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An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: Free energy calculations involving mutant and native structures bound to methotrexate

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Abstract

Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this paper, we describe the role played by hydrophobic residues lining the active site region, particularly 79 Ile and 176 Phe, in the binding of methotrexate to the Escherichia coli (E. coli) thymidylate synthase (TS) enzyme, using the thermodynamic cycle perturbation (TCP) approach. The computed binding free energy differences on the binding of methotrexate to the native and some mutant E. coli TS structures have been compared with experimental results. Computationally, four different ‘mutations’ have been simulated on the TS enzyme with methotrexate (MTX): 79 Ile →  79 Val; 79 Ile → 79 Ala; 79 Ile → 79 Leu; and 176 Phe →  176 Ile. The calculated results indicate that in each of these cases, the native residues (79 Ile and 176 Phe) interact more favorably with methotrexate than the mutant residues and these results are corroborated by experimental measurements. Binding preference to wild type residues can be rationalized in terms of their better hydrophobic contacts with the phenyl ring of methotrexate.

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References

  1. Matthews DA, Appelt K, Oatley SJ, Xuong NgH (1990) J Mol Biol 214:923–926

    Article  CAS  Google Scholar 

  2. Jones T, Calvert A, Jackman AL, Eakin MA, Smithers MJ, Betteridge RF, Newell DR, Hayter AJ, Stocker A, Harland SJ, Davis LC, Harrap KR (1985) J Med Chem 28:1468–1476

    Article  CAS  Google Scholar 

  3. Jones TR, Varney MD, Webber SE, Lewis KK, Marzoni GP, Palmer CL, Kathardekar V, Welsh KM, Webber S, Matthews DA, Appelt K, Smith WW, Janson CA, Villfranca JE, Bacquet RJ, Howland EF, Bartlett CA, Morse CA (1996) J Med Chem 39:904–917

    Article  CAS  Google Scholar 

  4. Nair MG, Nanavati NT, Nair IG, Kialiuk RL, Gaumont Y, Hsiao MC, Kalman TI (1986) J Med Chem 29:1754–1760

    Article  CAS  Google Scholar 

  5. Matthews DA, Villafranca JE, Janson CA, Smith WW, Welsh K, Freer S (1990) J Mol Biol 214:937–948

    Article  CAS  Google Scholar 

  6. Liu L, Santi DV (1993) Biochem 32:9263–9267

    Article  CAS  Google Scholar 

  7. Liu L, Santi DV (1992) Biochem 31:5010–5014

    Article  Google Scholar 

  8. Appelt K, Bacquet RJ, Bartlett CA, Booth CL, Freer ST, Fuhry MAM, Gehring MR, Hermann SM, Howland EF, Janson CA, Jones TR, Kan C, Kathardekar V, Lewis KK, Marzoni GP, Matthews DA, Mohr C, Moomaw EW, Morse CA, Oatley SJ, Ogden RO, Reddy MR, Reich SH, Schoettlin WS, Smith WW, Varney MD, Villafranca JE, Ward RW, Webber SE, Welsh KM, White J (1991) J Med Chem 34:1925–1934

    Article  CAS  Google Scholar 

  9. Holloway K, Wai JM, Halgren TA, Fitzgerald PM, Vacca JP, Dorsey BD, Levin RB, Thompson WJ, Chen JL, deSolms JS, Gaffin N, Ghosh AK, Giuliani EA, Graham SL, Guare JP, Hungate RW, Lyle TA, Sanders WM, Tucker TJ, Wiggins M, Wiscount CM, Woltersdorf OW, Young SD, Darke PL, Zugay JA (1995) J Med Chem 38:305–317

    Article  CAS  Google Scholar 

  10. Varney MD, Appelt K, Kalish V, Reddy MR, Tatlock J, Palmer CL, Romies WH, Wu BW, Musick L (1994) J Med Chem 37:2274–2284

    Article  CAS  Google Scholar 

  11. Erion MD, Montgomery JA, Niwas S, Rose JD, Ananthan S, Allen M, Secrist JA, Babu SY, Bugg CE, Guida WC, Ealick SE (1993) J Med Chem 36:3771–3783

    Article  CAS  Google Scholar 

  12. Erion MD, Dang Q, Reddy MR, Rao KS, Huang J, Lipscomb WN, van Poelje PD (2007) J Am Chem Soc 129:15480–15490

    Article  CAS  Google Scholar 

  13. Dang Q, Rao KS, Reddy KR, Jiang T, Reddy MR, Potter SC, Fujitaki JM, van Poelje PD, Huang J, Lipscomb WN, Erion MD (2007) J Am Chem Soc 129:15491–15502

    Article  CAS  Google Scholar 

  14. Reddy MR, Erion MD, Agarwal A (2001) In: Lipkowitz KB and Boyd DB (eds) Reviews in Computational Chemistry, vol 16. Wiley, New York, NY, pp 217–304

