Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design

TOKLUMAN, Tenzile Deniz; Erdem Yurter, Hayat; TATAR, Gamze Bora; Yelekci, Kemal

Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design

Gamze Bora TATAR, (Hacettepe Üniversitesi Tıp Fakültesi Tıbbi Biyoloji Anabilim Dalı, Ankara, Türkiye)

Tenzile Deniz TOKLUMAN, (Hacettepe Üniversitesi Tıp Fakültesi Tıbbi Biyoloji Anabilim Dalı, Ankara, Türkiye)

Kemal YELEKÇİ, (Kadir Has Üniversitesi Fen Edebiyat Fakültesi, İstanbul, Türkiye)

Hayat YURTER (Hacettepe Üniversitesi Tıp Fakültesi Tıbbi Biyoloji Anabilim Dalı, Ankara, Türkiye)

Turkish Journal of Chemistry

7 0

Yıl: 2011 Cilt: 35 Sayı: 6 Sayfa Aralığı: 861 - 870 Metin Dili: İngilizce İndeks Tarihi: 29-07-2022

Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design

Öz:

In-vitro inhibition activity screening and in-silico 3D molecular modeling approaches are important tools for design and development of specific histone deacetylase (HDAC) inhibitors. The objective of this study was to investigate the consistency between these 2 approaches. The HDAC 8 inhibition activities of 8 randomly selected different carboxylic acid derivatives were screened and in-vitro experimental results were compared with in-silico molecular modeling calculations. This study demonstrated that there is no sole gold standard technique for inhibitor design, and it was concluded that a combination of molecular modeling and activity screening assays will ensure more comprehensive and dependable results.

Anahtar Kelime:

Konular: Mühendislik, Kimya

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

1. Haberland, M.; Montgomery, R. L.; Olson, E. N. Nat. Rev. Genet. 2009, 10, 32-42.
2. Marsoni, S.; Damia G.; Camboni, G. Epigenetics 2008, 3, 164-172.
3. Paris, M.; Porcelloni, M.; Binaschi, M.; Fattori, D. J. Med. Chem. 2008, 51, 1505-1529.
4. Hahnen, E.; Hauke, J.; Tr¨ankle, C.; Ey¨upoglu, I. Y.; Wirth, B.; Bl¨umcke, I. Expert Opin. Investig. Drugs. 2008, 17, 169-184.
5. Sleiman, S. F.; Basso, M.; Mahishi, L.; Kozikowski, A. P.; Donohoe, M. E.; Langley, B.; Ratan, R. R. Expert Opin. Investig. Drugs. 2009, 18, 573-584.
6. Balasubramanian, S.; Verner, E.; Buggy, J. J. Cancer Lett. 2009, 280, 211-221.
7. Bieliauskas, A. V.; Pflum, M. K. Chem. Soc. Rev. 2008, 37, 1402-1413.
8. Zhang, L.; Fang, H.; Xu, W. Med. Res. Rev. 2010, 30, 585-602.
9. Marks, P. A.; Richon, V. M.; Miller, T.; Kelly, W. K. Adv. Cancer Res. 2004, 91, 137-168.
10. Vannini, A.; Volpari, C.; Filocamo, G.; Casavola, E. C.; Brunetti, M.; Renzoni, D.; Chakravarty, P.; Paolini, C.; De Francesco, R.; Gallinari, P.; Steink¨uhler, C.; Di Marco, S. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15064-15069.
11. Vannini, A.; Volpari, C.; Gallinari, P.; Jones, P.; Mattu, M.; Carf´ı, A.; De Francesco, R.; Steink¨uhler, C. ; Di Marco, S. EMBO Rep. 2007, 8, 879-884.
12. Somoza, J. R.; Skene, R. J.; Katz, B. A.; Mol, C.; Ho, J. D.; Jennings, A. J.; Luong, C.; Arvai, A.; Buggy, J. J.; Chi, E.; Tang, J.; Sang, B. C.; Verner, E.; Wynands, R.; Leahy, E. M.; Dougan, D. R.; Snell, G.; Navre, M.; Knuth, M. W.; Swanson, R. V.; McRee, D. E.; Tari, L. W. Structure 2004, 12, 1325-1334.
13. Bora-Tatar, G.; Dayanga¸c-Erden, D.; Demir, A. S.; Dalkara, S.; Yelek¸ci, K.; Erdem-Yurter, H. Bioorgan Med. Chem. 2009, 17, 5219-5228.
14. He, J.; Liu, H.; Chen, Y. J. Huazhong Univ. Sci. Technolog. Med. Sci. 2006, 26, 531-533.
15. Graphpad Prism Software version 4.0., La Jolla California, U.S.A.
16. http://www.rcsb.org. The Protein Data Bank. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242.
17. Accelrys Software Inc, Discovery Studio, Release 3.00, San Diego, USA: Accelrys Software Inc., 2007.
18. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K.; Olson, A. J. J. Comput. Chem 1998, 19, 1639-1662.
19. Morris G. M.; Huey, R.; Lindstrom, W.; Sanner M. F.; Belew R. K.; Goodsell D. S.; Olson A. J. J Comput Chem. 2009 30, 2785-2791.
20. Balasubramanian, S.; Ramos, J.; Luo, W.; Sirisawad, M.; Verner, E.; Buggy, J. J. Leukemia 2008, 22, 1026-34.
21. Wang, D. Curr. Top. Med. Chem. 2009, 9, 241-256.

APA	TATAR G, TOKLUMAN T, Yelekci K, Erdem Yurter H (2011). Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. , 861 - 870.
Chicago	TATAR Gamze Bora,TOKLUMAN Tenzile Deniz,Yelekci Kemal,Erdem Yurter Hayat Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. (2011): 861 - 870.
MLA	TATAR Gamze Bora,TOKLUMAN Tenzile Deniz,Yelekci Kemal,Erdem Yurter Hayat Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. , 2011, ss.861 - 870.
AMA	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. . 2011; 861 - 870.
Vancouver	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. . 2011; 861 - 870.
IEEE	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H "Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design." , ss.861 - 870, 2011.
ISNAD	TATAR, Gamze Bora vd. "Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design". (2011), 861-870.

APA	TATAR G, TOKLUMAN T, Yelekci K, Erdem Yurter H (2011). Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. Turkish Journal of Chemistry, 35(6), 861 - 870.
Chicago	TATAR Gamze Bora,TOKLUMAN Tenzile Deniz,Yelekci Kemal,Erdem Yurter Hayat Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. Turkish Journal of Chemistry 35, no.6 (2011): 861 - 870.
MLA	TATAR Gamze Bora,TOKLUMAN Tenzile Deniz,Yelekci Kemal,Erdem Yurter Hayat Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. Turkish Journal of Chemistry, vol.35, no.6, 2011, ss.861 - 870.
AMA	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. Turkish Journal of Chemistry. 2011; 35(6): 861 - 870.
Vancouver	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design. Turkish Journal of Chemistry. 2011; 35(6): 861 - 870.
IEEE	TATAR G,TOKLUMAN T,Yelekci K,Erdem Yurter H "Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design." Turkish Journal of Chemistry, 35, ss.861 - 870, 2011.
ISNAD	TATAR, Gamze Bora vd. "Power of inhibition activity screening and 3D molecular modeling approaches in HDAC 8 inhibitor design". Turkish Journal of Chemistry 35/6 (2011), 861-870.