Design of Virtual Libraries of Umami-Tasting Molecules

The introduction of molecular tools in food research offers the possibility to the food industry to benefit from the experience gained in the field by pharmaceutical companies. In this work we are showing how in silico virtual screening techniques based on molecular similarity were applied for identifying novel umami-tasting compounds. The results obtained suggest that 5'-ribonucleotides and monosodium glutamate might elicit the fifth basic taste via the same molecular mechanism. New algorithms were developed and used in this work, such as the dimension reduction of data sets by singular value decomposition and the introduction of the correlation dimension as a natural dimension of a chemical space. It is shown that the representations of molecular data sets in chemical spaces possess self-similar properties, characteristic of fractal objects.

[1]  A. H. A. Oord,et al.  Umami peptides: assessment of their alleged taste properties , 1997 .

[2]  Leonard A. Smith,et al.  Monte Carlo SSA: Detecting irregular oscillations in the Presence of Colored Noise , 1996 .

[3]  Tamar Schlick,et al.  An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization , 2000, J. Chem. Inf. Comput. Sci..

[4]  Jayaram Chandrashekar,et al.  An amino-acid taste receptor , 2002, Nature.

[5]  H Matter,et al.  Random or rational design? Evaluation of diverse compound subsets from chemical structure databases. , 1998, Journal of medicinal chemistry.

[6]  N. Chaudhari,et al.  A metabotropic glutamate receptor variant functions as a taste receptor , 2000, Nature Neuroscience.

[7]  C. Southan,et al.  The impact of genomics on drug discovery. , 2000, Progress in medicinal chemistry.

[8]  M. Clifford,et al.  Apparent molar volumes and tastes of molecules with more than one sapophore , 1987 .

[9]  P. Grassberger,et al.  Characterization of Strange Attractors , 1983 .

[10]  E. Kikuchi,et al.  The Relationship between Taste and Primary Structure of “Delicious Peptide” (Lys-Gly-Asp-Glu-Glu-Ser-Leu-Ala) from Beef Soup , 1989 .

[11]  H. Nishizaki,et al.  Synthesis of bitter peptides composed of aspartic acid and glutamic acid. , 1988 .

[12]  G. P. King,et al.  Extracting qualitative dynamics from experimental data , 1986 .

[13]  Hans Matter,et al.  Comparing 3D Pharmacophore Triplets and 2D Fingerprints for Selecting Diverse Compound Subsets , 1999, J. Chem. Inf. Comput. Sci..

[14]  P. Malherbe,et al.  Effect of the umami peptides on the ligand binding and function of rat mGlu4a receptor might implicate this receptor in the monosodium glutamate taste transduction , 1999, British journal of pharmacology.

[15]  C. Eckart,et al.  The approximation of one matrix by another of lower rank , 1936 .

[16]  E. Fluder,et al.  Latent semantic structure indexing (LaSSI) for defining chemical similarity. , 2001, Journal of medicinal chemistry.

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

[18]  H. Matter,et al.  Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors. , 1997, Journal of medicinal chemistry.

[19]  A. Ghose,et al.  Atomic Physicochemical Parameters for Three‐Dimensional Structure‐Directed Quantitative Structure‐Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity , 1986 .

[20]  W. Arnoldi The principle of minimized iterations in the solution of the matrix eigenvalue problem , 1951 .

[21]  T. Landauer,et al.  Indexing by Latent Semantic Analysis , 1990 .

[22]  P. Grassberger,et al.  Measuring the Strangeness of Strange Attractors , 1983 .

[23]  Xiaodong Li,et al.  Human receptors for sweet and umami taste , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  L. Mirsky SYMMETRIC GAUGE FUNCTIONS AND UNITARILY INVARIANT NORMS , 1960 .

[25]  Andreas Buja,et al.  XGobi: Interactive Dynamic Data Visualization in the X Window System , 1998 .

[26]  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..

[27]  William Fisanick,et al.  Similarity searching on CAS Registry substances. 1. Global molecular property and generic atom triangle geometric searching , 1992, J. Chem. Inf. Comput. Sci..

[28]  W. Bremser Hose — a novel substructure code , 1978 .

[29]  C. Lanczos An iteration method for the solution of the eigenvalue problem of linear differential and integral operators , 1950 .

[30]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[31]  Klaus Fraedrich,et al.  Estimating the Dimensions of Weather and Climate Attractors , 1986 .

[32]  S. Arai,et al.  Tastes of L-Glutamyl Oligopeptides in Relation to Their Chromatographic Properties , 1973 .

[33]  F. Bellisle Glutamate and the UMAMI taste: sensory, metabolic, nutritional and behavioural considerations. A review of the literature published in the last 10 years , 1999, Neuroscience & Biobehavioral Reviews.

[34]  E. Schmidt Zur Theorie der linearen und nichtlinearen Integralgleichungen , 1907 .

[35]  S. Arai,et al.  Isolation and identification of acidic oligopeptides occurring in a flavor potentiating fraction from a fish protein hydrolysate. , 1975, Journal of agricultural and food chemistry.