Deciphering cryptic similarities in protein binding sites.

Rapid expansion in the number of plausible drug targets arising from genomics research has created new pressures for increased efficiency in discovery of high specificity candidate drug compounds. Improved understanding of conserved features among protein structures provides a promising route to achieving this goal. Indirect evidence implies that important similarities are now ripe for elucidation by emerging experimental approaches.

[1]  I D Kuntz,et al.  Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. , 1997, Chemistry & biology.

[2]  R. M. Williamson.  Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. , 1995, Journal of theoretical biology.

[3]  M. Lyttle.  Combinatorial chemistry: A conservative perspective , 1995 .

[4]  F. LaBella.  Molecular basis for binding promiscuity of antagonist drugs. , 1991, Biochemical pharmacology.

[5]  I D Kuntz,et al.  Predicting the structure of protein complexes: a step in the right direction. , 1996, Chemistry & biology.

[6]  H O Villar,et al.  Amino acid preferences at protein binding sites , 1994, FEBS letters.

[7]  Robert D Clark,et al.  Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. , 1996, Journal of medicinal chemistry.

[8]  Cecilia Holm,et al.  Hormone-sensitive Lipase Is Structurally Related to Acetylcholinesterase, Bile Salt-stimulated Lipase, and Several Fungal Lipases , 1996, The Journal of Biological Chemistry.

[9]  P. Vyas,et al.  The mode of action of aspirin-like drugs: effect on inducible nitric oxide synthase. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[10]  W. Punch,et al.  Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. , 1997, Journal of molecular biology.

[11]  E. Seidemann,et al.  Probability model for molecular recognition in biological receptor repertoires: significance to the olfactory system. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Yvonne C. Martin,et al.  Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection , 1996, J. Chem. Inf. Comput. Sci..

[13]  M J Sippl,et al.  Optimum superimposition of protein structures: ambiguities and implications. , 1996, Folding & design.

[14]  M. Murakami.  Critical amino acids responsible for converting specificities of proteins and for enhancing enzyme evolution are located around β-turn potentials: Data-based prediction , 1993, Journal of protein chemistry.

[15]  Daniel A. Gschwend,et al.  Molecular docking towards drug discovery , 1996, Journal of molecular recognition : JMR.

[16]  S. L. Mayo,et al.  Probing the role of packing specificity in protein design. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  N. Go,et al.  A method to search for similar protein local structures at ligand-binding sites and its application to adenine recognition , 1997, European Biophysics Journal.

[18]  H. Villar,et al.  Glubodies: randomized libraries of glutathione transferase enzymes. , 1996, Chemistry & biology.

[19]  J. Berg,et al.  A direct comparison of the properties of natural and designed zinc-finger proteins. , 1995, Chemistry & biology.

[20]  H. Villar,et al.  Novel procedure for structure refinement in homology modeling and its application to the human class Mu glutathione S-transferases. , 1994, Protein engineering.

[21]  W. Smith,et al.  Selective inhibition of prostaglandin endoperoxide synthase-1 (cyclooxygenase-1) by valerylsalicylic acid. , 1995, Archives of biochemistry and biophysics.

[22]  Colin McMartin,et al.  QXP: Powerful, rapid computer algorithms for structure-based drug design , 1997, J. Comput. Aided Mol. Des..

[23]  S. Schreiber,et al.  Small molecule-dependent genetic selection in stochastic nanodroplets as a means of detecting protein-ligand interactions on a large scale. , 1997, Chemistry & biology.

[24]  W. Gilbert,et al.  How big is the universe of exons? , 1990, Science.

[25]  F. Luscinskas,et al.  Salicylates inhibit I kappa B-alpha phosphorylation, endothelial-leukocyte adhesion molecule expression, and neutrophil transmigration. , 1996, Journal of immunology.

[26]  A. Goldman,et al.  Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein , 1991, Science.

[27]  Ajay N. Jain.  Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities , 1996, J. Comput. Aided Mol. Des..

[28]  I. Kuntz,et al.  Molecular similarity based on DOCK-generated fingerprints. , 1996, Journal of medicinal chemistry.

[29]  C. Crews.  Deciphering isozyme function: exploring cell biology with chemistry in the post-genomic era. , 1996, Chemistry & biology.

[30]  S. Subramaniam,et al.  Computer-aided molecular modeling of the binding site architecture for eight monoclonal antibodies that bind a high potency guanidinium sweetener. , 1994, Journal of molecular graphics.

[31]  D Eisenberg,et al.  A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. , 1997, Journal of molecular biology.

[32]  H O Villar,et al.  Ligand‐based protein alignment and isozyme specificity of glutathione S‐transferase inhibitors , 1997, Proteins.

[33]  L. Pearl.  Similarity of active-site structures , 1993, Nature.

[34]  J. Thornton,et al.  Protein recognition of adenylate: an example of a fuzzy recognition template. , 1996, Journal of molecular biology.

[35]  P. Hajduk,et al.  Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.

[36]  H O Villar,et al.  Protein affinity map of chemical space. , 1998, Journal of chromatography. B, Biomedical sciences and applications.

[37]  L. Gold,et al.  Post-SELEX combinatorial optimization of aptamers. , 1997, Bioorganic & medicinal chemistry.

[38]  R. Jackson,et al.  Update on computer-aided drug design. , 1995, Current opinion in biotechnology.

[39]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[40]  Mutagenesis using trinucleotide beta-cyanoethyl phosphoramidites. , 1995, BioTechniques.

[41]  Suppression of P450IIC12 gene expression and elevation of actin messenger ribonucleic acid levels in the livers of female rats after injection of the interferon inducer poly rI.poly rC. , 1991, Biochemical pharmacology.

[42]  Gennady M Verkhivker,et al.  Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[43]  G. Bemis,et al.  The properties of known drugs. 1. Molecular frameworks. , 1996, Journal of medicinal chemistry.

[44]  David M. Rocke,et al.  Predicting ligand binding to proteins by affinity fingerprinting. , 1995, Chemistry & biology.