Natural products (NPs) are a rich source of novel compound classes and new drugs. In the present study we have used chemical space navigation tool ChemGPS-NP to evaluate occupancy by NPs bioactive medicinal chemistry compounds from database WOMBAT. The two sets differ notably in coverage space, tangible leadlike were found cover regions that lack representation Property based similarity calculations performed identify NP neighbors approved Several revealed this method confirmed exhibit same...

Natural compounds are evolutionary selected and prevalidated by Nature, displaying a unique chemical diversity corresponding of biological activities. These features make them highly interesting for studies biology, in the pharmaceutical industry development new leads. Of utmost importance, discovery biologically active compounds, is identification charting relevant space. The primary key to this coverage natural products' Here we introduce ChemGPS-NP, tool tuned handling encountered...

Addressing drug-like/lead-like properties of biologically active small molecules early in a lead generation program is the current paradigm within drug discovery community. Lipinski's "rule five" has become most commonly used tool to assess relationship between structures and drug-like properties. Sixty percent 126 140 unique compounds The Dictionary Natural Products had no violations five". We have isolated 814 natural products based on their expected generate product library (NPL) which...

The design of chemical libraries, an early step in agrochemical discovery programs, is frequently addressed by means qualitative physicochemical and/or topological rule-based methods. aim this study to develop quantitative estimates herbicide- (QEH), insecticide- (QEI), fungicide- (QEF), and, finally, pesticide-likeness (QEP). In the assessment these definitions, we relied on concept desirability functions.We found a simple function, shared three classes pesticides, parameterized...

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation assays, identification new starting points for exploration. Extracting entities from patents through manual extraction expert curators take substantial amount time resources. Text mining methods help to ease this process. To validate performance such methods, a...

Mid-infrared spectra of whey and casein hydrolysates were recorded using Fourier transform infrared (FTIR) spectroscopy. Multivariate data analysis techniques used to investigate the capacity FTIR classify study ability predict bitterness, solubility, emulsifying, foaming properties hydrolysates. Principal component revealed that prepared from different protein sources or with classes proteolytic enzymes are distinguished effectively on basis their spectra. Moreover, multivariate regression...

Although a thorough characterization of binding parameters is essential for application β-lactoglobulin as carrier variety small hydrophobic ligands, the derived in various studies using techniques are inconsistent. The bindings several ligands detected by fluorometry and equilibrium dialysis were compared. Fluorescence spectroscopy showed that β-ionone, retinol, fatty acid lactones all bound vicinity tryptophan residue. Retinol lactone competed same site. Exclusively quench fluorescence...

Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and complementarity of nine two-dimensional (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, ALOGP) retrieving active molecules by similarity searching against a set query compounds. For purpose, biological data from HTS campaigns four protein families (GPCRs, kinases, ion channels, proteases). We have established threshold...

Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature assay data have advanced dramatically. In parallel, commercial sources that extract curate such from journals patents also been expanding. This work updates a previous comparative study of chosen because bioactive content, availability downloads facility to select informative subsets. Where they could be calculated, extracted...

There is a strong interest in drug discovery and development to advance the understanding of pharmacological promiscuity. Improved how molecular structure related promiscuity could help reduce attrition compounds process. For this purpose, descriptor introduced that describes structural complexity compound based on size its framework (MF) relation overall size. It defined as fraction versus whole molecule (f(MF)). demonstrated correlates with f(MF) for large values. The observed correlation...

We have systematically enumerated graph representations of scaffold topologies for up to eight-ring molecules and four-valence atoms, thus providing coverage the lower portion chemical space small (Pollock et al. J. Chem. Inf. Model., this issue). Here, we examine topology distributions several databases: ChemNavigator PubChem commercially available chemicals, Dictionary Natural Products, a set 2742 launched drugs, WOMBAT, database medicinal chemistry compounds, two subsets PubChem,...

Correctness of structures and associated metadata within public commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure-property relationships modelling compound novelty checking. MOL files, SMILES notations, IUPAC names, InChI strings are ubiquitous file formats systematic identifiers for structures. While interchangeable many cheminformatics purposes there have been no studies on the inconsistency these structure due to various...

Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both hypothetical successful human drug target statistics. However, listings research targets that define area between these two extremes are sparse because challenges collating published information at necessary scale. We addressed this by interrogating databases, populated expert curation, bioactivity data extracted from patents journal papers over last 30 years.From...

Abstract ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target are resources of curated chemistry‐to‐protein relationships widely used in chemogenomic arena. In this work we have extended an earlier analysis (PMID 22821596) by comparing chemistry protein target content between 2010 2013. For former, details presented for overlaps differences, statistics stereochemistry as well stereo representation MW profiles four databases. 2013 our results indicate quality improvements,...

Patent specifications are one of many information sources needed to progress drug discovery projects. Understanding compound prior art and novelty checking, validation biological assays, identification new starting points for chemical explorations a few areas where patent analysis is an important component. Cheminformatics methods can be used facilitate the so-called key compounds in specifications. Such methods, relying on structural extracted from documents by expert curation or text...

The text mining of patents pharmaceutical interest poses a number unique challenges not encountered in other fields mining. Unlike fields, such as bioinformatics, where the terms is enumerable and essentially static, systematic chemical nomenclature can describe an infinite molecules. Hence, dictionary- ontology-based techniques that are commonly used for gene names, diseases, species, etc., have limited utility when searching novel therapeutic compounds patents. Additionally, length...

The statistics of drug development output and declining yield approved medicines has been the subject many recent reviews. However, assessing research productivity that feeds is more difficult. Here we utilise an extensive database structure-activity relationships extracted from papers patents. We have used this to analyse published compounds cumulatively linked nearly 4000 protein target identifiers multiple species over last 20 years. compound increases up 2005 followed by a decline...