Design of virtual libraries of umami-tasting molecules

Bioactive and Sensory Di- and Tripeptides Generated during Dry-Curing of Pork Meat

Dry-cured pork products, such as dry-cured ham, undergo an extensive proteolysis during manufacturing process which determines the organoleptic properties of the final product. As a result of endogenous pork muscle endo- and exopeptidases, many medium- and short-chain peptides are released from muscle proteins. Many of them have been isolated, identified, and characterized, and some peptides have been reported to exert relevant bioactivity with potential benefit for human health. However, little attention has been given to di- and tripeptides, which are far less known, although they have received increasing attention in recent years due to their high potential relevance in terms of bioactivity and role in taste development. This review gathers the current knowledge about di- and tripeptides, regarding their bioactivity and sensory properties and focusing on their generation during long-term processing such as dry-cured pork meats.

Toxicology studies with N-acetylglycine

N-acetylglycine (NAGly) has been identified as a minor constituent of numerous foods. The current paper reports the outcome of in vitro and in vivo genotoxicity, acute oral and repeated dose dietary toxicology studies conducted with NAGly. No evidence of genotoxicity was observed with NAGly in vitro bacterial tester strains or in vivo bone marrow micronucleus studies conducted in mice. No mortalities or evidence of adverse effects were observed in Sprague-Dawley rats following acute oral gavage with NAGly at a dose of 2000 mg/kg of body weight or following repeated dose dietary exposure to NAGly at targeted doses of 100, 500, or 1000 mg/kg of body weight/day for 28 days. No biologically significant or test substance related differences were observed in body weights, feed consumption, or clinical pathology response variables in any of the treatment groups. Based on these results it was concluded that NAGly is not genotoxic or acutely toxic. Further, the no-observed adverse-effect-level (NOAEL) for systemic toxicity from repeated dose dietary exposure to NAGly was 898.9 mg/kg of body weight/day for male rats and 989.9 mg/kg of body weight/day for female rats.

Assessing the Predictive Power of Unsupervised Visualization Techniques to Improve the Identification of GPCR-Focused Compound Libraries

Principal component analysis and self-organizing maps (SOMs) were compared to cluster and visualize the chemical space of a large and diverse data set. The data set comprised about 3000 G-protein-coupled receptor (GPCR) ligands for about 130 receptors and 3000 non-GPCR ligands from the World Drug Index. The molecules were described with a topological pharmacophore point histogram descriptor and a chemical fingerprint descriptor. To assess the predictive power of the clustering, a leave-multiple-out cross validation with k nearest neighbor classification was performed. The results of the classification tests and the visualization showed a clear superiority of the SOM method. SOM correctly divided the data set into two main clusters, one for the GPCR and the other for the non-GPCR ligands. Our results suggest that a continuous GPCR-ligand space exists.

Chemical Boundaries for Detection of Eye Irritation in Humans from Homologous Vapors

In a series of experiments, we looked at a "cutoff" effect for the detection of eye irritation from neat vapors of homologous n-alkylbenzenes and 2-ketones. Stimuli comprised pentyl, hexyl, and heptyl benzene, 2-dodecanone, and 2-tridecanone, presented to each eye at 4 and 8 l/min for 6 sec, using a three-alternative forced-choice procedure against blanks. Detection probability corrected for chance (i.e., detectability) decreased with carbon chain length such that heptyl benzene and 2-tridecanone were virtually undetectable, irrespective of flow rate to the eye. Heating both stimuli sources to 37 degrees C (body temperature) from 23 degrees C (room temperature) increased vapor concentration by 5.0 and 6.9 times, respectively, for heptyl benzene and 2-tridecanone. Still, both chemicals failed to show increased detection for 13 of the 21 participants. In addition, plots of experimentally measured and calculated eye irritation thresholds as a function of carbon chain length for each series indicated that, based on the trend, the concentration of the two cutoff homologs at 37 degrees C should have been high enough to allow detection. Taken together, the results suggest that these cutoffs rest on limitations related to the dimension of the molecules rather than on limitations related to their vapor concentration. For example, the stimulus molecule could exceed the size that allows it to fit into the receptor pocket of a receptive protein. Plots of calculated molecular dimensions across homologous alkylbenzenes, from ethyl to dodecylbenzene, and across 2-ketones, from 2-octanone to 2-octadecanone, provided additional support to the above conclusion.

Descriptor-based protein remote homology identification

Here, we report a novel protein sequence descriptor-based remote homology identification method, able to infer fold relationships without the explicit knowledge of structure. In a first phase, we have individually benchmarked 13 different descriptor types in fold identification experiments in a highly diverse set of protein sequences. The relevant descriptors were related to the fold class membership by using simple similarity measures in the descriptor spaces, such as the cosine angle. Our results revealed that the three best-performing sets of descriptors were the sequence-alignment-based descriptor using PSI-BLAST e-values, the descriptors based on the alignment of secondary structural elements (SSEA), and the descriptors based on the occurrence of PROSITE functional motifs. In a second phase, the three top-performing descriptors were combined to obtain a final method with improved performance, which we named DescFold. Class membership was predicted by Support Vector Machine (SVM) learning. In comparison with the individual PSI-BLAST-based descriptor, the rate of remote homology identification increased from 33.7% to 46.3%. We found out that the composite set of descriptors was able to identify the true remote homolog for nearly every sixth sequence at the 95% confidence level, or some 10% more than a single PSI-BLAST search. We have benchmarked the DescFold method against several other state-of-the-art fold recognition algorithms for the 172 LiveBench-8 targets, and we concluded that it was able to add value to the existing techniques by providing a confident hit for at least 10% of the sequences not identifiable by the previously known methods.