IDENTIFICATION OF POTENT BROMODOMAIN4 (BRD4) INHIBITORS BY ENERGY-PHARMACOPHORE BASED VIRTUAL SCREENING TO TARGET BRD4-NUT MIDLINE CARCINOMA
Keywords:
Bromo-domain, Cancer, Epigenetic, Molecular Docking, Protein-protein interactions, Pharmacophore modelling, Transcription, Virtual screeningAbstract
Objective: Protein-protein interactions (PPI's) have been used as a target in various diseases. One such major role of PPI's comes when the protein Bromodomain4 (BRD4) reads the epigenetic changes in the histones and regulates transcription. This protein has been shown by various research groups to be linked to a rare form of cancer called BRD4-NUT midline carcinoma. The present study incorporates understanding the role of BRD4 in such cancer and as is directed towards finding new lead compounds to target the PPI involved.
Methods: To find potential lead molecules against BRD4 protein, contact based and e-pharmacophore based virtual screening studies approach was adopted with the use of PHASE and E-pharmacophore module of the Schrödinger Maestro tool. Based on the pharmacophore hypothesis developed, virtual screening was performed for 22, 70, 000 Clean Lead-like compounds from the ZINC database by Virtual Screening Workflow of Schrödinger Maestro. Further Molecular dynamics simulations by GROMACS 4.5.5 were performed to study the energetics and stability of the top most docked ligands with BRD4 protein.
Results: Pharmacophore based virtual screening studies results in the retrieval of three potential lead molecules, ZINC68155904, ZINC67910065, and ZINC6710456 from ZINC database which interacts with BRD4 protein with Glide score of-9.98,-8.31,-7.61 kJ/mol respectively. The desired interaction of this ligands with Asn140, Pro82 and Tyr 97 of BRD4 protein showed that the final hits have the potency of forming a stable complex. Molecular dynamics simulations studies also support the stability of the BRD4-ligand docked complex.
Conclusion: The above study shows three compounds obtained viz ZINC68155904, ZINC67910065, and ZINC6710456 may serve as potential lead compounds which can act against BRD4 protein.
Â
Downloads
References
French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA. BRD4-NUT fusion oncogene a novel mechanism in aggressive carcinoma. Cancer Res 2003;63(2):304-7.
Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, et al. Selective inhibition of BET bromodomains. Nature 2010;468(7327):1067-73.
Sanchez R, Zhou M-M. The role of human bromodomains in chromatin biology and gene transcription. Curr Opin Drug Discovery Dev 2009;12(5):659.
Dey A, Nishiyama A, Karpova T, McNally J, Ozato K. Brd4 marks select genes on mitotic chromatin and directs postmitotic transcription. Mol Biol Cell 2009;20(23):4899-909.
Chiang C-M. Brd4 engagement from chromatin targeting to transcriptional regulation: selective contact with acetylated histone H3 and H4. F1000 biology reports; 2009. p. 1.
Wu S-Y, Chiang C-M. The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J Biol Chem 2007;282(18):13141-5.
Owen DJ, Ornaghi P, Yang JC, Lowe N, Evans PR, Ballario P, et al. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J 2000;19(22):6141-9.
Berger SL. Histone modifications in transcriptional regulation. Curr Opin Genet Dev 2002;12(2):142-8.
Yang X-J. Multisite protein modification and intramolecular signaling. Oncogene 2004;24(10):1653-62.
Yang Z, Yik JH, Chen R, He N, Jang MK, Ozato K, et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 2005;19(4):535-45.
Ai N, Hu X, Ding F, Yu B, Wang H, Lu X, et al. Signal-induced Brd4 release from chromatin is essential for its role transition from chromatin targeting to transcriptional regulation. Nucleic Acids Res 2011;39(22):9592-604.
Dey A, Ellenberg J, Farina A, Coleman AE, Maruyama T, Sciortino S, et al. A bromodomain protein, MCAP, associates with mitotic chromosomes and affects G2-to-M transition. Mol Cell Biol 2000;20(17):6537-49.
Dey A, Chitsaz F, Abbasi A, Misteli T, Ozato K. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc Natl Acad Sci 2003;100(15):8758-63.
Bisgrove DA, Mahmoudi T, Henklein P, Verdin E. Conserved P-TEFb-interacting domain of BRD4 inhibits HIV transcription. Proc Natl Acad Sci 2007;104(34):13690-5.
Krueger BJ, Varzavand K, Cooper JJ, Price DH. The mechanism of release of P-TEFb and HEXIM1 from the 7SK snRNP by viral and cellular activators includes a conformational change in 7SK. PloS One 2010;5(8):e12335.
Filippakopoulos P, Picaud S, Fedorov O, Keller M, Wrobel M, Morgenstern O, et al. Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family. Bioorg Med Chem 2012;20(6):1878-86.
