The influence of glycerol on the binding of methotrexate to Mycobacterium tuberculosis dihydrofolate reductase: a molecular modelling study

References

• Corbett EL, Watt CJ, Walker N, Maher D, Williams BG, Raviglione MC, Dye C. The growing burden of tuberculosis. Arch Int Med. 2003;163(9):1009–1021. doi:10.1001/archinte.163.9.1009.
   PubMed Web of Science ®Google Scholar
• Nachega JB, Chaisson RE. Tuberculosis drug resistance: a global threat. Clin Infect Dis. 2003;36(Suppl 1):S24–S30. doi:10.1086/344657.
   PubMed Web of Science ®Google Scholar
• Raviglione M, Smith I. XDR tuberculosis – implications for global public health. N Engl J Med. 2007;356(7):656–659. doi:10.1056/NEJMp068273.
   PubMed Web of Science ®Google Scholar
• Blakley RL, In: Blakley RL, Benkovic SJ, editors. Folates and Pterines. New York: Wiley; 1984. p. 191–253.
   Google Scholar
• Blakley RL. Eukaryotic dihydrofolate reductase. Adv Enzymol Relat Areas Mol Biol. 1995;70:23–102.
   PubMedGoogle Scholar
• Blakley RL. Dihydrofolate reductase. In: Blakley RL & Benkovic SJ, editors. Folates and Pterines. New York: Wiley; 1984, vol. 1, pp. 191–253.
   Google Scholar
• Schweitzer BI, Dicker AP, Bertino JR. Dihydrofolate reductase as a therapeutic target. FASEB J. 1990;4:2441–2452.
   PubMed Web of Science ®Google Scholar
• White EL, Ross LJ, Cunningham A, Escuyer V. Cloning, expression, and characterization of Mycobacterium tuberculosis dihydrofolate reductase. FEMS Microbiol Lett. 2004;232(1):101–105. doi:10.1016/S0378-1097(04)00038-2.
   PubMed Web of Science ®Google Scholar
• Li R, Sirawaraporn R, Chitnumsub P, Sirawaraporn W, Wooden J, Athappilly F, Turley S, Hol WG. Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. J Mol Biol. 2000;295(2):307–323. doi:10.1006/jmbi.1999.3328.
   PubMed Web of Science ®Google Scholar
• Cody V, Galitsky N, Luft JR, Pangborn W, Rosowsky A, Blakley RL. Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523. Biochemistry. 1997;36(45):13897–13903. doi:10.1021/bi971711l.
   PubMed Web of Science ®Google Scholar
• El-Hamamsy MHRI, Smith AW, Thompson AS, Threadgill MD. Structure-based design, synthesis and preliminary evaluation of selective inhibitors of dihydrofolate reductase from Mycobacterium tuberculosis. Bioorg Med Chem Lett. 2007;15(13):4552–4576. doi:10.1016/j.bmc.2007.04.011.
   Web of Science ®Google Scholar
• Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Götz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh MJ, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, and Kollman PA. AMBER 12. San Francisco: University of California; 2012.
   Google Scholar
• Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA.; Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, and Pople JA, Gaussian 03, Revision C.02, Gaussian, Inc. Wallingford CT; 2004.
   Google Scholar
• Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem. 1993;97(40):10269–10280. doi:10.1021/j100142a004.
   Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174. doi:10.1002/jcc.20035.
   PubMed Web of Science ®Google Scholar
• Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997;267(3):727–748. doi:10.1006/jmbi.1996.0897.
   PubMed Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: an n⋅log(n) method for Ewald sums in large systems. J Chem Phys. 1993;98(12):10089–10092. doi:10.1063/1.464397.
   Web of Science ®Google Scholar
• Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81(8):3684–3690. doi:10.1063/1.448118.
   Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. Vmd: visual molecular dynamics. J Mol Graph. 1996;14(1):33–38. doi:10.1016/0263-7855(96)00018-5.
   PubMedGoogle Scholar
• Balsera MA, Wriggers W, Oono Y, Schulten K. Principal-component-analysis eigenvalue spectra from data with symmetry-breaking structure. Phys Rev E. 1996;69:1–13.
   Google Scholar
• Sherer EC, Harris SA, Soliva R, Orozco M, Laughton CA. Molecular dynamics studies of DNA a-tract structure and flexibility. J Am Chem Soc. 1999;121(25):5981–5991. doi:10.1021/ja983715z.
   Web of Science ®Google Scholar
• Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules:¿ combining molecular mechanics and continuum models. Acc Chem Res. 2000;33(12):889–897. doi:10.1021/ar000033j.
   PubMed Web of Science ®Google Scholar
• Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc. 1990;112(16):6127–6129. doi:10.1021/ja00172a038.
   Web of Science ®Google Scholar
• Orozco M, Luque FJ. Theoretical methods for the description of the solvent effect in biomolecular systems. Chem Rev. 2000;100(11):4187–4226. doi:10.1021/cr990052a.
   PubMed Web of Science ®Google Scholar