4 DNA Dependent DNA Polymerases as Targets for Low-Weight …
135
144. Pungitore CR, Ayub MJ, García M, Borkowski EJ, Sosa ME, Ciuffo G, Tonn CE (2004)
Iridoids as allelochemicals and DNA polymerase inhibitors. J Nat Prod 67:357–361
145. Li J, Du Y, Liu X, Shen QC, Huang AL, Zheng MY, Luo XM, Jiang HL (2013) Binding
sensi-tivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies. Acta Pharmacol Sin 34(2):319–328
146. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative
protein modeling by MODELLER. Proteins 23: 318–326
147. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck—a program to
check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291
148. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput
Chem 26: 1668–1688
149. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR et al (2004)
Gaussian 03, Revision B.05. Gaussian, Inc, Wallingford, CT
150. Bayly CI, Cieplak P, Cornell W, Kollman PA (1993) A well-behaved electrostatic potential
based method susing charge restraints for deriving atomic charges: the RESP model. J Phys
Chem 97(40):10269–10280
151. Wang JM, Wang W, Kollman PA (2001) Automatic atom type and bond type perception in
molecular mechanical calculations. J Mol Graph Model 25(2):247–260
152. Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate parameters
for use with the AMBER force field. J Comput Chem 24:1016–1025
153. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of
a general amber force field. J Comput Chem 25:1157–1174
154. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang
W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897
155. Daga PR, Duan J, Doerksen RJ (2010) Computational model of hepatitis B virus DNA
polymerase: molecular dynamics and docking to understand resistant mutations. Protein Sci
19:796–807
156. Yarmolyuk SM, Nyporko AYu, Bdzhola VG (2013) Rational design of protein kinase inhibitors. Biopolym Cell 29(4):339–347
157. Richartz A, Höltje M, Brandt B, Schäfer-Korting M, Höltje HD (2008) Targeting human
DNA polymerase α for the inhibition of keratinocyte proliferation. Part 1. Homology model,
active site architecture and ligand binding. J Enzyme Inhib Med Chem 23(1):94–100
158. Edelson RE, Gorycki PD, MacDonald TL (1990) The mechanism of aphidicolin bioinactivation by rat liver in vitro systems. Xenobiotica 20:273–287
159. Höltje M, Richartz A, Zdrazil B, Schwanke A, Dugovic B, Murruzzu C, Reissig HU, Korting
HC, Kleuser B, Höltje HD, Schäfer-Korting M. (2010) Human polymerase α inhibitors for
skin tumors. Part 2. Modeling, synthesis and influence on normal and transformed keratinocytes of new thymidine and purine derivatives. J Enzyme Inhib Med Chem 25(2):250–265
160. Schwanke A, Murruzzu C, Zdrazil B, Zuhse R, Natek M, Höltje M, Korting HC, Reissig HU,
Höltje HD, Schäfer-Korting M (2010) Antitumor effects of guanosine-analog phosphonates
identified by molecular modelling. Int J Pharm 397(1–2):9–18
161. Zdrazil B, Schwanke A, Schmitz B, Schäfer-Korting M, Höltje HD (2011) Molecular modelling studies of new potential human DNA polymerase α inhibitors. J Enzyme Inhib Med
Chem 26(2):270–279
162. Karampuri S, Bag P, Yasmin S, Chouhan DK, Bal C, Mitra D, Chattopadhyay D, Sharon A
(2012) Structure based molecular design, synthesis and biological evaluation of α-pyrone
analogs as anti-HSV agent. Bioorg Med Chem Lett 22(19):6261–6266
135
144. Pungitore CR, Ayub MJ, García M, Borkowski EJ, Sosa ME, Ciuffo G, Tonn CE (2004)
Iridoids as allelochemicals and DNA polymerase inhibitors. J Nat Prod 67:357–361
145. Li J, Du Y, Liu X, Shen QC, Huang AL, Zheng MY, Luo XM, Jiang HL (2013) Binding
sensi-tivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies. Acta Pharmacol Sin 34(2):319–328
146. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative
protein modeling by MODELLER. Proteins 23: 318–326
147. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck—a program to
check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291
148. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput
Chem 26: 1668–1688
149. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR et al (2004)
Gaussian 03, Revision B.05. Gaussian, Inc, Wallingford, CT
150. Bayly CI, Cieplak P, Cornell W, Kollman PA (1993) A well-behaved electrostatic potential
based method susing charge restraints for deriving atomic charges: the RESP model. J Phys
Chem 97(40):10269–10280
151. Wang JM, Wang W, Kollman PA (2001) Automatic atom type and bond type perception in
molecular mechanical calculations. J Mol Graph Model 25(2):247–260
152. Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate parameters
for use with the AMBER force field. J Comput Chem 24:1016–1025
153. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of
a general amber force field. J Comput Chem 25:1157–1174
154. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang
W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889–897
155. Daga PR, Duan J, Doerksen RJ (2010) Computational model of hepatitis B virus DNA
polymerase: molecular dynamics and docking to understand resistant mutations. Protein Sci
19:796–807
156. Yarmolyuk SM, Nyporko AYu, Bdzhola VG (2013) Rational design of protein kinase inhibitors. Biopolym Cell 29(4):339–347
157. Richartz A, Höltje M, Brandt B, Schäfer-Korting M, Höltje HD (2008) Targeting human
DNA polymerase α for the inhibition of keratinocyte proliferation. Part 1. Homology model,
active site architecture and ligand binding. J Enzyme Inhib Med Chem 23(1):94–100
158. Edelson RE, Gorycki PD, MacDonald TL (1990) The mechanism of aphidicolin bioinactivation by rat liver in vitro systems. Xenobiotica 20:273–287
159. Höltje M, Richartz A, Zdrazil B, Schwanke A, Dugovic B, Murruzzu C, Reissig HU, Korting
HC, Kleuser B, Höltje HD, Schäfer-Korting M. (2010) Human polymerase α inhibitors for
skin tumors. Part 2. Modeling, synthesis and influence on normal and transformed keratinocytes of new thymidine and purine derivatives. J Enzyme Inhib Med Chem 25(2):250–265
160. Schwanke A, Murruzzu C, Zdrazil B, Zuhse R, Natek M, Höltje M, Korting HC, Reissig HU,
Höltje HD, Schäfer-Korting M (2010) Antitumor effects of guanosine-analog phosphonates
identified by molecular modelling. Int J Pharm 397(1–2):9–18
161. Zdrazil B, Schwanke A, Schmitz B, Schäfer-Korting M, Höltje HD (2011) Molecular modelling studies of new potential human DNA polymerase α inhibitors. J Enzyme Inhib Med
Chem 26(2):270–279
162. Karampuri S, Bag P, Yasmin S, Chouhan DK, Bal C, Mitra D, Chattopadhyay D, Sharon A
(2012) Structure based molecular design, synthesis and biological evaluation of α-pyrone
analogs as anti-HSV agent. Bioorg Med Chem Lett 22(19):6261–6266