On modeling peptidomimetics in complex with the SH2 domain of Stat3

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Volumn , Issue , 2011, Pages 3229-3232

  Dhanik, Ankur ^a   McMurray, John S ^b   Kavraki, Lydia ^a  

^a Rice University   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTODOCK; BINDING AFFINITIES; DOCKING PROGRAMS; DRUG COMPOUNDS; HUMAN CANCER; MOLECULAR DOCKING; PEPTIDOMIMETICS; PHOSPHOPETIDES; POTENT INHIBITOR; SH2 DOMAIN; SIGNAL TRANSDUCERS;

DISEASES; KNOWLEDGE BASED SYSTEMS; MOLECULAR MODELING;

BINDING ENERGY;

LIGAND; STAT3 PROTEIN;

ARTICLE; CHEMISTRY; MOLECULAR MIMICRY; PROTEIN CONFORMATION; SRC HOMOLOGY DOMAIN;

LIGANDS; MOLECULAR MIMICRY; PROTEIN CONFORMATION; SRC HOMOLOGY DOMAINS; STAT3 TRANSCRIPTION FACTOR;

EID: 84862593859     PISSN: 1557170X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2011.6090878     Document Type: Conference Paper

References (21)

1. [Online]. Available: http://www.who.int/mediacentre/factsheets/fs297/en/ index.html
2. D. E. Levy and J. E. Darnell, "Stats: transcriptional control and biological impact." Nature reviews. Molecular cell biology, vol. 3, no. 9, pp. 651-62, Sept. 2002.
3. H. Yu and R. Jove, "The STATs of cancer-new molecular targets come of age." Nature reviews. Cancer, vol. 4, no. 2, pp. 97-105, Feb. 2004.
4. J. S. Mcmurray, "Structural basis for the binding of high affinity phosphpeptides to Stat3," Biopolymers, vol. 90, no. 1, 2007.
5. G. Schneider, "Virtual screening: an endless staircase?" Nature reviews. Drug discovery, vol. 9, no. 4, pp. 273-6, Apr. 2010.
6. I. Kuntz, "A geometric approach to macromolecule-ligand interactions," Journal of Molecular Biology, vol. 161, no. 2, pp. 269-288, Oct. 1982.
7. R. Abagyan, M. Totrov, and D. Kuznetsov, "ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation," Journal of Computational Chemistry, vol. 15, no. 5, pp. 488-506, May 1994.
8. G. Jones, P. Willett, and R. C. Glen, "Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation." Journal of molecular biology, vol. 245, no. 1, pp. 43-53, Jan. 1995.
9. M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, "A fast flexible docking method using an incremental construction algorithm." Journal of molecular biology, vol. 261, no. 3, pp. 470-89, Aug. 1996.
10. G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, and A. J. Olson, "Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function," Journal of Computational Chemistry, vol. 19, no. 14, pp. 1639-1662, Nov. 1998.
11. A. N. Jain, "Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine." Journal of medicinal chemistry, vol. 46, no. 4, pp. 499-511, Feb. 2003.
12. O. Trott and A. J. Olson, "Software News and Update AutoDock Vina : Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading," Journal of Computational Chemistry, 2009.
13. S. Becker, B. Groner, and C. W. Müller, "Three-dimensional structure of the Stat3 homodimer bound to DNA." Nature, vol. 394, no. 6689, pp. 145-51, July 1998.
14. M. F. Sanner, "Python: a programming language for software integration and development." Journal of molecular graphics & modelling, vol. 17, no. 1, pp. 57-61, Feb. 1999.
15. D. R. Coleman, Z. Ren, P. K. Mandal, A. G. Cameron, G. a. Dyer, S. Muranjan, M. Campbell, X. Chen, and J. S. McMurray, "Investigation of the binding determinants of phosphopeptides targeted to the SRC homology 2 domain of the signal transducer and activator of transcription 3. Development of a high-affinity peptide inhibitor." Journal of medicinal chemistry, vol. 48, no. 21, pp. 6661-70, Oct. 2005.
16. D. Coleman, K. Kaluarachchi, Z. Ren, X. Chen, and J. McMurray, "Solid phase synthesis of phosphopeptides incorporating 2,2-dimethyloxazolidine pseudoproline analogs: Evidence for trans leupro peptide bonds in stat3 inhibitors," International Journal of Peptide Research and Therapeutics, vol. 14, pp. 1-9, 2008.
17. P. K. Mandal, D. Limbrick, D. R. Coleman, G. a. Dyer, Z. Ren, J. S. Birtwistle, C. Xiong, X. Chen, J. M. Briggs, and J. S. McMurray, "Conformationally constrained peptidomimetic inhibitors of signal transducer and activator of transcription 3: Evaluation and molecular modeling." Journal of medicinal chemistry, vol. 52, no. 8, pp. 2429-42, Apr. 2009.
18. P. K. Mandal, Z. Ren, X. Chen, C. Xiong, and J. S. McMurray, "Structure-affinity relationships of glutamine mimics incorporated into phosphopeptides targeted to the SH2 domain of signal transducer and activator of transcription 3." Journal of medicinal chemistry, vol. 52, no. 19, pp. 6126-41, Oct. 2009.
19. P. K. Mandal, F. Gao, Z. Lu, Z. Ren, R. Ramesh, J. S. Birtwistle, K. Kaluarachchi, X. Chen, R. C. Bast Jr., and M. J. S. Liao, W S, "Potent and Selective Phosphopeptide Mimetic Prodrugs Targeted to the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 3," Manuscript submitted.
20. [Online]. Available: http://www.schrodinger.com/products/14/12/
21. M. W. Chang, C. Ayeni, S. Breuer, and B. E. Torbett, "Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina." PloS one, vol. 5, no. 8, pp. 1-9, Jan. 2010.