Peng J, Zhu Y, Milton JT, Price DH. Identification of multiple cyclin subunits of human P-TEFb. Genes Dev 1998;12(5):755-62.
Marshall NF, Price DH. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J Biol Chem 1995;270(21):12335-8.
Marshall NF, Peng J, Xie Z, Price DH. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J Biol Chem 1996;271(43):27176-83.
Phelps MA, Lin TS, Johnson AJ, Hurh E, Rozewski DM, Farley KL, et al. Clinical response and pharmacokinetics from a phase 1 study of an active dosing schedule of flavopiridol in relapsed chronic lymphocytic leukemia. Blood 2009;113(12):2637-45.
Yang Z, He N, Zhou Q. Brd4 recruits P-TEFb to chromosomes at late mitosis to promote G1 gene expression and cell cycle progression. Mol Cell Biol 2008;28(3):967-76.
Maruyama T, Farina A, Dey A, Cheong J, Bermudez VP, Tamura T, et al. A mammalian bromodomain protein, Brd4, interacts with replication factor C and inhibits progression to S phase. Mol Cell Biol 2002;22(18):6509-20.
French CA, Miyoshi I, Aster JC, Kubonishi I, Kroll TG, Dal Cin P, et al. BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t (15;19). Am J Pathol 2001;159(6):1987-92.
Zhou M, Huang K, Jung K-J, Cho W-K, Klase Z, Kashanchi F, et al. Bromodomain protein Brd4 regulates human immunodeficiency virus transcription through phosphorylation of CDK9 at threonine 29. J Virol 2009;83(2):1036-44.
Lin A, Wang S, Nguyen T, Shire K, Frappier L. The EBNA1 protein of Epstein-Barr virus functionally interacts with Brd4. J Virol 2008;82(24):12009-19.
Gagnon D, Joubert S, Sénéchal H, Fradet-Turcotte A, Torre S, Archambault J. Proteasomal degradation of the papillomavirus E2 protein is inhibited by overexpression of bromodomain-containing protein 4. J Virol 2009;83(9):4127-39.
Chung C-w, Coste H, White JH, Mirguet O, Wilde J, Gosmini RL, et al. Discovery and characterization of small molecule inhibitors of the BET family bromodomains. J Med Chem 2011;54(11):3827-38.
Hewings DS, Wang M, Philpott M, Fedorov O, Uttarkar S, Filippakopoulos P, et al. 3, 5-Dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands. J Med Chem 2011;54(19):6761-70.
Chung C-w, Dean AW, Woolven JM, Bamborough P. Fragment-based discovery of bromodomain inhibitors part 1: inhibitor binding modes and implications for lead discovery. J Med Chem 2012;55(2):576-86.
Bamborough P, Diallo H, Goodacre JD, Gordon L, Lewis A, Seal JT, et al. Fragment-based discovery of bromodomain inhibitors part 2:optimization of phenylisoxazole sulfonamides. J Med Chem 2012;55(2):587-96.
SS, Protein Preparation Wizard; Epik version 2.3, Schrödinger L, New York, NY, 2012;, Impact version 5.8 S, LLC,, New York N, 2012;Prime version 3.1, Schrödinger,, et al.
S Lig Prep v, Schrödinger L: New York N; 2012.
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47(7):1739-49.
Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004;47(7):1750-9.
Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput-Aided Mol Des 2006;20(10-11):647-71.
Dixon SL, Smondyrev AM, Rao SN. PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Design 2006;67(5):370-2.
Salam NK, Nuti R, Sherman W. Novel method for generating structure-based pharmacophores using energetic analysis. J Chem Inf Model 2009;49(10):2356-68.
Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 2012;52(7):1757-68.
Wan H. What ADME tests should be conducted for preclinical studies? ADMET DMPK 2013;1(3):19-28.
S, QikProp v, Schrödinger L, New York N; 2012.
S, Canvas v, Schrödinger L, New York N; 2012.
Duan J, Dixon SL, Lowrie JF, Sherman W. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods. J Mol Graphics Modell 2010;29(2):157-70.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. GROMACS 4.5:a high-throughput and highly parallel open source molecular simulation toolkit. Bioinf 2013:29(7):845-54.
Schuttelkopf AW, Van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr Sect D: Biol Crystallogr 2004;60(8):1355-63.
Kalyaanamoorthy S, Chen Y-PP. Energy based pharmacophore mapping of HDAC inhibitors against class I HDAC enzymes. Biochim Biophys Acta Proteins Proteomics 2013;1834(1):317-28.
Pham DT, Dimov SS, Nguyen C. Selection of K in K-means clustering. Proc Inst Mech Eng Part C 2005;219(1):103-19.