Design and molecular docking studies of new inhibitor candidates for EBNA1 DNA binding site: a computational study

References

• Bochkarev A, Barwell JA, Pfuetzner RA, et al. Crystal-structure of the DNA-binding domain of the Epstein-Barr-virus origin-binding protein Ebna1. Cell. 1995;83(1):39–46.
   PubMed Web of Science ®Google Scholar
• Yasuda A, Noguchi K, Minoshima M, et al. DNA ligand designed to antagonize EBNA1 represses Epstein-Barr virus-induced immortalization. Cancer Sci. 2011;102(12):2221–2230.
   PubMed Web of Science ®Google Scholar
• Garai-Ibabe G, Grinyte R, Canaan A, et al. Homogeneous assay for detection of active Epstein-Barr nuclear antigen 1 by thrombin activity modulation. Anal Chem. 2012;84(14):5834–5837.
   PubMed Web of Science ®Google Scholar
• Pope JH, Horne MK, Scott W. Transformation of foetal human leukocytes in vitro by filtrates of a human leukaemic cell line containing herpes-like virus. Int J Cancer. 1968;3(6):857–866.
   PubMed Web of Science ®Google Scholar
• Haque TJ, Crawford DH. Transmission of Epstein-Barr virus during transplantation. Rev Med Virol. 1996;6(2):77–84.
   PubMed Web of Science ®Google Scholar
• Taylor GS, Long HM, Brooks JM, et al. The immunology of Epstein-Barr virus-induced disease. Annu Rev Immunol. 2015;33:787–821.
   PubMed Web of Science ®Google Scholar
• Tikhmyanova N, Schultz DC, Lee T, et al. Identification of a new class of small molecules that efficiently reactivate latent Epstein-Barr virus. ACS Chem Biol. 2014;9(3):785–795.
   PubMed Web of Science ®Google Scholar
• Matsuura H, Kirschner AN, Longnecker R, et al. Crystal structure of the Epstein-Barr virus (EBV) glycoprotein H/glycoprotein L (gH/gL) complex. Proc Natl Acad Sci USA. 2010;107(52):22641–6.
   PubMed Web of Science ®Google Scholar
• Okano M. Epstein-Barr virus infection and its role in the expanding spectrum of human diseases. Acta Paediatr. 1998;87(1):11–18.
   PubMed Web of Science ®Google Scholar
• Leight ER, Sugden B. EBNA-1: a protein pivotal to latent infection by Epstein-Barr virus. Rev Med Virol. 2000;10(2):83–100.
   PubMed Web of Science ®Google Scholar
• Zhou X., Xiao X., Chen F., et al. Cancer and inflammation mechanisms: chemical, biological, and clinical aspects. Hoboken (NJ): John Wiley & Sons; 2014.
   Google Scholar
• Gianti E, Messick TE, Lieberman PM, et al. Computational analysis of EBNA1 “druggability” suggests novel insights for Epstein-Barr virus inhibitor design. J Comput Aided Mol Des.. 2016;30(4):285–303.
   PubMed Web of Science ®Google Scholar
• Young LS, Rickinson AB. Epstein-Barr virus: 40 years on. Nat Rev Cancer. 2004;4(10):757–768.
   PubMed Web of Science ®Google Scholar
• Lindner SE, Sugden B. The plasmid replicon of Epstein-Barr virus: mechanistic insights into efficient, licensed, extrachromosomal replication in human cells. Plasmid. 2007;58(1):1–12.
   PubMed Web of Science ®Google Scholar
• Frappier L. Ebna1. Curr Top Microbiol Immunol. 2015;391:3–34.
   PubMed Web of Science ®Google Scholar
• Li N, Thompson S, Schultz DC, et al. Discovery of selective inhibitors against EBNA1 via high throughput in silico virtual screening. PLoS One. 2010;5(4):e10126.
   PubMed Web of Science ®Google Scholar
• Bochkarev, A., E. Bochkareva, L. Frappier, and A.M. Edwards, The 2.2 angstrom structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1. J Mol Biol. 1998. 284(5): p. 1273-1278.
   PubMed Web of Science ®Google Scholar
• Wang J, Lindner SE, Leight ER, et al. Essential elements of a licensed, mammalian plasmid origin of DNA synthesis. Mol Cell Biol. 2006;26(3):1124–1134.
   PubMed Web of Science ®Google Scholar
• Garber AC, Hu J, Renne R. Latency-associated nuclear antigen (LANA) cooperatively binds to two sites within the terminal repeat, and both sites contribute to the ability of LANA to suppress transcription and to facilitate DNA replication. J Biol Chem. 2002;277(30):27401–27411.
   PubMed Web of Science ®Google Scholar
• Rishi V, Potter T, Laudeman J, et al. A high-throughput fluorescence-anisotropy screen that identifies small molecule inhibitors of the DNA binding of B-ZIP transcription factors. Anal Biochem. 2005;340(2):259–271.