    Google Scholar 

  15. Reddy MR, Viswanadhan VN, Weinstein JN (1991) Proc Natl Acad Sci USA 88:10287–10291

    Article  CAS  Google Scholar 

  16. Ferguson DM, Radmer RJ, Kollman PA (1991) J Med Chem 34:2654–2659

    Article  CAS  Google Scholar 

  17. Tropshaw AJ, Hermans J (1999) J Prot Eng 5:29–33

    Article  Google Scholar 

  18. Rao BG, Tilton RF, Singh UC (1992) J Am Chem Soc 114:4447–4452

    Article  CAS  Google Scholar 

  19. Fleischman SH, Brooks CL (1990) Proteins: Struct Funct and Genet 7:52–61

    Article  CAS  Google Scholar 

  20. Merz KM, Kollman PA (1989) J Am Chem Soc 111:5649–5658

    Article  CAS  Google Scholar 

  21. Reddy MR, Varney MD, Kalish V, Viswanadhan VN, Appelt K (1994) J Med Chem 114:10117–10122

    Google Scholar 

  22. Erion MD, van Poelje PD, Reddy MR (2000) J Am Chem Soc 122:6114–6115

    Article  CAS  Google Scholar 

  23. Reddy MR, Erion MD (2001) J Am Chem Soc 123:6246–6252

    Article  CAS  Google Scholar 

  24. Singh UC (1988) Proc Natl Acad Sci 85:4280–4284

    Article  CAS  Google Scholar 

  25. Reddy MR, Bacquet RJ, Zichi D, Matthews DA, Welsh KM, Jones TR, Freer S (1992) J Am Chem Soc 114:10117–10122

    Article  CAS  Google Scholar 

  26. Rastelli G, Thomas B, Kollman PA, Santi DV (1995) J Am Chem Soc 117:7213–7227

    Article  CAS  Google Scholar 

  27. Lee T-S, Kollman PA (2001) In : Reddy MR, Erion MD (eds) Free Energy Calculations in Rational Drug Design. Kluwer, New York, NY, pp 335–343

  28. Ravichandra Mutyala, Reddy RN, Sumakanth M, Reddanna P, Reddy MR (2007) J Comp Chem 28:932–937

    Article  Google Scholar 

  29. Galaxy Molecular Modeling Software and AM2000 Macromolecular Simulation package (1995) AM Technologies, Inc. San Antonio, TX, Copyright

  30. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagoha G, Profeta S Jr, Weiner PK (1984) J Am Chem Soc 106:765–784

    Article  CAS  Google Scholar 

  31. Singh UC, Weiner PK, Caldwell JK, Kollman PA (1986) AMBER version 3.0. University of California at San Francisco

    Google Scholar 

  32. Berendsen HJC, Grigera JR, Straatsma TP (1987) J Phys Chem 91:6269–6271

    Article  CAS  Google Scholar 

  33. Reddy MR, Berkowitz M (1989) Chem Phys Lett 155:173–176

    Article  CAS  Google Scholar 

  34. Frisch MJ, Head-Gordon HB, Schlegel K, Raghavachari JS, Binkley C, Gonzalez DJ, Defrees DJ, Fox RJ, Whiteside R, Seeger CF, Melius J, Baker R, Martin LR, Kahn JJP, Stewart EM, Fluder S, Topiol JA, Pople JA (1994) Gaussian Inc, Pittsburgh, PA

  35. Chirlian LE, Francl MM (1987) J Comp Chem 8:894–905

    Article  CAS  Google Scholar 

  36. Verlet L (1967) Phys Rev 159:98–103

    Article  CAS  Google Scholar 

  37. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comp Phys 23:327–341

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Rational Labs Pvt. Limited, Plot #177, IDA Mallapur, Hyderabad, 500 076, India

    Ramirededy Nageswara Reddy & Ravichandra Reddy Mutyala

  2. RR Labs Inc., 8013 Los Sabalos Street, San Diego, CA, 92126, USA

    Ravichandra Reddy Mutyala & Mutyala Rami Reddy

  3. School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India

    Polamarasetty Aparoy & Pallu Reddanna

  4. Metabasis Therapeutics Inc., 11119 North Torrey Pines Road, La Jolla, CA, 92037, USA

    Mutyala Rami Reddy

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  1. Ramirededy Nageswara Reddy
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  2. Ravichandra Reddy Mutyala
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  3. Polamarasetty Aparoy
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  4. Pallu Reddanna
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Correspondence to Mutyala Rami Reddy.

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Reddy, R.N., Mutyala, R.R., Aparoy, P. et al. An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: Free energy calculations involving mutant and native structures bound to methotrexate. J Mol Model 16, 203–209 (2010). https://doi.org/10.1007/s00894-009-0535-9

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  • DOI: https://doi.org/10.1007/s00894-009-0535-9

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