메뉴 건너뛰기




Volumn 51, Issue 4, 2011, Pages 777-787

Improving VEGFR-2 docking-based screening by pharmacophore postfiltering and similarity search postprocessing

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY;

EID: 79955388686     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci1002763     Document Type: Article
Times cited : (16)

References (48)
  • 1
    • 28144462911 scopus 로고    scopus 로고
    • Expression of vascular endothelial growth factor (VEGF) and VEGF receptors in tumor angiogenesis and malignancies
    • DOI 10.1177/1534735405282557
    • Pradeep, C. R.; Sunila, E. S.; Kuttan, G. Expression of vascular endothelial growth factor (VEGF) and VEGF receptors in tumor angiogenesis and malignancies Integr. Cancer Ther. 2005, 4, 315-321 (Pubitemid 41698180)
    • (2005) Integrative Cancer Therapies , vol.4 , Issue.4 , pp. 315-321
    • Pradeep, C.R.1    Sunila, E.S.2    Kuttan, G.3
  • 5
    • 60449096371 scopus 로고    scopus 로고
    • 1, 2, 3-Triazol-4-yl) benzenamines: Synthesis and activity against VEGF receptors 1 and 2
    • Kiselyov, A. S.; Semenova, M.; Semenov, V. V. 1, 2, 3-Triazol-4-yl) benzenamines: Synthesis and activity against VEGF receptors 1 and 2 Bioorg. Med. Chem. Lett. 2009, 5, 1344-1348
    • (2009) Bioorg. Med. Chem. Lett. , vol.5 , pp. 1344-1348
    • Kiselyov, A.S.1    Semenova, M.2    Semenov, V.V.3
  • 6
    • 46849115345 scopus 로고    scopus 로고
    • Design, synthesis, and biological evaluation of novel 3-aryl-4-(1H-indole- 3yl)-1,5-dihydro-2H-pyrrole-2-ones as vascular endothelial growth factor receptor (VEGF-R) inhibitors
    • DOI 10.1021/jm8001185
    • Peifer, C.; Selig, R.; Kinkel, K.; Ott, D.; Totzke, F.; Schachtele, C.; Heidenreich, R.; Rocken, M.; Schollmeyer, D.; Laufer, S. Design, synthesis, and biological evaluation of novel 3-aryl-4-(1 H -indole-3-yl)-1,5-dihydro-2 H -pyrrol-2-ones as vascular endothelial growth factor receptor (VEGF-R) inhibitors J. Med. Chem. 2008, 13, 3814-3824 (Pubitemid 351956512)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.13 , pp. 3814-3824
    • Peifer, C.1    Selig, R.2    Kinkel, K.3    Ott, D.4    Totzke, F.5    Schachtele, C.6    Heidenreich, R.7    Rocken, M.8    Schollmeyer, D.9    Laufer, S.10
  • 7
    • 71749102468 scopus 로고    scopus 로고
    • N-(4-(6, 7-Disubstituted-quinolin-4-yloxy)-3-fluorophenyl)-2-oxo-3- phenylimidazolidine-1-carboxamides: A novel series of dual c-Met/VEGFR2 receptor tyrosine kinase inhibitors
    • Mannion, M.; Raeppel, S.; Claridge, S.; Zhou, N.; Saavedra, O.; Isakovic, L.; Zhan, L.; Gaudette, F.; Raeppel, F.; Déziel, R. N-(4-(6, 7-Disubstituted-quinolin-4-yloxy)-3-fluorophenyl)-2-oxo-3-phenylimidazolidine-1- carboxamides: A novel series of dual c-Met/VEGFR2 receptor tyrosine kinase inhibitors Bioorg. Med. Chem. Lett. 2009, 23, 6552-6556
    • (2009) Bioorg. Med. Chem. Lett. , vol.23 , pp. 6552-6556
    • Mannion, M.1    Raeppel, S.2    Claridge, S.3    Zhou, N.4    Saavedra, O.5    Isakovic, L.6    Zhan, L.7    Gaudette, F.8    Raeppel, F.9    Déziel, R.10
  • 11
    • 67650097331 scopus 로고    scopus 로고
    • Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
    • Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy J. Chem. Inf. Model. 2009, 6, 1455-1474
