Construction and Validation of Virtual Screening Based on Code Structure of PDB3MQE, 3NTG, and 3LN0 To Discover Cyclooxygenase Inhibitor-2 (COX-2)

  • ESTI MUMPUNI UNIVERSITAS PANCASILA
  • ARGUN WIDARSA UNIVERSITAS PANCASILA
  • YANTI SUSILAWATI UNIVERSITAS PANCASILA
  • OISAN OISAN UNIVERSITAS PANCASILA
  • ARIEF NURROCHMAD UNIVERSITAS GADJAH MADA
  • HARNO DWI PRANOWO UNIVERSITAS GADJAH MADA
  • UMAR ANGGARA JENIE UNIVERSITAS GADJAH MADA
  • ENADE PERDANA ISTYASTONO UNIVERSITAS SANATA DHARMA

Abstract

Cyclooxygenase-2 (COX-2) inhibitors are high demand drugs in the market. However, available COX-2 inhibitors nowadays have many side effects. Therefore, there is still a need to develop more potent selective COX-2 inhibitors and one of the method that has been prove the effectivity and eficiency for new drugs research is in silico. Structure-based virtual screening (SBVS) protocols were developed to find COX-2 inhibitors using the Protein-Ligand ANT System (PLANTS) docking software, SPORES, BKChem and Open Babel. The directory of useful decoys (DUD) dataset for COX-2 was used to validate the protocols retrospectively; the DUD consist of 426 known COX-2 inhibitors and 13289 decoys. Based on criteria value of EF20% and EFmax used in the article from Huang et al (2006) and Yuniarti et al (2011), two validated protocol, AYO_COX2_v.1.1 and AYO_COX2_v.1.2 , showed good results

References

1. Agarwal S, Reddy GV, and Reddanna P. Eicosanoids in inflammation and cancer: the role of COX-2. Expert Rev. Clin. Immunol. 2009. 5:145-65.
2. Inotai A, Hanko B, and Meszaros A. Trends in the non-steroidal anti-inflammatory drug market in six Central-Eastern European countries based on retail information. Pharmacoepidemiol. Drug Saf. 2010. 19:183-90.
3. Glover JA, Hughes CM, Cantwell MM, Murray LJ. A systematic review to establish the frequency of cyclooxygenase-2 expression in normal breast epithelium, ductal carcinoma in situ, microinvasive carcinoma of the breast and invasive breast cancer. Br. J. Cancer. 2011. 105:13-7.
4. Huang N, Shoichet BK, and Irwin JJ. Benchmarking sets for molecular docking. J. Med. Chem. 2006. 49:6789-801.
5. Yuniarti N, Ikawati Z, and Istyastono EP. The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign. Bioinformation. 2011. 6:164-6.
6. Kellenberger E, Foata N, and Rognan D. Ranking targets in structure-based virtual screening of three dimensional protein libraries: methods and problems. J. Chem. Inf. Model. 2008. 48:1014-25.
7. Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins. 2004. 57:225-42.
8. De Graaf C and Rognan D. Customizing G Protein-coupled receptor models for structure-based virtual screening. Curr. Pharm. Des. 2009. 15:4026-48.
9. Prasojo SL, Hartanto FAD, Yuniarti N, Ikawati Z, Istyastono EP. Docking of 1-phenylsulfonamide-3-trifluoromethyl-5-parabromophenyl-pyrazole to cyclooxygenase-2 using PLANTS. Indonesian Journal of Chemistry. 2010. 10:348-51.
10. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R, Participants of GPCR Dock 2010. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011. 19(8): 1108-26.
Published
2014-04-30
How to Cite
MUMPUNI, ESTI et al. Construction and Validation of Virtual Screening Based on Code Structure of PDB3MQE, 3NTG, and 3LN0 To Discover Cyclooxygenase Inhibitor-2 (COX-2). JURNAL ILMU KEFARMASIAN INDONESIA, [S.l.], v. 12, n. 1, p. 117-123, apr. 2014. ISSN 2614-6495. Available at: <http://jifi.farmasi.univpancasila.ac.id/index.php/jifi/article/view/196>. Date accessed: 19 may 2024.
Section
Articles