Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment

Journal of Biomedical Materials Research - Part B Applied Biomaterials

Volumn 88, Issue 2, 2009, Pages 447-457

  Vaidyanathan, J ^a   Vaidyanathan, T K ^a   Ravichandran, S ^b  

^a RUTGERS SCHOOL OF DENTAL MEDICINE   (United States)

^b SAIC FREDERICK INC   (United States)

Author keywords

Adhesion; Collagen; Computer modeling simulation; Dental craniofacial material; Tissue adhesion

Indexed keywords

ADHESIVE LIGANDS; BINDING INTERACTIONS; CHEMICAL FUNCTIONS; COMPUTER MODELING/SIMULATION; DENTAL/CRANIOFACIAL MATERIAL; DENTIN ADHESIVES; DENTIN BONDINGS; DOCKING SIMULATIONS; EXPERIMENTAL EVALUATIONS; HYDROPHILIC MONOMERS; INTER-MOLECULAR INTERACTIONS; LOW-ENERGY CONFORMATIONS; PHARMACOPHORE MODELS; TISSUE ADHESION; VIRTUAL SCREENINGS;

ADHESION; ALIGNMENT; BINDING ENERGY; BIOLOGICAL MATERIALS; BIOMATERIALS; CHEMICAL ANALYSIS; COLLAGEN; DOCKING; HYDROPHILICITY; LIGANDS; MONOMERS; TARGETS; THREE DIMENSIONAL;

CONFORMATIONS;

COLLAGEN; DENTIN BONDING AGENT; LIGAND; MONOMER;

ANALYTIC METHOD; ARTICLE; COMPUTER SIMULATION; CONFORMATION; DENTIN; ENERGY; HYDROPHILICITY; MOLECULAR DOCKING; MOLECULAR INTERACTION; PHARMACOPHORE; SCREENING;

COMPUTER SIMULATION; DENTIN; HUMANS; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, ELECTRON, SCANNING; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE;

EID: 60849120756     PISSN: 15524973     EISSN: 15524981     Source Type: Journal    
DOI: 10.1002/jbm.b.31134     Document Type: Article

References (20)

1. Nakabayashi N, Pashley DH. Hybridization of Dental Hard Tissues. Chicago: Quintessence Publishing Co.; 1998. pp 37-83.
2. Vaidyanathan J, Kasinathan C, Vaidyanathan TK. Biomimetic recognition and immunochemical binding assay of collagen-ligand binding. J Adhes Dent 2003;5:7-17.
3. Ehrlich P. Ueber den jetztigen Stand der Chemotherapie. Berichte der Deutschen chemischen Gesellschaft (Reports of the German Chemical Society) 1909;42:17-47.
4. Gund P. Three-dimensional pharmacaphore pattern searching. Prog Mol Subcell Biol 1977;5:117-143.
5. Milne GWA. Pharmacophore and drug discovery. In: Schleyer PvR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF III, Schreiner PR, editors. Encyclopedia of Computational Chemistry, Vol. 3. Chichester (UK): Wiley; 1998. pp 2046-2056.
6. Dror O, Shulman-Peleg A, Nussinov R, Wolfson HJ. Predicting molecular interactions in silico. I. A guide to pharmaco-phore identification and its applications to drug design. Curr Med Chem 2004;11:71-90.
7. Miller MD. Molecular superposition. In: Schleyer PvR, Allin-ger NL, Clark T, Gasteiger J, Kollman PA, Schaefer HF III, Schreiner PR, editors. Encyclopedia of Computational Chemistry, Vol. 3. Chichester (UK): Wiley; 1998. pp 1693-1697.
8. Marshall G, Barry C, Bosshard H, Dammkoehler R, Dunn D. The conformational parameter in drug design: The active analog approach. In: Olson E, Christoffersen R, editors. Computer-Assisted Drug Design. Washington DC: American Chemical Society; 1979. pp 205-226.
9. Beusen DD, Marshall GR. Pharmacophore definition using the active analog approach. In: Guner OF, editor. Pharmacophore Perception, Development, and Use in Drug Design. La Jolla: International University Line; 2000. pp 21-45.
10. Guner OF. History and evolution of the pharmacophore concept in computer-aided drug design. Curr Top Med Chem 2002;2:1321-1332.
11. Vaidyanathan J, Vaidyanathan TK, Ramasubbu N, Ravichan-dran S. A computational and experimental analysis of ligand binding to type 1 collagen. Curr Comput Aided Drug Des 2005;1:397-422.
12. Clement O, Mehl AT. HipHop: Pharmacophores based on multiple common-feature alignments. In: Guner OF, editor. Phar-macophore Perception, Development, and Use in Drug Design. La Jolla: International University Line; 2000. pp 71-84.
13. Li H, Sutter J, Hoffmann R. HypoGen: An automated system for generating 3D predictive pharmacophore models. In: Guner OF, editor. Pharmacophore Perception, Development, and Use in Drug Design. La Jolla: International University Line; 2000. pp 171-189.
14. Sutter J, Güner OF, Hoffmann R, Li H, Waldman M. Effect of variable weights and tolerances on predictive model generation. In: Guner OF, editor. Pharmacophore Perception, Development, and Use in Drug Design. La Jolla: International University Line; 2000. pp 499-511.
15. B rooks BR, Bruccoleri RE, Olafson BD, States DJ, Swamina-than S, Karplus M. CHARMM: A program for macromolecu-lar energy minimization and dynamics calculations. J Comput Chem 1983;4:187-217.
16. Smellie A, Teig SL, Towbin P. Poling: Promoting conforma-tional variation. J Comput Chem 1995;16:171-187.
17. Vaidyanathan J, Vaidyanathan TK, Kerrigan J. Evaluation of intermolecular interactions of self-etch dentin adhesive primer molecules with type 1 collagen: Computer modeling and in vitro binding analysis. Acta Biomaterialia 2007;3:705-714.
18. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
19. Namork E, Heier HE. Silver enhancement of gold probes (540 nm): Single and double labeling of antigenic sites on cell surfaces imaged with backscattered electrons. J Electron Microsc Tech 1988;11:102-108.
20. Hacker GW, Gu J. Gold and Silver Staining: Techniques in Molecular Staining Morphology. Advances in Pathology Microscopy and Molecular Morphology Series. Boca Raton: CRC Press; 2002.