    • (2009) J. Chem. Inf. Model. , vol.6 , pp. 1455-1474
    • Cross, J.B.1    Thompson, D.C.2    Rai, B.K.3    Baber, J.C.4    Fan, K.Y.5    Hu, Y.6    Humblet, C.7
  • 12
    • 66149103553 scopus 로고    scopus 로고
    • Comparative Assessment of Scoring Functions on a Diverse Test Set
    • Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative Assessment of Scoring Functions on a Diverse Test Set J. Chem. Inf. Model. 2009, 4, 1079-1093
    • (2009) J. Chem. Inf. Model. , vol.4 , pp. 1079-1093
    • Cheng, T.1    Li, X.2    Li, Y.3    Liu, Z.4    Wang, R.5
  • 14
    • 65349136650 scopus 로고    scopus 로고
    • Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
    • Rohrer, S. G.; Baumann, K. Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data J. Chem. Inf. Model. 2009, 2, 169-184
    • (2009) J. Chem. Inf. Model. , vol.2 , pp. 169-184
    • Rohrer, S.G.1    Baumann, K.2
  • 16
    • 0342645331 scopus 로고    scopus 로고
    • 2008.10 release; Chemical Computing Group, Inc.: Montreal, Canada.
    • MOE (Molecular Operating Environment), 2008.10 release; Chemical Computing Group, Inc.: Montreal, Canada, 2004.
    • (2004) MOE (Molecular Operating Environment)
  • 18
    • 76449085493 scopus 로고    scopus 로고
    • Computation of 3D queries for ROCS based virtual screens
    • Tawa, G. J.; Baber, J. C.; Humblet, C. Computation of 3D queries for ROCS based virtual screens J. Comput.-Aided Mol. Des. 2009, 12, 853-868
    • (2009) J. Comput.-Aided Mol. Des. , vol.12 , pp. 853-868
    • Tawa, G.J.1    Baber, J.C.2    Humblet, C.3
  • 19
    • 33751272653 scopus 로고    scopus 로고
    • Structural biology of protein tyrosine kinases
    • DOI 10.1007/s00018-006-6202-8
    • Cowan-Jacob, S. W. Structural biology of protein tyrosine kinases Cell. Mol. Life Sci. 2006, 22, 2608-2625 (Pubitemid 44800715)
    • (2006) Cellular and Molecular Life Sciences , vol.63 , Issue.22 , pp. 2608-2625
    • Cowan-Jacob, S.W.1
  • 22
    • 41349106585 scopus 로고    scopus 로고
    • Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
    • DOI 10.1007/s10822-007-9163-6
    • Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-What can we learn from earlier mistakes? J. Comput.-Aided Mol. Des. 2008, 3, 213-228 (Pubitemid 351447959)
    • (2008) Journal of Computer-Aided Molecular Design , vol.22 , Issue.3-4 , pp. 213-228
    • Kirchmair, J.1    Markt, P.2    Distinto, S.3    Wolber, G.4    Langer, T.5
  • 24
    • 74049133612 scopus 로고    scopus 로고
    • Optimal assignment methods for ligand-based virtual screening
    • Jahn, A.; Hinselmann, G.; Fechner, N.; Zell, A. Optimal assignment methods for ligand-based virtual screening J. Cheminf. 2009, 1, 14-37
    • (2009) J. Cheminf. , vol.1 , pp. 14-37
    • Jahn, A.1    Hinselmann, G.2    Fechner, N.3    Zell, A.4
  • 25
    • 70349373859 scopus 로고    scopus 로고
    • Combining docking with pharmacophore filtering for improved virtual screening
    • Peach, M. L.; Nicklaus, M. C. Combining docking with pharmacophore filtering for improved virtual screening J. Cheminf. 2009, 1, 6-21
    • (2009) J. Cheminf. , vol.1 , pp. 6-21
    • Peach, M.L.1    Nicklaus, M.C.2
  • 27
    • 41349122416 scopus 로고    scopus 로고
    • Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?
