메뉴 건너뛰기




Volumn 28, Issue 2, 2009, Pages 113-130

Characterization of an inhibitory dynamic pharmacophore for the ERCC1-XPA interaction using a combined molecular dynamics and virtual screening approach

Author keywords

Clustering; DrugBank; ERCC1; NCI dtp database; Pharmacophore; UCN01; Virtual screening; XPA

Indexed keywords

CLUSTERING; DRUGBANK; ERCC1; NCI DTP DATABASE; PHARMACOPHORE; UCN01; VIRTUAL SCREENING; XPA;

EID: 70349303452     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.04.009     Document Type: Article
Times cited : (31)

References (57)
  • 1
    • 2142694056 scopus 로고    scopus 로고
    • Cisplatin and platinum drugs at the molecular level
    • Boulikas T., and Vougiouka M. Cisplatin and platinum drugs at the molecular level. Oncol. Rep. 10 (2003) 1663-1682
    • (2003) Oncol. Rep. , vol.10 , pp. 1663-1682
    • Boulikas, T.1    Vougiouka, M.2
  • 2
    • 6844222840 scopus 로고    scopus 로고
    • Carboplatin versus cisplatin in solid tumors: an analysis of the literature
    • Lokich J., and Anderson N. Carboplatin versus cisplatin in solid tumors: an analysis of the literature. Ann. Oncol. 9 (1998) 13-21
    • (1998) Ann. Oncol. , vol.9 , pp. 13-21
    • Lokich, J.1    Anderson, N.2
  • 4
    • 0018568039 scopus 로고
    • Mechanisms of action of cis-dichlorodiamineplatinum (II)
    • Zwelling L.A., and Kohn K.W. Mechanisms of action of cis-dichlorodiamineplatinum (II). Cancer Treat Rep. 63 (1979) 1439-1444
    • (1979) Cancer Treat Rep. , vol.63 , pp. 1439-1444
    • Zwelling, L.A.1    Kohn, K.W.2
  • 5
    • 0019767317 scopus 로고
    • The role of DNA repair in the recovery of human cells from cisplatin toxicity
    • Pera M.F., Rawlings C.J., and Roberts J.J. The role of DNA repair in the recovery of human cells from cisplatin toxicity. Chem. Biol. Interact. 37 (1981) 245-261
    • (1981) Chem. Biol. Interact. , vol.37 , pp. 245-261
    • Pera, M.F.1    Rawlings, C.J.2    Roberts, J.J.3
  • 6
    • 0001685401 scopus 로고
    • The major adduct of the antitumor drug cis-dichlorodiamineplatinum with DNA bends the duplex by approximate equal to 40 degrees toward the major groove
    • Rice J.A., Crothers D.M., and Pinto A.L. The major adduct of the antitumor drug cis-dichlorodiamineplatinum with DNA bends the duplex by approximate equal to 40 degrees toward the major groove. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 4158-4161
    • (1988) Proc. Natl. Acad. Sci. U.S.A. , vol.85 , pp. 4158-4161
    • Rice, J.A.1    Crothers, D.M.2    Pinto, A.L.3
  • 7
    • 0018746983 scopus 로고
    • Excision repair of cis-dichlorodiamineplatinum-induced damage to DNA of Chinese hamster cells
    • Fraval H.N., and Roberts J.J. Excision repair of cis-dichlorodiamineplatinum-induced damage to DNA of Chinese hamster cells. Cancer Res. 39 (1979) 1793-1797
    • (1979) Cancer Res. , vol.39 , pp. 1793-1797
    • Fraval, H.N.1    Roberts, J.J.2
  • 8
    • 0000714484 scopus 로고
    • Platinum-DNA adducts in leukocyte DNA correlate with disease response in ovarian cancer patients receiving platinum-based chemotherapy
    • Reed E., Ozols R.F., Tarone R., Yuspa S.H., and Poirier M.C. Platinum-DNA adducts in leukocyte DNA correlate with disease response in ovarian cancer patients receiving platinum-based chemotherapy. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 5024-5028
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 5024-5028
    • Reed, E.1    Ozols, R.F.2    Tarone, R.3    Yuspa, S.H.4    Poirier, M.C.5
  • 9
    • 0031745255 scopus 로고    scopus 로고
    • Chemotherapy of advanced ovarian cancer
    • McGuire W., and Ozols R.F. Chemotherapy of advanced ovarian cancer. Semin. Oncol. 25 (1998) 340-348
    • (1998) Semin. Oncol. , vol.25 , pp. 340-348
    • McGuire, W.1    Ozols, R.F.2
  • 10
    • 0027379862 scopus 로고
    • Clinical reversal of drug resistance in ovarian cancer
    • Ozols R.F., O'Dwyer P.J., and Hamilton T.C. Clinical reversal of drug resistance in ovarian cancer. Gynecol. Oncol. 51 (1993) 90-96
