Multi-objective evolutionary design of adenosine receptor ligands

Journal of Chemical Information and Modeling

Volumn 52, Issue 7, 2012, Pages 1713-1721

  Van Der Horst, Eelke ^a   Marqués Gallego, Patricia ^a   Mulder Krieger, Thea ^a   Van Veldhoven, Jacobus ^a   Kruisselbrink, Johannes ^b   Aleman, Alexander ^b   Emmerich, Michael T M ^b   Brussee, Johannes ^a   Bender, Andreas ^a   Ijzerman, Adriaan P ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ITERATIVE METHODS; PHARMACODYNAMICS; SCAFFOLDS; STRUCTURAL DESIGN; SUPPORT VECTOR MACHINES;

MOLECULAR FINGERPRINT; MULTI OBJECTIVE EVOLUTIONARY ALGORITHMS; MULTI-OBJECTIVE EVOLUTIONARY; PHARMACOPHORE MODELING; PROOF OF PRINCIPLES; STRUCTURE GENERATION; SUBSTITUTION PATTERNS; SUPPORT VECTOR MACHINE MODELS;

EVOLUTIONARY ALGORITHMS;

ADENOSINE RECEPTOR STIMULATING AGENT; LIGAND;

ALGORITHM; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; HUMAN; MOLECULAR EVOLUTION; ARTICLE;

ALGORITHMS; BINDING SITES; DRUG DESIGN; EVOLUTION, MOLECULAR; HUMANS; LIGANDS; MODELS, MOLECULAR; PURINERGIC P1 RECEPTOR AGONISTS;

EID: 84864202186     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci2005115     Document Type: Article

References (35)

