Molecular shape and electrostatics in the encoding of relevant chemical information
Tóm tắt
We propose a molecule’s chemistry can be hidden by representations of its shape and electrostatic field while retaining crucial, pharmaceutically relevant, information. Necessary, but not sufficient, to this proposition are the importance of shape and electrostatics to activity, the facility to easily represent, store and compare field properties, and knowledge of the density of possible drug-like molecules within a given radius of physical similarity. We provide methods and evidence to support the conclusion that a useful encoding is practical and propose tests for falsification.
Tài liệu tham khảo
Hohenberg P., Kohn W., (1964) Phys. Rev. B, 136:864
Bissantz C., Folkers G., Rognan D., (2000) J. Med. Chem. 43: 4759
Nicholls A., MacCuish N.E., MacCuish J.D., (2004) JCAMD, 18: 451
Rush T.S., Grant J.A., Mosyak L., Nicholls A., (2005) J. Med. Chem. 48(5): 1489
Katz, A.H., Tawa, G.J., Mason, K., Gove, S. and Alvarez, J.C., Comput. Chem., 92 (2004), ACS, Anaheim
Tawa, G.J., Katz, A.H. and Alvarez, J.C., Comput. Chem., 244 (2004) ACS, Philadelphia
Petit-Zeman, S., 4th Horizon Symposium, Oct. 23–25, 2003
Bohacek R.S., McMartin C., Guida W.C., (1996) Med. Res. Rev. 16: 3
Masek B.B, Merchant A., Matthews J.B., (1993) Proteins 17: 193
Grant J.A., Pickup B.T., (1995) J. Phys. Chem. 99: 3503
Grant J.A., Pickup B.T., (1996) J. Comput. Chem, 17: 1653
Grant, J.A., Haigh, J.A., Nicholls, A. and Pickup, B.T., JCICS, Vol. 20, (2005) (In press)
Nicholls, A., Daylight Users Group Meeting, Feb. 24–27th, 1998
Hall, D.W. and Spencer, G.L., Elementary Topology, Wiley, 1955, p. 59ff
Fink T., Bruggesser H., Reymond J.-L, 2005 Angew. Chem. Int. Ed. 44: 1504
Putta S., Christian L., Beroza P., Greene J., 2002 JCICS 42: 1230
Kearsley S.K., Smith G.M., (1990) Tet. Comp. Met 3: 615
Good A.C., Hodgkin E.E., Richards W.G., (1992) JCICS. 32: 188
Good A.C., Richards W.G., (1993) J. Chem. Inf. Comput. Sci., 33: 112
Lin, J.-H. and Clark, T., J. Chem. Inf. Model (2005) 45 (in␣press)
Kazhdan, M.M., Thesis Dissertation, Comp. Sci. Dept., Princeton, June 2004
Duncan B.S., Olson A.J, 1993 Biopolymers 33: 219
Leicester S.E., Finney J.L., Bywater R.P, 1988 J. Mol. Graphics 6: 104
Max N.L., Getzoff E.D., 1988 IEEE Comput. Graphics Appl. 8: 42
Ritchie, D.W. and Kemp, G.J., Proteins: Structure, Function & Genetics, John Wiley & Sons, 1999
Ritchie D.W., Kemp G.J.L., 1999 J. Comput. Chem. 20(4): 383
Grant, J.A. and Pickup, B.T., In W. Gunsteren and P.K. Weiner (Eds.), Computer Simulation of Biomolecular Systems, Vol. 3, Kluwer, 1997
Perola E., Charifson P., (2004) J. Med. Chem. 47:2499
Boström J., Norby P.-O., Liljefors T., (1998) JCAMD 12:383
ROCS 2.0, Omega 1.1, WABE 0.9, EON 1.0, OpenEye Scientific Software, Santa Fe, NM (www.eyesopen.com)
Bostrom J., Greenwood J.R., Gottfries J., (2003) J. Mol. Graph Model 5:449
Gasteiger, J. and Marsili, M., Tetrahedron Lett. (1978) 3181
Durant J.L., Leland B.A., Henry D.R., Nourse J.G., (2002) J. Chem. Inf. Comput. Sci., 42: 1273
Fingerprint, M., Mesa Analytics & Computing, LLC, Santa Fe, NM, www.mesaac.com
Lu H., Chang D.J., Baratte B., Meijer L., Schulze-Gahmen U., (2005) J. Med. Chem. 48: 737
MDDR (MDL Drug Data Report), MDL, Inc and Prous Science (1995–2005)
Corina, Molecular Networks, GmbH Computerchemie Langemarckplatz 1, Erlangen, Germany
Jones, H. Thesis Dissertation, Chemistry Dept., University of Sheffield, 2004
Smith D.J., Forrest S., Hightower R.R., Perelson A.S., (1997) J. Theor. Biol. 189: 141
Lapedes, A. and Farber R., Santa Fe Institute working paper 00-01-006
Abagyan, R., Raush, E. and Budagyan, L. Safe Exchange of Chemical Information Symposium, March 14th 2005, San Diego, ACS
vonNeumann, J. and Morgenstern, O., Theory of Games and Economic Behavior, Princeton Univ. Press, 1944
Schneier, B., Applied Cryptography, Wiley, 1995