4 DNA Dependent DNA Polymerases as Targets for Low-Weight …
133
107. Andrei G, De Clercq E, Snoeck R (2009) Viral DNA polymerase inhibitors. In: Raney KD,
Götte M, Cameron CE (eds) Viral genome replication. Springer, New York, p 481–526
108. Schnute ME, Cudahy MM, Brideau RJ, Homa FL, Hopkins TA, Knechtel ML, Oien NL,
Pitts TW, Poorman RA, Wathen MW, Wieber JL (2005) 4-Oxo-4,7-dihydrothieno[2,3-b]
pyridines as non-nucleoside inhibitors of human cytomegalovirus and related herpesvirus
polymerases. J Med Chem 48(18):5794–5804
109. Schnute ME, Anderson DJ, Brideau RJ, Ciske FL, Collier SA, Cudahy MM, Eggen M, Genin
MJ, Hopkins TA, Judge TM, Kim EJ, Knechtel ML, Nair SK, Nieman JA, Oien NL, Scott
A, Tanis SP, Vaillancourt VA, Wathen MW, Wieber JL (2007) 2-Aryl-2-hydroxyethylamine
substituted 4-oxo-4,7-dihydrothieno[2,3-b]pyridines as broad-spectrum inhibitors of human
herpesvirus polymerases. Bioorg Med Chem Lett 17(12):3349–3353
110. Larsen SD, Zhang Z, DiPaolo BA, Manninen PR, Rohrer DC, Hageman MJ, Hopkins TA,
Knechtel ML, Oien NL, Rush BD, Schwende FJ, Stefanski KJ, Wieber JL, Wilkinson KF,
Zamora KM, Wathen MW, Brideau RJ (2007) 7-Oxo-4,7-dihydrothieno[3,2-b]pyridine6-carboxamides: synthesis and biological activity of a new class of highly potent inhibitors
of human cytomegalovirus DNA polymerase. Bioorg Med Chem Lett 17(14):3840–3844
111. Hu H, Zhang J, Lee HJ, Kim SH, Lü J (2009) Penta-O-galloyl-beta-d-glucose induces Sand G(1)-cell cycle arrests in prostate cancer cells targeting DNA replication and cyclin D1.
Carcinogenesis 30(5):818–823
112. Zhang J, Li L, Kim SH, Hagerman AE, Lu J (2009) Anti-cancer, anti-diabetic and other
pharmacologicand biological activities of penta-galloyl-glucose. Pharm res 26:2066–2080
113. Chai Y, Lee HJ, Shaik AA, Nkhata K, Xing C, Zhang J, Jeong SJ, Kim SH, Lu J (2010)
Penta-O-galloyl-beta-d-glucose induces G1 arrest and DNA replicative S-phase arrest independently of cyclin-dependent kinase inhibitor 1A, cyclin-dependent kinase inhibitor 1B
and P53 in human breast cancer cells and is orally active against triple negative xenograft
growth. Breast Cancer Res 12(5):R67
114. Mizushina Y, Kasai N, Sugawara F, Iida A, Yoshida H, Sakaguchi K (2001) Three-dimensional structural model analysis of the binding site of lithocholic acid, an inhibitor of DNA
polymerase β and DNA topoisomerase II. J Biochem 130(5):657–664
115. Mizushina Y, Kasai N, Miura K, Hanashima S, Takemura M, Yoshida H, Sugawara F, Sakaguchi K (2004) Structural relationship of lithocholic acid derivatives binding to the N-terminal 8-kDa domain of DNA polymerase β. Biochemistry 43(33):10669–10677
116. Shi S, Yan L, Yang Y, Fisher-Shaulsky J, Thacher T (2003) An extensible and systematic
force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems.