    • Good, A. C.; Oprea, T. I. Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J. Comput.-Aided Mol. Des. 2008, 3, 169-178
    • (2008) J. Comput.-Aided Mol. Des. , vol.3 , pp. 169-178
    • Good, A.C.1    Oprea, T.I.2
  • 28
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for evaluation of computational methods
    • Jain, A. N.; Nicholls, A. Recommendations for evaluation of computational methods J. Comput.-Aided Mol. Des. 2008, 3, 133-139
    • (2008) J. Comput.-Aided Mol. Des. , vol.3 , pp. 133-139
    • Jain, A.N.1    Nicholls, A.2
  • 29
    • 66249144110 scopus 로고    scopus 로고
    • Better than Random? the Chemotype Enrichment Problem
    • Mackey, M. D.; Melville, J. L. Better than Random? The Chemotype Enrichment Problem J. Chem. Inf. Model. 2009, 5, 1154-1162
    • (2009) J. Chem. Inf. Model. , vol.5 , pp. 1154-1162
    • MacKey, M.D.1    Melville, J.L.2
  • 30
    • 17144385534 scopus 로고    scopus 로고
    • Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
    • DOI 10.1021/jm049092j
    • Triballeau, N.; Acher, F.; Brabet, I.; Pin, J. P.; Bertrand, H. O. Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4 J. Med. Chem. 2005, 7, 2534-2547 (Pubitemid 40520517)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.-P.4    Bertrand, H.-O.5
  • 31
    • 41349102961 scopus 로고    scopus 로고
    • Evaluating docking programs: Keeping the playing field level
    • Liebeschuetz, J. W. Evaluating docking programs: keeping the playing field level J. Comput.-Aided Mol. Des. 2008, 3, 229-238
    • (2008) J. Comput.-Aided Mol. Des. , vol.3 , pp. 229-238
    • Liebeschuetz, J.W.1
  • 32
    • 41349090342 scopus 로고    scopus 로고
    • Can we use docking and scoring for hit-to-lead optimization?
    • Enyedy, I. J.; Egan, W. J. Can we use docking and scoring for hit-to-lead optimization? J. Comput.-Aided Mol. Des. 2008, 3, 161-168
    • (2008) J. Comput.-Aided Mol. Des. , vol.3 , pp. 161-168
    • Enyedy, I.J.1    Egan, W.J.2
  • 34
    • 33750981540 scopus 로고    scopus 로고
    • Do structurally similar ligands bind in a similar fashion?
    • DOI 10.1021/jm060167o
    • Bostrom, J.; Hogner, A.; Schmitt, S. Do structurally similar ligands bind in a similar fashion? J. Med. Chem. 2006, 23, 6716-6725 (Pubitemid 44749739)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.23 , pp. 6716-6725
    • Bostrom, J.1    Hogner, A.2    Schmitt, S.3
  • 35
    • 37649009919 scopus 로고    scopus 로고
    • Molecule-pharmacophore superpositioning and pattern matching in computational drug design
    • Wolber, G.; Seidel, T.; Bendix, F.; Langer, T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design Drug Discovery Today 2008, 13, 23-29
    • (2008) Drug Discovery Today , vol.13 , pp. 23-29
    • Wolber, G.1    Seidel, T.2    Bendix, F.3    Langer, T.4
  • 37
    • 33847207834 scopus 로고    scopus 로고
    • Molecular similarity analysis in virtual screening: Foundations, limitations and novel approaches
    • Eckert, H.; Bajorath, J. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches Drug Discovery Today 2007, 5-6, 225-233
    • (2007) Drug Discovery Today , vol.56 , pp. 225-233
    • Eckert, H.1    Bajorath, J.2
  • 38
    • 61349117968 scopus 로고    scopus 로고
    • The importance of discerning shape in molecular pharmacology