    • (1993) Gynecol. Oncol. , vol.51 , pp. 90-96
    • Ozols, R.F.1    O'Dwyer, P.J.2    Hamilton, T.C.3
  • 11
    • 33846404174 scopus 로고    scopus 로고
    • Molecular mechanisms of resistance and toxicity associated with platinating agents
    • Cara A., Rabik M., and Dolan E. Molecular mechanisms of resistance and toxicity associated with platinating agents. Cancer Treat Rev. 33 (2007) 9-23
    • (2007) Cancer Treat Rev. , vol.33 , pp. 9-23
    • Cara, A.1    Rabik, M.2    Dolan, E.3
  • 12
    • 21644466123 scopus 로고    scopus 로고
    • Excision repair cross complementing group 1; gene expression and platinum resistance
    • Altaha R., Liang X., Yu J.J., and Reed E. Excision repair cross complementing group 1; gene expression and platinum resistance. Int. J. Mol. 14 (2004) 559-570
    • (2004) Int. J. Mol. , vol.14 , pp. 559-570
    • Altaha, R.1    Liang, X.2    Yu, J.J.3    Reed, E.4
  • 13
    • 0028141961 scopus 로고
    • Messenger RNA levels of XPAC and ERCC1 in ovarian cancer tissue correlate with response to platinum-based chemotherapy
    • Dabholkar M., Vionnet J., Bostick-Bruton F., Yu J.J., and Reed E. Messenger RNA levels of XPAC and ERCC1 in ovarian cancer tissue correlate with response to platinum-based chemotherapy. J. Clin. Invest. 94 (1994) 703-708
    • (1994) J. Clin. Invest. , vol.94 , pp. 703-708
    • Dabholkar, M.1    Vionnet, J.2    Bostick-Bruton, F.3    Yu, J.J.4    Reed, E.5
  • 14
    • 0346103811 scopus 로고    scopus 로고
    • Sensitization to the cytotoxicity of cisplatin by transfection with nucleotide excision repair gene xeroderma pigmentosum group A antisense RNA in human lung adenocarcinoma cells
    • Wu X., Fan W., Xu S., and Zhou Y. Sensitization to the cytotoxicity of cisplatin by transfection with nucleotide excision repair gene xeroderma pigmentosum group A antisense RNA in human lung adenocarcinoma cells. Clin. Cancer Res. 9 (2003) 5874-5879
    • (2003) Clin. Cancer Res. , vol.9 , pp. 5874-5879
    • Wu, X.1    Fan, W.2    Xu, S.3    Zhou, Y.4
  • 15
    • 0034117603 scopus 로고    scopus 로고
    • Clinical perspectives on platinum resistance
    • Giaccone G. Clinical perspectives on platinum resistance. Drugs 5 (2000) 9-17
    • (2000) Drugs , vol.5 , pp. 9-17
    • Giaccone, G.1
  • 17
    • 0033566758 scopus 로고    scopus 로고
    • Efficient nucleotide excision repair of cisplatin, oxaliplatin, and bis-aceto-ammine-dichloro-cyclohexylamine-platinum(IV) (JM216) platinum intrastrand DNA diadducts
    • Reardon J.T., Vaisman A., Chaney S.G., and Sancar A. Efficient nucleotide excision repair of cisplatin, oxaliplatin, and bis-aceto-ammine-dichloro-cyclohexylamine-platinum(IV) (JM216) platinum intrastrand DNA diadducts. Cancer Res. 59 (1999) 3968-3971
    • (1999) Cancer Res. , vol.59 , pp. 3968-3971
    • Reardon, J.T.1    Vaisman, A.2    Chaney, S.G.3    Sancar, A.4
  • 19
    • 0035811260 scopus 로고    scopus 로고
    • Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment containing the ERCC1-binding region and the minimal DNA-binding domain (M59-F219)
    • Buchko G.W., Isern N.G., Spicer L.D., and Kennedy M.A. Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment containing the ERCC1-binding region and the minimal DNA-binding domain (M59-F219). Mutat. Res. 486 (2001) 1-10
    • (2001) Mutat. Res. , vol.486 , pp. 1-10
    • Buchko, G.W.1    Isern, N.G.2    Spicer, L.D.3    Kennedy, M.A.4
  • 20
    • 0029828941 scopus 로고    scopus 로고
    • Sequential binding of DNA repair proteins RPA and ERCC1 to XPA in vitro
    • Saijo M., Kuraoka I., Masutani C., Hanaoka F., and Tanaka K. Sequential binding of DNA repair proteins RPA and ERCC1 to XPA in vitro. Nucleic Acids Res. 24 (1996) 4719-4724
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4719-4724
    • Saijo, M.1    Kuraoka, I.2    Masutani, C.3    Hanaoka, F.4    Tanaka, K.5
  • 21
    • 0033545701 scopus 로고    scopus 로고
