Thermodynamic analysis of thrombin inhibition by benzamidine and p-methylbenzamidine via free-energy perturbations: Inspection of intraperturbed-group contributions using the finite difference thermodynamic integration (FDTI) algorithm

Journal of Physical Chemistry B

Volumn 106, Issue 2, 2002, Pages 466-476

  Guimarães, Cristiano Ruch Werneck ^a   De Alencastro, Ricardo Bicca ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BLOOD; CHEMICAL BONDS; COAGULATION; ELECTROSTATICS; ENZYME INHIBITION; FREE ENERGY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES; PROTEINS;

HYDROPHOBIC INTERACTIONS;

THERMODYNAMICS;

EID: 0037123056     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp013563l     Document Type: Article

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9. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
10. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
11. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
12. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
13. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
14. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
15. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
16. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
17. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
18. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
19. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
20. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
21. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
22. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
23. Singh, U.C.; Brown, F.K.; Bash, P.A.; Kollman, P.A. J. Am. Chem. Soc. 1987, 109 (6), 1607. Jorgensen, W.L.; Buckner, J.K.; Boudon, S.; Tirado-Rives, J. J. Chem. Phys. 1988, 89 (6), 3742. Jorgensen, W.L.; Blake, J.F.; Buckner, J.K. Chem. Phys. 1989, 129, 193. Essex, J.W.; Reynolds, C.A.; Richards, W.G. J. Chem. Soc., Chem. Commun. 1989, 1152. Dang, L.X.; Merz, K.M., Jr.; Kollman, P.A. J. Am. Chem. Soc. 1989, 111, 8505. Hirono, S.; Kollman, P.A. J. Mol. Biol. 1990, 212, 197. Jorgensen, W.L.; Briggs, J.M.; Contreras, M.L. J. Phys. Chem. 1990, 94, 1683. Caldwell, J.W.; Agard, D.A.; Kollman, P.A. Proteins 1991, 10, 140. Dunn, W.J., III; Nagy, P.I. J. Comput. Chem. 1992, 13 (4), 468. Sun, Y.; Spellmeyer, D.; Pearlman, D.A.; Kollman, P.A. J. Am. Chem. Soc. 1992, 114, 6798. Myamoto, S.; Kollman, P.A. Proteins 1993, 16, 226. Miyamoto, S.; Kollman, P.A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402. Pang, Y.-P.; Kollman, P.A. Perspect. Drug Discovery Des. 1995, 3, 106. Jorgensen, W.L.; Tirado-Rives, J. Perspect. Drug Discovery Des. 1995, 3, 123. Rao, B.G.; Kim, E.E.; Murcko, M.A. J. Comput.-Aided Mol. Des. 1996, 10, 23. Rastelli, G.; Costantino, L.; Vianello, P.; Barlocco, D. Tetrahedron 1998, 54, 9415. Pitera, J.; Kollman, P.A. J. Am. Chem. Soc. 1998, 120, 7557. McCarrick, M.A.; Kollman, P.A. J. Comput.-Aided Mol. Des. 1999, 13, 109. Best, S.A.; Merz, K.M., Jr.; Reynolds, C.H. J. Phys Chem. B 1999, 103, 714. Eriksson, M.A.L.; Pitera, J.; Kollman, P.A. J. Med. Chem. 1999, 42, 868.
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