   PubMed Web of Science ®Google Scholar
• Kiessling A, Sperl B, Hollis A, et al. Selective inhibition of c-Myc/Max dimerization and DNA binding by small molecules. Chem Biol. 2006;13(7):745–751.
   PubMed Web of Science ®Google Scholar
• Bowser TE, Bartlett VJ, Grier MC, et al. Novel anti-infection agents: small-molecule inhibitors of bacterial transcription factors. Bioorg Med Chem Lett. 2007;17(20):5652–5655.
   PubMed Web of Science ®Google Scholar
• Mao C, Patterson NM, Cherian MT, et al. A new small molecule inhibitor of estrogen receptor alpha binding to estrogen response elements blocks estrogen-dependent growth of cancer cells. J Biol Chem. 2008;283(19):12819–12830.
   PubMed Web of Science ®Google Scholar
• Vangrevelinghe E, Zimmermann K, Schoepfer J, et al. Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. J Med Chem. 2003;46(13):2656–2662.
   PubMed Web of Science ®Google Scholar
• Siddiquee K, Zhang S, Guida WC, et al. Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity. Proc Natl Acad Sci USA. 2007;104(18):7391–7396.
   PubMed Web of Science ®Google Scholar
• Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron. 1980;36(22):3219–3228.
   Web of Science ®Google Scholar
• Irwin J. ZINC15.docking.org: over 1.5 billion compounds you can search and buy; 550 million lead-like you can dock. Abstracts of Papers of the American Chemical Society; 2019. p. 257.
   Google Scholar
• Marvin was used for drawing, displaying and characterizing chemical structures, substructures and reactions. 2017, ChemAxon.
   Google Scholar
• Biovia DS. Discovery visualizer studio. San Diego: Dassault Systèmes; 2019.
   Google Scholar
• Zoete V, Daina A, Bovigny C, et al. Swisssimilarity: a web tool for low to ultra high throughput ligand-based virtual screening. J Chem Inf Model. 2016;56(8):1399–1404.
   PubMed Web of Science ®Google Scholar
• Feltrin L. KNIME an open source solution for predictive analytics in the Geosciences. IEEE Geosci Remote Sens Mag. 2015;3(4):28.
   Web of Science ®Google Scholar
• Sander T, Freyss J, von Korff M, et al. Datawarrior: an open-source program for chemistry aware data visualization and analysis. J Chem Inf Model. 2015;55(2):460–473.
   PubMed Web of Science ®Google Scholar
• Pierce AC, Rao G, Bemis GW. BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV protease. J. Med. Chem.. 2004;47(11):2768–2775.
   PubMed Web of Science ®Google Scholar
• Schrödinger, Schrödinger Release 2019-3. Maestro, 2019. New York (NY): LLC; 2019.
   Google Scholar
• Frisch M. J., Trucks G. W., Schlegel H. B., et al. Gaussian 09 Revision E.01. Wallingford (CT): Gaussian Inc.; 2016.
   Google Scholar
• Morris GM, Huey R, Lindstrom W, et al. Autodock4 and autodocktools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791.
   PubMed Web of Science ®Google Scholar
• Hu L, Zhang Y, Zhu H, et al. Filicinic acid based meroterpenoids with anti-Epstein-Barr virus activities from hypericum japonicum. Org Lett. 2016;18(9):2272–2275.
   PubMed Web of Science ®Google Scholar
• Wu T, Wang Q, Jiang C, et al. Neo-clerodane diterpenoids from Scutellaria barbata with activity against Epstein-Barr virus lytic replication. J Nat Prod. 2015;78(3):500–509.
   PubMed Web of Science ®Google Scholar
• Ukiya M, Akihisa T, Tokuda H, et al. Sunpollenol and five other rearranged 3,4-seco-tirucallane-type triterpenoids from sunflower pollen and their inhibitory effects on Epstein-Barr virus activation. J Nat Prod.. 2003;66(11):1476–1479.
   PubMed Web of Science ®Google Scholar
• Akihisa T, Hamasaki Y, Tokuda H, et al. Microbial transformation of isosteviol and inhibitory effects on Epstein-Barr virus activation of the transformation products. J Nat Prod.. 2004;67(3):407–410.
   PubMed Web of Science ®Google Scholar
• Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28(1):235–242.
   PubMed Web of Science ®Google Scholar
• Perryman AL, McCammon JA. Autodocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. J Med Chem. 2002;45(26):5624–5627.
   PubMed Web of Science ®Google Scholar
• Wolf A, Zimmermann M, Hofmann-Apitius M. Alternative to consensus scoring–a new approach toward the qualitative combination of docking algorithms. J Chem Inf Model. 2007;47(3):1036–1044.
   PubMed Web of Science ®Google Scholar
• Chen D, Menche G, Power TD, et al. Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins. Proteins. 2007;67(3):593–605.
   PubMed Web of Science ®Google Scholar