Rational and efficient geometric definition of pharmacophores is essential for the patent process

Drug Discovery Today

Volumn 11, Issue 21-22, 2006, Pages 991-998

  Guérin, Georges Alexandre ^a   Pratuangdejkul, Jaturong ^b,c,d   Alemany, Monica ^e   Launay, Jean Marie ^b,c,d   Manivet, Philippe ^b,c,d  

^a BioQuanta Corporation   (United States)

^b ASSISTANCE PUBLIQUE HÔPITAUX DE PARIS   (France)

^c Laboratoire de Biologie Cellulaire   (France)

^d MAHIDOL UNIVERSITY   (Thailand)

^e INSTITUT D INVESTIGACIONS BIOMÈDIQUES AUGUST PI I SUNYER IDIBAPS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

SEROTONIN; SEROTONIN AGONIST; SEROTONIN ANTAGONIST; SEROTONIN RECEPTOR; SEROTONIN UPTAKE INHIBITOR;

ALGORITHM; BINDING SITE; CHIRALITY; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPUTER MODEL; CRYSTAL STRUCTURE; DIASTEREOISOMER; DRUG DESIGN; DRUG SCREENING; ENANTIOMER; GEOMETRY; HYDROGEN BOND; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; PATENT; PHARMACOPHORE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; STEREOISOMERISM; STRUCTURE ACTIVITY RELATION; VIRTUAL REALITY; X RAY CRYSTALLOGRAPHY;

COMPUTER-AIDED DESIGN; CONSENSUS; DRUG DESIGN; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PATENTS; PATENTS AS TOPIC; PHARMACEUTICAL PREPARATIONS; STEREOISOMERISM; TERMINOLOGY; TERMINOLOGY AS TOPIC;

EID: 33750087317     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2006.09.003     Document Type: Review

References (27)

1. Ehrlich P. Über den jetzigen stand der chemotherapie. Chem. Ber. 42 (1909) 17
2. Gund P. Three-dimensional pharmacophoric pattern searching. Prog. Mol. Subcell. Biol. 5 (1977) 117-143
3. Wermuth C.-G., et al. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure Appl. Chem. 70 (1998) 1129-1143
4. Güner, O.F. (2000). Pharmacophore Perception, Development, and Use in Drug Design (Güner O.F., ed.) Biotechnology Series 2, International University Line
5. Shimbo I., et al. Patent protection for protein structure analysis. Nat. Biotechnol. 22 (2004) 109-112
6. Masuoka K. Study on the ways of protection of post-genome research products. Institute of Intellectual Property (Japan) Bull. (2002) 84-95
7. Buckminster Fuller R. SYNERGETICS. Explorations in the Geometry of Thinking (1975), Macmillan
8. Federico, P.J. (1982). Descartes on Polyhedra. A Study of the 'De Solidorum Elementis', Sources in the History of Mathematics and Physical Sciences 4, Springer
9. Kurogi Y., and Guner O.F. History and evolution of the pharmacophore concept in computer-aided drug design. Curr. Top. Med. Chem. 2 (2002) 1321-1332
10. Guner, O.F. (2000) Pharmacophore Perception, Development, and Use in Drug Design, Biotechnology Series 2, International University Line
11. Bolstatd P. GIS Fundamentals: A First Text on Geographic Information Systems. 2nd edn (2005), Eider Press
12. Richmond N.J., et al. Alignment of three-dimensional molecules using an image recognition algorithm. J. Mol. Graph. Model. 23 (2004) 199-209
13. Wolber, G. and Dornhofer, A.A. (2006). Efficient overlay of molecular 3D pharmacophores. American Chemical Society Symposium on Advances in Pharmacophores and 3-D screening, 26-30 March 2006, Atlanta, GA, USA
14. Lemmen C., and Lengauer T. Time-efficient flexible superposition of medium-sized molecules. J. Comput. Aided Mol. Des. 11 (1997) 357-368
15. Agranat I., et al. Putting chirality to work: the strategy of chiral switches. Nat. Rev. Drug Discov. 1 (2002) 753-768
16. Agranat I., and Caner H. Intellectual property and chirality of drugs. Drug Discov. Today 4 (1999) 313-321
17. Cramer III R.D., et al. Comparative molecular field analysis (CoMFA). Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 110 (1988) 5959-5967
18. Bohm M., and Klebe G. Development of new hydrogen-bond descriptors and their application to comparative molecular field analyses. J. Med. Chem. 45 (2002) 1585-1597
19. Cruciani G., and Watson K.A. Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b. J. Med. Chem. 37 (1994) 2589-2601
20. Manivet P., et al. The serotonin binding site of human and murine 5-HT2B receptors: molecular modeling and site-directed mutagenesis. J. Biol. Chem. 277 (2002) 17170-17178
21. Pratuangdejkul J., et al. Definition of an uptake pharmacophore of the serotonin transporter through 3D-QSAR analysis. Curr. Med. Chem. 12 (2005) 2393-23410
22. Rashid A., et al. Identification of the binding sites and the selectivity of sarpogrelate, a novel 5HT2 antagonist, to human 5HT2A, 5HT2B and 5HT2C receptor subtypes by molecular modelling. Life Sci. 73 (2005) 193-207
23. Golbraikh A., et al. Novel chirality descriptors derived from molecular topology. J. Chem. Inf. Comput. Sci. 41 (2001) 147-158
24. Stahlberg J., et al. Structural basis for enantiomer binding and separation of a common beta-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 Å resolution. J. Mol. Biol. 305 (2001) 79-93
25. Datta S., and Grant D.J. Crystal structures of drugs: advances in determination, prediction and engineering. Nat. Rev. Drug Discov. 3 (2004) 42-57
26. Guner O., et al. Pharmacophore modeling and three dimensional database searching for drug design using catalyst: recent advances. Curr. Med. Chem. 11 (2004) 2991-3005
27. Wolber G., and Langer T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J. Chem. Inf. Model 45 (2005) 160-169