A high throughput in vivo assay for taste quality and palatability.

Taste quality and palatability are two of the most important properties measured in the evaluation of taste stimuli. Human panels can report both aspects, but are of limited experimental flexibility and throughput capacity. Relatively efficient animal models for taste evaluation have been developed, but each of them is designed to measure either taste quality or palatability as independent experimental endpoints.

Pharmacologic antagonism of the oral aversive taste-directed response to capsaicin in a mouse brief access taste aversion assay.

Chemosensory signaling by the tongue is a primary determinant of ingestive behavior and is mediated by specific interactions between tastant molecules and G protein-coupled and ion channel receptors. The functional relationship between tastant and receptor should be amenable to pharmacologic methods and manipulation. We have performed a pharmacologic characterization of the taste-directed licking of mice presented with solutions of capsaicin and other transient receptor potential vanilloid-1 (TRPV1) agonists using a brief access taste aversion assay.

Quantitative assessment of TRPM5-dependent oral aversiveness of pharmaceuticals using a mouse brief-access taste aversion assay.

Many orally administered pharmaceuticals are regarded by humans as aversive, most often described as 'bitter'. Taste aversiveness often leads to patient noncompliance and reduced treatment effectiveness. 'Bitter' taste is mediated by T2R G-protein coupled receptors through a peripheral signaling pathway critically dependent upon function of the TRPM5 ion channel.

A comparison of the chemical properties of drugs and FEMA/FDA notified GRAS chemical compounds used in the food industry.

The range of molecular properties of generally recognized as safe (GRAS) compounds that are typically used in food and beverage products is compared to marketed drugs. It is observed that GRAS compounds differ from marketed drugs with respect to several molecular descriptors, including molecular weight, H-bond acceptor count, H-bond donor count, aromatic ring count, basic group count, acidic group count, molecular flexibility, enhanced ether and ester bearing compound populations, and reduced nitrogen and halogen bearing compound populations. It was observed that log(P) and log(S), which provide computed estimates of compound solubility in organic and aqueous solvents, respectively, have significant overlap in the two populations.

Thermodynamic stability of carbonic anhydrase: measurements of binding affinity and stoichiometry using ThermoFluor.

ThermoFluor (a miniaturized high-throughput protein stability assay) was used to analyze the linkage between protein thermal stability and ligand binding. Equilibrium binding ligands increase protein thermal stability by an amount proportional to the concentration and affinity of the ligand. Binding constants (K(b)) were measured by examining the systematic effect of ligand concentration on protein stability.

Decrypting the biochemical function of an essential gene from Streptococcus pneumoniae using ThermoFluor technology.

The protein product of an essential gene of unknown function from Streptococcus pneumoniae was expressed and purified for screening in the ThermoFluor affinity screening assay. This assay can detect ligand binding to proteins of unknown function. The recombinant protein was found to be in a dimeric, native-like folded state and to unfold cooperatively.

Chemical genomics as an emerging paradigm for postgenomic drug discovery.

Chemical genomics approaches are evolving to overcome key problems limiting the efficiency of drug discovery in the postgenomic era. Many of these stem from the low success rates in finding drugs for novel genomics targets whose biochemical properties and therapeutic relevance is poorly understood. The fundamental objective of chemical genomics is to find and optimize chemical compounds that can be used to directly test the therapeutic relevance of new targets revealed through genome sequencing.

Applications of calorimetric methods to drug discovery and the study of protein interactions.

Recent studies report the application of isothermal titration calorimetry and differential scanning calorimetry to the study of protein-ligand interactions, allosteric cooperativity and aspects of protein folding. New methods of data analysis compare alternative methods for determining ligand binding enthalpy and analyze potential sources of error in the experimental measurement of other thermodynamic parameters. Several reports examine issues concerning drug design and the correlation of thermodynamic and X-ray structural data.

Combinatorial informatics in the post-genomics ERA.

The multitude of potential drug targets emerging from genome sequencing demands new approaches to drug discovery. A chemogenomics strategy, which involves the generation of small-molecule compounds that can be used both as tools to probe biological mechanisms and as leads for drug-property optimization, provides a highly parallel, industrialized solution. Key to the success of this strategy is an integrated suite of chemi-informatics applications that can allow the rapid and directed optimization of chemical compounds with drug-like properties using 'just-in-time' combinatorial chemical synthesis.

High-density miniaturized thermal shift assays as a general strategy for drug discovery.

More general and universally applicable drug discovery assay technologies are needed in order to keep pace with the recent advances in combinatorial chemistry and genomics-based target generation. Ligand-induced conformational stabilization of proteins is a well-understood phenomenon in which substrates, inhibitors, cofactors, and even other proteins provide enhanced stability to proteins on binding. This phenomenon is based on the energetic coupling of the ligand-binding and protein-melting reactions.

Non-peptidic phenyl-based thrombin inhibitors: exploring structural requirements of the S1 specificity pocket with amidines.

We expand the structural requirements and structure-activity relationship of a novel class of non-peptidic aryl-based thrombin inhibitors through exploration of the S1 specificity pocket of thrombin using flexible and constrained amidines. The most active compound of this class is 11 with Ki = 69 nM, which is ca. 15-fold less potent than constrained guanidine 5.

Structure-activity and crystallographic analysis of a new class of non-amide-based thrombin inhibitor.

