The use of local surface properties for molecular superimposition.
This study employed surface-based properties for use in the superimposition of three series of molecules. The properties used were derived from semiempirical molecular orbital calculations and can be related to the physics of intermolecular interactions. In each case, the superimposition of the compounds was within 0.6 A of the experimental overlay. The superimposition cases presented differing levels of involvement of electrostatic interactions, and in only one case did shape similarity provide the best overlay. Two test compounds were applied to an example exploring non-nucleoside HIV-1 reverse transcriptase inhibitors and only one of these compounds overlaid in the same manner as their crystal structure complexes. This served to highlight the need for molecules to occupy the same region of space when employing this technique. Nevertheless, the method can be used to generate pharmacophores and ultimately could be used to interrogate databases for molecules that match the key surface properties, thus allowing scaffold hopping.
Manallack
David T
DT
Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia, David.Manallack@vcp.monash.edu.au
D000590:Amino Acid Chloromethyl Ketones / Q000737:chemistry; D019380:Anti-HIV Agents / Q000737:chemistry*; D000925:Anticoagulants / Q000737:chemistry; D000964:Antimetabolites, Antineoplastic / Q000737:chemistry; D018360:Crystallography, X-Ray; D004151:Dipeptides / Q000737:chemistry; D005492:Folic Acid / Q000031:analogs & derivatives / Q000737:chemistry; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D006801:Humans; D007093:Imidazoles / Q000737:chemistry; D008024:Ligands; D008727:Methotrexate / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D010880:Piperidines / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry; D011810:Quinoxalines / Q000737:chemistry; D018894:Reverse Transcriptase Inhibitors / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013457:Sulfur Compounds / Q000737:chemistry; D013499:Surface Properties; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry
D000590:Amino Acid Chloromethyl Ketones; D019380:Anti-HIV Agents; D000925:Anticoagulants; D000964:Antimetabolites, Antineoplastic; D004151:Dipeptides; D017320:HIV Protease Inhibitors; D007093:Imidazoles; D008024:Ligands; D010880:Piperidines; D011506:Proteins; D011810:Quinoxalines; D018894:Reverse Transcriptase Inhibitors; D013457:Sulfur Compounds; C010920:dihydrofolate; C038708:N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide; D005492:Folic Acid; D013762:Tetrahydrofolate Dehydrogenase; C040308:phenylalanyl-prolyl-arginine-chloromethyl ketone; C433874:capravirine; C093110:HBY 097; D008727:Methotrexate