1. Fredholm, B. B.; IJzerman, A. P.; Jacobson, K. A.; Klotz, K. N.; Linden, J. International Union of Pharmacology. XXV. Nomenclature and classification of adenosine receptors Pharmacol. Rev. 2001, 53, 527-552 (Pubitemid 33136237)
2. Ralevic, V.; Burnstock, G. Receptors for purines and pyrimidines Pharmacol. Rev. 1998, 50, 413-492 (Pubitemid 28477681)
3. Jacobson, K. A.; Gao, Z. G. Adenosine receptors as therapeutic targets Nat. Rev. Drug Discovery 2006, 5, 247-264 (Pubitemid 43336037)
4. Muller, C. E.; Jacobson, K. A. Recent developments in adenosine receptor ligands and their potential as novel drugs Biochim. Biophys. Acta, Biomembr. 2011, 1808, 1290-1308
5. Muller, C. E. A(1)-adenosine receptor antagonists Expert Opin. Ther. Pat. 1997, 7, 419-440
6. Baraldi, P. G.; Tabrizi, M. A.; Gessi, S.; Borea, P. A. Adenosine receptor antagonists: Translating medicinal chemistry and pharmacology into clinical utility Chem. Rev. 2008, 108, 238-263 (Pubitemid 351176408)
7. Lameijer, E. W.; Kok, J. N.; Bäck, T.; IJzerman, A. P. The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules J. Chem. Inf. Model. 2006, 46, 545-552
8. Lameijer, E. W.; Tromp, R. A.; Spanjersberg, R. F.; Brussee, J.; IJzerman, A. P. Designing active template molecules by combining computational de novo design and human chemist's expertise J. Med. Chem. 2007, 50, 1925-1932 (Pubitemid 46626601)
9. Nicolaou, C. A.; Brown, N.; Pattichis, C. S. Molecular optimization using computational multi-objective methods Curr. Opin. Drug Discovery Dev. 2007, 10, 316-324 (Pubitemid 46800225)
10. Molecule Commander, version 4.2; Cidrux Pharminformatics B.V.: Haarlem, The Netherlands.
11. Bender, A.; Young, D. W.; Jenkins, J. L.; Serrano, M.; Mikhailov, D.; Clemons, P. A.; Davies, J. W. Chemogenomic data analysis: Prediction of small-molecule targets and the advent of biological fingerprints Comb. Chem. High Throughput Screening 2007, 10, 719-731 (Pubitemid 350099316)
12. Bender, A.; Scheiber, J.; Glick, M.; Davies, J. W.; Azzaoui, K.; Hamon, J.; Urban, L.; Whitebread, S.; Jenkins, J. L. Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure ChemMedChem 2007, 2, 861-873
13. Morphy, R.; Kay, C.; Rankovic, Z. From magic bullets to designed multiple ligands Drug Discovery Today 2004, 9, 641-651 (Pubitemid 38981718)
14. de Matos, P.; Alcantara, R.; Dekker, A.; Ennis, M.; Hastings, J.; Haug, K.; Spiteri, I.; Turner, S.; Steinbeck, C. Chemical Entities of Biological Interest: an update Nucleic Acids Res. 2010, 38, D249-254
15. Irwin, J. J.; Shoichet, B. K. ZINC-A Free Database of Commercially Available Compounds for Virtual Screening J. Chem. Inf. Model. 2005, 45, 177-182 (Pubitemid 40736970)
16. Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks J. Med. Chem. 1996, 39, 2887-2893 (Pubitemid 26251026)
17. Bemis, G. W.; Murcko, M. A. Properties of Known Drugs. 2. Side Chains J. Med. Chem. 1999, 42, 5095-5099 (Pubitemid 30020260)
18. Ertl, P.; Rohde, B.; Selzer, P. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties J. Med. Chem. 2000, 43, 3714-3717
19. Scitegic Pipeline Pilot, 6.1.5.0 Student ed.; Accelrys, Inc.: San Diego, CA, 2007.
20. Kazius, J.; McGuire, R.; Bursi, R. Derivation and Validation of Toxicophores for Mutagenicity Prediction J. Med. Chem. 2005, 48, 312-320 (Pubitemid 40105270)
21. Chang, L. C. W.; Spanjersberg, R. F.; Kunzel, J. K. V.; Mulder-Krieger, T.; van den Hout, G.; Beukers, M. W.; Brussee, J.; IJzerman, A. P. 2,4,6-trisubstituted pyrimidines as a new class of selective adenosine A(1) receptor antagonists J. Med. Chem. 2004, 47, 6529-6540 (Pubitemid 39657315)
22. Molecular Operating Environment, 2008.10; Chemical Computing Group: Montreal, Quebec, Canada, 2008.
23. Trautmann, H.; Weihs, C. On the distribution of the desirability index using Harrington's desirability function Metrika 2006, 63, 207-213 (Pubitemid 43473646)
24. Ivanciuc, O. Applications of Support Vector Machines in Chemistry Rev. Comput. Chem. 2007, 23, 291-400
25. Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space J. Chem. Inf. Model. 2009, 49, 108-119
26. Kruisselbrink, J. W.; Emmerich, M. T. M.; Bäck, T.; Bender, A.; IJzerman, A. P.; van der Horst, E. Combining Aggregation with Pareto Optimization: A Case Study in Evolutionary Molecular Design. In Evolutionary Multi-Criterion Optimization; Springer-Verlag: Berlin/Heidelberg, 2009; Vol. 5467, pp 453-467.
27. Kruisselbrink, J. W.; Aleman, A.; Emmerich, M. T. M.; IJzerman, A. P.; Bender, A.; Bäck, T.; van der Horst, E. Enhancing search space diversity in multi-objective evolutionary drug molecule design using niching. In Proceedings of the 11th Annual conference on Genetic and evolutionary computation, Montreal, Québec, Canada, 2009; ACM: New York, 2009; pp 217-224.
28. Shir, O.; Preuss, M.; Naujoks, B.; Emmerich, M. Enhancing Decision Space Diversity in Evolutionary Multiobjective Algorithms. In Proceedings of the 5th International Conference on Evolutionary Multi-Criterion Optimization, Nantes, France, 2009; Springer: Berlin/Heidelberg, 2009; pp 95-109.
29. Nicolaou, C. A.; Apostolakis, J.; Pattichis, C. S. De Novo Drug Design Using Multiobjective Evolutionary Graphs J. Chem. Inf. Model. 2009, 49, 295-307
30. Preuss, M.; Schönemann, L.; Emmerich, M. Counteracting genetic drift and disruptive recombination in (μpluskommaλ)-EA on multimodal fitness landscapes. In Proceedings of the 2005 conference on Genetic and evolutionary computation; ACM: Washington, DC, 2005; pp 865-872. (Pubitemid 43226387)
31. Bender, A.; Glen, R. C. Molecular similarity: a key technique in molecular informatics Org. Biomol. Chem. 2004, 2, 3204-3218
32. Borrmann, T.; Hinz, S.; Lertarelli, D. C. G.; Li, W. J.; Florin, N. C.; Scheiff, A. B.; Muller, C. E. 1-Alkyl-8-(piperazine-1-sulfonyl)phenylxanthines: Development and Characterization of Adenosine A(2B) Receptor Antagonists and a New Radioligand with Subnanomolar Affinity and Subtype Specificity J. Med. Chem. 2009, 52, 3994-4006
33. Muller, C. E.; Diekmann, M.; Thorand, M.; Ozola, V. [H-3]8-ethyl-4- methyl-2-phenyl-(8R)-4,5,7,8-tetrahydro-1H-imidazo[2,1-i] -purin-5-one ([H-3]PSB-11), a novel high-affinity antagonist radioligand for human A(3) adenosine receptors Bioorg. Med. Chem. Lett. 2002, 12, 501-503 (Pubitemid 34113933)
34. Da Settimo, F.; Primofiore, G.; Taliani, S.; Marini, A. M.; La Motta, C.; Novellino, E.; Greco, G.; Lavecchia, A.; Trincavelli, L.; Martini, C. 3-Aryl[1,2,4]triazino[4,3-a]benzimidazol-4(10H)-ones: A New Class of Selective A1 Adenosine Receptor Antagonists J. Med. Chem. 2001, 44, 316-327 (Pubitemid 32113581)
35. Da Settimo, F.; Primofiore, G.; Taliani, S.; La Motta, C.; Novellino, E.; Greco, G.; Lavecchia, A.; Cosimelli, B.; Iadanza, M.; Klotz, K.-N.; Tuscano, D.; Trincavelli, M. L.; Martini, C. A1 adenosine receptor antagonists, 3-aryl[1,2,4]triazino[4,3-a]benzimidazol-4-(10H)-ones (ATBIs) and N-alkyl and N-acyl-(7-substituted-2-phenylimidazo[1,2-a][1,3,5]triazin-4-yl)amines (ITAs): Different recognition of bovine and human binding sites Drug Dev. Res. 2004, 63, 1-7 (Pubitemid 40076273)