honarparvar, B. Differential flap dynamics in l,d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics. Mol. Biosyst., 2017, 13(6), 1223-1234.
[http://dx.doi.org/10.1039/C7MB00110J] [PMID: 28480928]
[87]
Billones, J.B.; Carrillo, M.C.O.; Organo, V.G.; Macalino, S.J.Y.; Sy, J.B.A.; Emnacen, I.A.; Clavio, N.A.B.; Concepcion, G.P. Toward antituberculosis drugs: in silico screening of synthetic compounds against Mycobacterium tuberculosisl,d-transpeptidase 2. Drug Des. Devel. Ther., 2016, 10, 1147-1157.
[http://dx.doi.org/10.2147/DDDT.S97043] [PMID: 27042006]
[88]
Chen, F.; Li, W.; Zhou, Y.; Shen, J.; Wu, Z.; Liu, G.; Lee, P.W.; Tang, Y. admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J. Chem. Inf. Model., 2012, 52(11), 3099-3105.
[http://dx.doi.org/10.1021/ci300367a] [PMID: 23092397]
[89]
Baldin, S.; Misiura, N.; Švedas, V. Building a full-atom model of L, Dtranspeptidase 2 from Mycobacterium tuberculosis for screening new inhibitors. Acta naturae, 2017, 9(1), 44-51.
[PMID: 28461973]
[90]
Ntombela, T.; Fakhar, Z.; Ibeji, C.U.; Govender, T.; Maguire, G.E.M.; Lamichhane, G.; Kruger, H.G.; Honarparvar, B. Molecular insight on the non-covalent interactions between carbapenems and L,D-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study. J. Comput. Aided Mol. Des., 2018, 32(6), 687-701.
[http://dx.doi.org/10.1007/s10822-018-0121-2] [PMID: 29845435]
[91]
Hugonnet, J.E.; Tremblay, L.W.; Boshoff, H.I.; Barry, C.E., III; Blanchard, J.S. Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis. Science, 2009, 323(5918), 1215-1218.
[http://dx.doi.org/10.1126/science.1167498] [PMID: 19251630]
[92]
Cohen, K.A.; El-Hay, T.; Wyres, K.L.; Weissbrod, O.; Munsamy, V.; Yanover, C.; Aharonov, R.; Shaham, O.; Conway, T.C.; Goldschmidt, Y.; Bishai, W.R.; Pym, A.S. Paradoxical hypersusceptibility of drug-resistant Mycobacterium tuberculosis to β-lactam antibiotics. EBioMedicine, 2016, 9, 170-179.
[http://dx.doi.org/10.1016/j.ebiom.2016.05.041] [PMID: 27333036]