The structure activity relationships of a novel series of non-amide-based thrombin inhibitors are described. Exploration of the P2 and the aryl binding region for this series has identified optimal groups for achieving nanomolar potency. The binding modes of these optimal groups have been confirmed by X-ray structural analysis.

Amidinohydrazones as guanidine bioisosteres: application to a new class of potent, selective and orally bioavailable, non-amide-based small-molecule thrombin inhibitors.

We describe a new class of potent, non-amide-based small molecule thrombin inhibitors in which an amidinohydrazone is used as a guanidine bioisostere on a non-peptide scaffold. Compound 4 exhibits nM inhibition of thrombin, is selective for thrombin, and shows 60 and 23% bioavailability in rabbits and dogs, respectively. Crystallographic analysis of 4 bound to thrombin confirmed the amindinohydrazone binding mode.

Advances in diversity profiling and combinatorial series design.

Rapid advances in synthetic and screening technology have recently enabled the simultaneous synthesis and biological evaluation of large chemical libraries containing hundreds to tens of thousands of compounds, using molecular diversity as a means to design and prioritize experiments. This paper reviews some of the most important computational work in the field of diversity profiling and combinatorial library design, with particular emphasis on methodology and applications. It is divided into four sections that address issues related to molecular representation, dimensionality reduction, compound selection, and visualization.

In vitro evaluation and crystallographic analysis of a new class of selective, non-amide-based thrombin inhibitors.

We describe the in vitro evaluation and crystallographic analysis of a new class of potent and selective, non-amino acid-based, small-molecule thrombin inhibitors, exemplified by 14. This class of achiral inhibitors lacks an amide-based backbone, exhibits nM inhibition of thrombin, and is selective for thrombin. Compound 14 does not interact with the active-site catalytic apparatus and is anchored to the enzyme via a single network of hydrogen bonds to Asp189 of the S1 pocket.

Serendipity meets precision: the integration of structure-based drug design and combinatorial chemistry for efficient drug discovery.

Structure-based drug design uses three-dimensional visualization of drug candidates bound to a target receptor to direct structural modifications that increase potency. This widely used approach is limited by the difficulty of accurately predicting drug-binding affinities from three-dimensional structures. The integration of structure-based drug design with combinatorial chemistry can overcome this limitation by providing an empirical understanding of drug-binding energies.

Crystallographic and thermodynamic comparison of structurally diverse molecules binding to streptavidin.

Crystallographic structures and thermodynamic binding parameters are compared for three structural classes of streptavidin ligand including d-biotin, 2-[(4'-hydroxyphenyl)-azo] benzoate and the peptide NH(2)-Phe-Ser-His-Pro-Gln-Asn-Thr-COOH. Descriptions of these structural and thermodynamic observations emphasize the diversity of potential strategies for improving ligand affinity.

Structural studies of the retroviral proteinase from avian myeloblastosis associated virus.

The structure of the retroviral proteinase from avian myeloblastosis associated virus (MAV) has been determined and refined at 2.2 A resolution. This structure is compared with those of homologous proteinases from Rous sarcoma virus (RSV) and human immunodeficiency type 1 virus (HIV).

Protein engineering for molecular electronics.

Recombinant DNA technology allows the manipulation of the physical properties of proteins that perform electron transport and photochemical processes. Recent work is reviewed that has a potential impact on the development of molecular electronic devices, within a general framework outlining strategies for device fabrication. This review is also published in Current Opinion in Structural Biology 1992, 2:587-592.

Permuteins of interleukin 1 beta--a simplified approach for the construction of permutated proteins having new termini.

A technique for the rapid and simple generation of permutated versions of the interleukin-1 beta (IL-1 beta) gene is described. In this method, the human IL-1 beta cDNA is twice amplified by the polymerase chain reaction (PCR) and the resulting DNA fragments are ligated in tandem. Between the two genes, the DNA sequence encodes a short four amino acid loop to link the native N- and C-terminal ends of the IL-1 beta protein.

PROBIT: a statistical approach to modeling proteins from partial coordinate data using substructure libraries.

A program (PROBIT) has been developed that allows the reconstruction of a complete set of three-dimensional protein coordinates from alpha-carbon coordinates. The program generates a statistical measure of polypeptide conformational behavior for substructures in a defined structural context from a library of highly refined protein structures. These statistics provide a prescription for substructure substitution from the database to allow regeneration of the complete protein structure.

Crystallographic refinement of bovine pro-phospholipase A2 at 1.6 A resolution.

Bovine pro-phospholipase A2 (Mr = 14,520), trigonal, P3(1)21, a = b = 46.5, c = 102.0 A, one molecule per asymmetric unit, lambda (Cu K alpha) = 1.

The identification of tyrosine as a common key residue in unrelated H-2Kd restricted antigenic peptides.

We have compared the activity of several Kd- or Ld-restricted antigenic peptides as competitors in a functional competition assay using cytolytic T lymphocyte (CTL) clones. All of four unrelated Kd-restricted peptides tested could compete with each other but not with the Ld-restricted peptide P91A-. 12-24 (P91A).

An independent crystallographic refinement of porcine phospholipase A2 at 2.4 A resolution.

Porcine phospholipase A2 (Mr = 13,980), trigonal, P3(1)21, a = b = 69.4, c = 70.4 A, one molecule per asymmetric unit, lambda (Cu K alpha) = 1.