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Molecular Docking and Drug-likeness Prediction of New Potent Tubulin Colchicine Binding Site Inhibitors for Potential Antitumor Drug

Year 2022, Volume 43, Issue 3, 398 - 403, 30.09.2022
https://doi.org/10.17776/csj.1063966

Abstract

Cancer is a real public health problem that figures among the main causes of morbidity and mortality in the world. The Colchicine Binding Site (CBS) is an important pocket for potential tubulin polymerization destabilizers. Colchicine binding site inhibitors (CBSI) exhibit their biological effects by inhibiting tubulin assembly and suppressing microtubule formation. In order to identify new potent CBSI, molecular docking and drug likeness prediction were performed. In this context, a collection of 850 similar compounds to combretastatinA-4from PubChem database was docked into the CBS. Out of these, compounds S1 and S2 were found to have highest negative binding energy of -9.462 and -9.017 Kcal/mol respectively. Furthermore, these two compounds were predicted to have satisfying drug likeness properties, indicating that they might be promising lead compounds for further antitumor drug research.

References

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Year 2022, Volume 43, Issue 3, 398 - 403, 30.09.2022
https://doi.org/10.17776/csj.1063966

Abstract

References

  • [1] Üstün E., Şahin N., Molecular Docking Studies of N-Heterocyclic Carbene Molecules with Thioredoxin Reductase and DNA, Cumhuriyet Sci. J., 42(3) (2021) 656-662.
  • [2] Sung H., Ferlay J., Siegel RL., Laversanne M., Soerjomataram I., Jemal A., Bray F., Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries, CA: Cancer. J. Clin., 71 (3) (2021) 209-249.
  • [3] International Agency for Research on Cancer, Global cancer observatory, GLOBOCAN 2020. Availabe at https://gco.iarc.fr/. Retrieved September 10, 2021.
  • [4] Taperaa M., Kekeçmuhammed H., Tüzün B., Sarıpınar E., Koçyiğit UM., Yıldırım E., Doğan M., Zorlu Y. Synthesis, Carbonic Anhydrase Inhibitory Activity, Anticancer Activity and Molecular Docking Studies of New Imidazolyl Hydrazone Derivatives, J. Mol. Struct., 1269 (2022) 133816.
  • [5] Sarkı G., Tüzün B., Ünlüer D., Kantekin H. Synthesis, characterization, chemical and biological activities of 4-(4-methoxyphenethyl)-5- benzyl-2-hydroxy-2H-1,2,4-triazole-3(4H)-one phthalocyanine derivatives, Inorg. Chim. Acta., Available online 30 July 2022, 121113.
  • [6] Koçyiğit UM., Doğan M., Muğlu H., Taslimi P., Tüzün B., Yakan H., Bal H., Güzel E., Gülçin I. Determination of biological studies and molecular docking calculations of isatin-thiosemicarbazone hybrid compounds, J. Mol. Struct., 1264 (2022) 133249.
  • [7] Cutts JH., Beer CT., Noble RL., Biological properties of Vincaleukoblastine, an alkaloid in Vinca rosea Linn, with reference to its antitumor action, Cancer. Res., 20 (1960) 1023–31.
  • [8] Person F., Wilczak W., Hube-Magg C., Burdelski C., Möller-Koop C., Simon R., Noriega M., Sauter G., Steurer S., Burdak-Rothkamm S., Jacobsen F., Prevalence of βIII-tubulin (TUBB3) expression in human normal tissues and cancers, Tumor. Biol., 39(10) (2017) 1010428317712166.
  • [9] Stengel C., Newman SP., Leese MP., Potter BVL., Reed MJ., Purohit A., Class III β-tubulin expression and in vitro resistance to microtubule targeting agents, Br. J. Cancer., 102(2) (2009) 316–324.
  • [10] Massarotti A., Coluccia A., Silvestri R., Sorba G., Brancale A., The Tubulin Colchicine Domain: a Molecular Modeling Perspective, Chem.Med.Chem., 7(1) (2012) 33–42.
  • [11] Halgren TA., Murphy RB., Friesner RA., Beard HS., Frye LL., Pollard WT., Banks JL., Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening, J. Med. Chem., 47(7) (2004) 1750–1759.
  • [12] Shelley JC., Cholleti A., Frye LL., Greenwood JR., Timlin MR., Uchimaya M., Epik: A Software Program For Pk A Prediction And Protonation State Generation For Drug-Like Molecules, J.Comput. Aided. Mol. Des., 21(12) (2007) 681–691.
  • [13] Jie Dong DSC., Wang NN., Yao ZJ., Zhang L., Cheng Y., Ouyang D., Lu AP., ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database, J. Cheminformatics., 10 (2018) 29.
  • [14] Hamelryck T., Manderick B., PDB File Parser And Structure Class Implemented in Python, Bioinformatics., 19(17) (2003) 2308–2310.
  • [15] O’Boyle NM., Banck M., James CA., Morley C., Vandermeersch T., Hutchison GR., Open Babel: An open chemical toolbox, J. Cheminformatics., 3(1) (2011) 33-3.
  • [16] PDBaser: A python tool for fast protein - ligand extraction, Available at https://github.com/mimminou/PDBASER. Retrived March 10, 2021.
  • [17] Hioual KS., Chikhi A., Bensegueni A., Merzoug A., Boucherit H., Teniou S., Mokrani EH., Merabti B., Successful challenge: A Key Step In Infectious Diseases Treatment Using Computer-Aided Drug Design, Int. J. Biol. Sci. App., 1(1) (2014) 11-14.
  • [18] Sandeli AK., Khiri-Meribout N., Benzerka S., Gürbüz N., Dündar M., Karcı H., Bensouici C., Mokrani EH., Ozdemir I., Koç A., Ozdemir N., Debache A., Ozdemir I., Silver (I)-N-heterocyclic carbene complexes: Synthesis and characterization, biological evaluation of Anti-Cholinesterase, anti-alpha-amylase, anti-lipase, and antibacterial activities, and molecular docking study, Inorg. Chim. Acta., 525 (2021) 120486.
  • [19] Mokrani EH., Bensegueni A., Chaput L., Beauvineau C., Djeghim H., Mouawad L., Identification Of New Potent Acetylcholinesterase Inhibitors Using Virtual Screening And In Vitro Approaches, Mol. Inform., 38 (2019) 1800118.

