In silico binding free energy predictability with π-π Interaction energy-augmented scoring function: Benzimidazole Raf inhibitors as a case study

Bioorganic and Medicinal Chemistry Letters

Volumn 22, Issue 9, 2012, Pages 3278-3283

  Chung, Jae Yoon ^a,b   Cho, Seung Joo ^c   Cho, Art E ^b   Hah, Jung Mi ^a  

^a Hanyang University   (South Korea)

^b Korea University   (South Korea)

^c Chosun University   (South Korea)

Author keywords

interaction; 3D QSAR; Active site; LMP2 calculation; Ring groups; Scoring function

Indexed keywords

B RAF KINASE INHIBITOR; BENZIMIDAZOLE DERIVATIVE; BENZIMIDAZOLE RAF; BENZIMIDAZOLE RAF INHIBITOR; SORAFENIB; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPUTER MODEL; ENERGY; PHI PHI INTERACTION ENERGY; PREDICTION; SCORING SYSTEM; STRUCTURE ACTIVITY RELATION;

BENZIMIDAZOLES; COMPUTER SIMULATION; DRUG DISCOVERY; ELECTRONS; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN KINASE INHIBITORS; RAF KINASES; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84859815041     PISSN: 0960894X     EISSN: 14643405     Source Type: Journal    
DOI: 10.1016/j.bmcl.2012.03.017     Document Type: Article

References (18)

1. C. Bissantz, B. Kuhn, and M. Stahl J. Med. Chem. 53 2010 5061
2. P. Gund J. Med. Chem. 52 2009 3428
3. A.R. Leach, B.K. Shoichet, and C.E. Peishoff J. Med. Chem. 49 2006 5851
4. Mr. Sándor, R.B. Kiss, and G.M. Keserü J. Chem. Inf. Model 50 2010 1165
5. R.D. Taylor, P.J. Jewsbury, and J.W. Essex J. Comput. Aided Mater. Des. 16 2002 151
6. I. Halperin, B. Ma, H. Wolfson, and R. Nussinov Proteins: Struct. Funct. Bioinfom. 47 2002 409
7. J.Y. Chung, J.-M. Hah, and A.E. Cho J. Chem. Inf. Model 49 2009 2382
8. C.A. Hunter, J. Singh, and J.M. Thornton J. Mol. Biol. 218 1991 837
9. A.E. Cho, J.Y. Chung, M. Kim, and K. Park J. Chem. Phys. 131 2009 134108
10. S. Ramurthy, S. Subramanian, M. Aikawa, P. Amiri, A. Costales, J. Dove, S. Fong, J.M. Jansen, B. Levine, S. Ma, C.M. McBride, J. Michaelian, T. Pick, D.J. Poon, S. Girish, C.M. Shafer, D. Stuart, L. Sung, and P.A. Renhowe J. Med. Chem. 51 2008 7049
11. P.T.C. Wan, M.J. Garnett, S.M. Roe, S. Lee, D. Niculescu-Duvaz, V.M. Good, C.G. Project, C.M. Jones, C.J. Marshall, C.J. Springer, D. Barford, and R. Marais Cell 116 2004 855
12. Glide v, Schrödinger; LLC: New York, NY, 2009.
13. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, H. Knoll, M. Shelley, J.K. Perry, D.E. Shaw, P. Francis, and P.S. Shenkin J. Med. Chem. 47 2004 1739
14. SYBYL 7.3 TI, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA.
15. Tripos Bookshelf 8.0 TI, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA.
16. J. Chung, A.E. Cho, and J.-M. Hah Bull. Korean Chem. Soc. 30 2009 2739
17. J. Chung, H. Chung, S. Cho, J.-M. Hah, and A.E. Cho J. Comput. Aided Mater. Des. 24 2010 385
18. C. Guimarães, and M. Cardozo J. Chem. Inf. Model 48 2008 958