    • Kortagere, S.; Krasowski, M. D.; Ekins, S. The importance of discerning shape in molecular pharmacology Trends Pharmacol. Sci. 2009, 3, 138-147
    • (2009) Trends Pharmacol. Sci. , vol.3 , pp. 138-147
    • Kortagere, S.1    Krasowski, M.D.2    Ekins, S.3
  • 39
    • 33751313329 scopus 로고    scopus 로고
    • Knowledge-based chemoinformatic approaches to drug discovery
    • DOI 10.1016/j.drudis.2006.10.012, PII S1359644606004338
    • Ghose, A. K.; Herbertz, T.; Salvino, J. M.; Mallamo, J. P. Knowledge-based chemoinformatic approaches to drug discovery Drug Discovery Today 2006, 23-24, 1107-1114 (Pubitemid 44803112)
    • (2006) Drug Discovery Today , vol.11 , Issue.23-24 , pp. 1107-1114
    • Ghose, A.K.1    Herbertz, T.2    Salvino, J.M.3    Mallamo, J.P.4
  • 41
    • 33947594733 scopus 로고    scopus 로고
    • Pharmacophore modeling and in silico screening for new KDR kinase inhibitors
    • DOI 10.1016/j.bmcl.2007.01.089, PII S0960894X0700162X
    • Yu, H.; Wang, Z.; Zhang, L.; Zhang, J.; Huang, Q. Pharmacophore modeling and in silico screening for new KDR kinase inhibitors Bioorg. Med. Chem. Lett. 2007, 8, 2126-2133 (Pubitemid 46484321)
    • (2007) Bioorganic and Medicinal Chemistry Letters , vol.17 , Issue.8 , pp. 2126-2133
    • Yu, H.1    Wang, Z.2    Zhang, L.3    Zhang, J.4    Huang, Q.5
  • 45
    • 49449117755 scopus 로고    scopus 로고
    • Discovery of 5-[[4-[(2,3-Dimethyl-2 H -indazol-6-yl)methylamino]-2- pyrimidinyl]amino]-2-methylbenzenesulfonamide (Pazopanib), a Novel and Potent Vascular Endothelial Growth Factor Receptor Inhibitor
    • Harris, P. A.; Boloor, A.; Cheung, M.; Kumar, R.; Crosby, R. M.; Davis-Ward, R. G.; Epperly, A. H.; Hinkle, K. W.; Hunter, R. N., III; Johnson, J. H. Discovery of 5-[[4-[(2,3-Dimethyl-2 H -indazol-6-yl)methylamino]-2- pyrimidinyl]amino]-2-methylbenzenesulfonamide (Pazopanib), a Novel and Potent Vascular Endothelial Growth Factor Receptor Inhibitor J. Med. Chem. 2008, 15, 4632-4640
    • (2008) J. Med. Chem. , vol.15 , pp. 4632-4640
    • Harris, P.A.1    Boloor, A.2    Cheung, M.3    Kumar, R.4    Crosby, R.M.5    Davis-Ward, R.G.6    Epperly, A.H.7    Hinkle, K.W.8    Hunter III, R.N.9    Johnson, J.H.10
  • 47
    • 34447308503 scopus 로고    scopus 로고
    • In-silico fragment-based identification of novel angiogenesis inhibitors
    • DOI 10.1016/j.bmcl.2007.05.104, PII S0960894X07006725
    • Dakshanamurthy, S.; Kim, M.; Brown, M. L.; Byers, S. W. In-silico fragment-based identification of novel angiogenesis inhibitors Bioorg. Med. Chem. Lett. 2007, 16, 4551-4556 (Pubitemid 47058948)
    • (2007) Bioorganic and Medicinal Chemistry Letters , vol.17 , Issue.16 , pp. 4551-4556
    • Dakshanamurthy, S.1    Kim, M.2    Brown, M.L.3    Byers, S.W.4
  • 48
    • 34547661861 scopus 로고    scopus 로고
    • Comparative performance of several flexible docking programs and scoring functions: Enrichment studies for a diverse set of pharmaceutically relevant targets
    • DOI 10.1021/ci7000346
    • Zhou, Z.; Felts, A. K.; Friesner, R. A.; Levy, R. M. Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets J. Chem. Inf. Model. 2007, 4, 1599-1608 (Pubitemid 47210063)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.4 , pp. 1599-1608
    • Zhou, Z.1    Felts, A.K.2    Friesner, R.A.3    Levy, R.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.