    • Defective repair of cisplatin-induced DNA damage caused by reduced XPA protein in testicular germ cell tumours
    • Koberle B., Masters J.R., Hartley J.A., and Wood R.D. Defective repair of cisplatin-induced DNA damage caused by reduced XPA protein in testicular germ cell tumours. Curr. Biol. 9 (1999) 273-276
    • (1999) Curr. Biol. , vol.9 , pp. 273-276
    • Koberle, B.1    Masters, J.R.2    Hartley, J.A.3    Wood, R.D.4
  • 22
    • 2442419814 scopus 로고    scopus 로고
    • Reduced levels of XPA, ERCC1 and XPF DNA repair proteins in testis tumor cell lines
    • Welsh C., Day R., McGurk C., Masters J.R., Wood R.D., and Köberle B. Reduced levels of XPA, ERCC1 and XPF DNA repair proteins in testis tumor cell lines. Int. J. Cancer 110 (2004) 352-361
    • (2004) Int. J. Cancer , vol.110 , pp. 352-361
    • Welsh, C.1    Day, R.2    McGurk, C.3    Masters, J.R.4    Wood, R.D.5    Köberle, B.6
  • 23
    • 0035863317 scopus 로고    scopus 로고
    • A truncated human xeroderma pigmentosum complementation group A protein expressed from an adenovirus sensitizes human tumor cells to ultraviolet light and cisplatin
    • Rosenberg E., Taher M.M., Kuemmerle N.B., Farnsworth J., and Valerie K. A truncated human xeroderma pigmentosum complementation group A protein expressed from an adenovirus sensitizes human tumor cells to ultraviolet light and cisplatin. Cancer Res. 61 (2001) 764-770
    • (2001) Cancer Res. , vol.61 , pp. 764-770
    • Rosenberg, E.1    Taher, M.M.2    Kuemmerle, N.B.3    Farnsworth, J.4    Valerie, K.5
  • 26
    • 33947716119 scopus 로고    scopus 로고
    • A semiempirical free energy force field with charge-based desolvation
    • Huey R., Morris G.M., Olson A.J., and Goodsell D.S. A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem. 28 (2007) 1145-1152
    • (2007) J. Comput. Chem. , vol.28 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 27
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: current status and future challenges
    • Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: current status and future challenges. Proteins 65 (2006) 15-26
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 29
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • Cavasotto C.N., and Abagyan R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 337 (2004) 209-225
    • (2004) J. Mol. Biol. , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 30
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto C.N., Kovacs J.A., and Abagyan R.A. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 127 (2005) 9632-9640
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 31
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: the relaxed complex scheme
    • Lin J.H., Perryman A.L., Schames J.R., and McCammon J.A. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J. Am. Chem. Soc. 124 (2002) 5632-5633
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5632-5633
    • Lin, J.H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 32
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase
    • Murray C.W., Baxter C.A., and Frenkel A.D. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J. Comput. Aided Mol. Des. 13 (1999) 547-562
    • (1999) J. Comput. Aided Mol. Des. , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 33
    • 0035416126 scopus 로고    scopus 로고
    • High-throughput docking for lead generation
    • Abagyan R., and Totrov M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 5 (2001) 375-382
    • (2001) Curr. Opin. Chem. Biol. , vol.5 , pp. 375-382
    • Abagyan, R.1    Totrov, M.2
  • 35
    • 70349342487 scopus 로고    scopus 로고
    • Last checked October 19, 2008
    • http://dtp.nci.nih.gov/branches/dscb/diversity_explanation.html (Last checked October 19, 2008).
  • 36
    • 0033568223 scopus 로고    scopus 로고
    • Cell cycle checkpoint Abrogator UCN-01 inhibits DNA repair
    • Hong J., and Li-Ying Y. Cell cycle checkpoint Abrogator UCN-01 inhibits DNA repair. Cancer Res. 59 (1999) 4529-4534