Details

Primary Language English
Subjects Pharmacology and Pharmacy
Journal Section Natural Sciences
Authors

El Hassen MOKRANI> (Primary Author)
Mentouri Brothers Constantine 1
0000-0002-2725-2940
Algeria


Amine ABDELAZIZ This is me
University Mentouri Brothers Constantine 1
0000-0002-4320-2927
Algeria


Naamane AKAKBA This is me
University Mentouri Brothers Constantine 1
0000-0003-0021-0334
Algeria


Soumıa TENIOU>
University Mentouri Brothers Constantine 1
0000-0002-6023-2538
Algeria


Rym Gouta DEMMAK This is me
University Mentouri Brothers Constantine 1
0000-0002-2793-5653
Algeria


Abderrahmane BENSEGUENI This is me
University Mentouri Brothers Constantine 1
0000-0003-3467-6749
Algeria

Publication Date September 30, 2022
Application Date January 29, 2022
Acceptance Date August 27, 2022
Published in Issue Year 2022, Volume 43, Issue 3

Cite

APA Mokranı, E. H. , Abdelazız, A. , Akakba, N. , Tenıou, S. , Demmak, R. G. & Benseguenı, A. (2022). Molecular Docking and Drug-likeness Prediction of New Potent Tubulin Colchicine Binding Site Inhibitors for Potential Antitumor Drug . Cumhuriyet Science Journal , 43 (3) , 398-403 . DOI: 10.17776/csj.1063966