J Comput Chem 24(9):1059–1076
117. Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9:1–5
118. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998)
Auto-mated docking using a lamarckian genetic algorithm and and empirical binding free
energy function J Comput Chem 19: 1639–1662
119. Murakami S, Kamisuki S, Takata K, Kasai N, Kimura S, Mizushina Y, Ohta K, Sugawara F,
Sakaguchi K (2006) Site-directed mutational analysis of structural interactions of low molecule compounds binding to the N-terminal 8 kDa domain of DNA polymerase β. Biochem
Biophys Res Commun 350(1):7–16
120. Clarkson J, Campbell ID (2003) Studies of protein-ligand interactions by NMR. Biochem
Soc Trans 31(Pt 5):1006–1009
121. Mayer M, Meyer B (2001, Jun 27) Group epitope mapping by saturation transfer difference
NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem
Soc 123(25):6108–6117
122. Meyer B, Klein J, Mayer M, Meinecke R, Möller H, Neffe A, Schuster O, Wülfken J, Ding
Y, Knaie O, Labbe J, Palcic MM, Hindsgaul O, Wagner B, Ernst B (2004) Saturation transfer
difference NMR spectroscopy for identifying ligand epitopes and binding specificities. Ernst
Schering Res Found Workshop 44:149–167
133
107. Andrei G, De Clercq E, Snoeck R (2009) Viral DNA polymerase inhibitors. In: Raney KD,
Götte M, Cameron CE (eds) Viral genome replication. Springer, New York, p 481–526
108. Schnute ME, Cudahy MM, Brideau RJ, Homa FL, Hopkins TA, Knechtel ML, Oien NL,
Pitts TW, Poorman RA, Wathen MW, Wieber JL (2005) 4-Oxo-4,7-dihydrothieno[2,3-b]
pyridines as non-nucleoside inhibitors of human cytomegalovirus and related herpesvirus
polymerases. J Med Chem 48(18):5794–5804
109. Schnute ME, Anderson DJ, Brideau RJ, Ciske FL, Collier SA, Cudahy MM, Eggen M, Genin
MJ, Hopkins TA, Judge TM, Kim EJ, Knechtel ML, Nair SK, Nieman JA, Oien NL, Scott
A, Tanis SP, Vaillancourt VA, Wathen MW, Wieber JL (2007) 2-Aryl-2-hydroxyethylamine
substituted 4-oxo-4,7-dihydrothieno[2,3-b]pyridines as broad-spectrum inhibitors of human
herpesvirus polymerases. Bioorg Med Chem Lett 17(12):3349–3353
110. Larsen SD, Zhang Z, DiPaolo BA, Manninen PR, Rohrer DC, Hageman MJ, Hopkins TA,
Knechtel ML, Oien NL, Rush BD, Schwende FJ, Stefanski KJ, Wieber JL, Wilkinson KF,
Zamora KM, Wathen MW, Brideau RJ (2007) 7-Oxo-4,7-dihydrothieno[3,2-b]pyridine6-carboxamides: synthesis and biological activity of a new class of highly potent inhibitors
of human cytomegalovirus DNA polymerase. Bioorg Med Chem Lett 17(14):3840–3844
111. Hu H, Zhang J, Lee HJ, Kim SH, Lü J (2009) Penta-O-galloyl-beta-d-glucose induces Sand G(1)-cell cycle arrests in prostate cancer cells targeting DNA replication and cyclin D1.
Carcinogenesis 30(5):818–823
112. Zhang J, Li L, Kim SH, Hagerman AE, Lu J (2009) Anti-cancer, anti-diabetic and other
pharmacologicand biological activities of penta-galloyl-glucose. Pharm res 26:2066–2080
113. Chai Y, Lee HJ, Shaik AA, Nkhata K, Xing C, Zhang J, Jeong SJ, Kim SH, Lu J (2010)
Penta-O-galloyl-beta-d-glucose induces G1 arrest and DNA replicative S-phase arrest independently of cyclin-dependent kinase inhibitor 1A, cyclin-dependent kinase inhibitor 1B
and P53 in human breast cancer cells and is orally active against triple negative xenograft
growth. Breast Cancer Res 12(5):R67
114. Mizushina Y, Kasai N, Sugawara F, Iida A, Yoshida H, Sakaguchi K (2001) Three-dimensional structural model analysis of the binding site of lithocholic acid, an inhibitor of DNA
polymerase β and DNA topoisomerase II. J Biochem 130(5):657–664
115. Mizushina Y, Kasai N, Miura K, Hanashima S, Takemura M, Yoshida H, Sugawara F, Sakaguchi K (2004) Structural relationship of lithocholic acid derivatives binding to the N-terminal 8-kDa domain of DNA polymerase β. Biochemistry 43(33):10669–10677
116. Shi S, Yan L, Yang Y, Fisher-Shaulsky J, Thacher T (2003) An extensible and systematic
force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems.
J Comput Chem 24(9):1059–1076
117. Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9:1–5
118. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998)
Auto-mated docking using a lamarckian genetic algorithm and and empirical binding free
energy function J Comput Chem 19: 1639–1662
119. Murakami S, Kamisuki S, Takata K, Kasai N, Kimura S, Mizushina Y, Ohta K, Sugawara F,
Sakaguchi K (2006) Site-directed mutational analysis of structural interactions of low molecule compounds binding to the N-terminal 8 kDa domain of DNA polymerase β. Biochem
Biophys Res Commun 350(1):7–16
120. Clarkson J, Campbell ID (2003) Studies of protein-ligand interactions by NMR. Biochem
Soc Trans 31(Pt 5):1006–1009
121. Mayer M, Meyer B (2001, Jun 27) Group epitope mapping by saturation transfer difference
NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem
Soc 123(25):6108–6117
122. Meyer B, Klein J, Mayer M, Meinecke R, Möller H, Neffe A, Schuster O, Wülfken J, Ding
Y, Knaie O, Labbe J, Palcic MM, Hindsgaul O, Wagner B, Ernst B (2004) Saturation transfer
difference NMR spectroscopy for identifying ligand epitopes and binding specificities. Ernst
Schering Res Found Workshop 44:149–167