    • (1999) Cancer Res. , vol.59 , pp. 4529-4534
    • Hong, J.1    Li-Ying, Y.2
  • 37
    • 0042415783 scopus 로고    scopus 로고
    • NAMD2: greater scalability for parallel molecular dynamics
    • Kalé L. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151 (1999) 283-312
    • (1999) J. Comput. Phys. , vol.151 , pp. 283-312
    • Kalé, L.1
  • 38
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • 65,712-65,725
    • Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., and Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 65,712-65,725
    • (2006) Proteins
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 42
    • 36649006642 scopus 로고    scopus 로고
    • Clustering molecular dynamics trajectories. 1. Characterizing the performance of different clustering algorithms
    • Shao J., Tanner S.W., Thompson N., and Cheatham T.E. Clustering molecular dynamics trajectories. 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3 (2007) 2312-2334
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2312-2334
    • Shao, J.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 43
    • 0000577041 scopus 로고
    • Large-amplitude nonlinear motions in proteins
    • Garcia A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68 (1992) 2696-2699
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 45
    • 41349089279 scopus 로고    scopus 로고
    • Convergence of sampling in protein simulations
    • Hess B. Convergence of sampling in protein simulations. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 65 (2002) 31910-31920
    • (2002) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. , vol.65 , pp. 31910-31920
    • Hess, B.1
  • 46
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: conformational flooding
    • Grubmuller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top. 52 (1995) 2893-2906
    • (1995) Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top. , vol.52 , pp. 2893-2906
    • Grubmuller, H.1
  • 47
    • 33749551180 scopus 로고    scopus 로고
    • Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
    • Kosztin I., Barz B., and Janosi L. Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality. J. Chem. Phys. 124 (2006) 64106-64111
    • (2006) J. Chem. Phys. , vol.124 , pp. 64106-64111
    • Kosztin, I.1    Barz, B.2    Janosi, L.3
  • 50
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges
    • Gasteiger J., and Marsili M. Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges. Tetrahedron 36 (1980) 3219-3228
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 54
    • 0005123846 scopus 로고
    • Automated chemical hypothesis generation and database searching with catalyst
    • Müller K. (Ed), ESCOM Science Publishers B.V., Leiden, The Netherlands
    • Sprague P.W. Automated chemical hypothesis generation and database searching with catalyst. In: Müller K. (Ed). Perspectives in Drug Discovery and Design vol.3 (1995), ESCOM Science Publishers B.V., Leiden, The Netherlands 1-20
    • (1995) Perspectives in Drug Discovery and Design , vol.3 , pp. 1-20
    • Sprague, P.W.1
  • 56
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate to sets of vectors
    • Kabsch W. A solution for the best rotation to relate to sets of vectors. Acta Crystallogr. A32 (1976) 922-923
    • (1976) Acta Crystallogr. , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 57
    • 0037053312 scopus 로고    scopus 로고
    • Analysis of conserved active site residues in monoamine oxidase A and B and their three-dimensional molecular modeling
    • Geha R.M., Chen K., Wouters J., Ooms F., and Shih J.C. Analysis of conserved active site residues in monoamine oxidase A and B and their three-dimensional molecular modeling. J. Biol. Chem. 277 (2002) 17209-17216
    • (2002) J. Biol. Chem. , vol.277 , pp. 17209-17216
    • Geha, R.M.1    Chen, K.2    Wouters, J.3    Ooms, F.4    Shih, J.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.