ISIDA Property‐Labelled Fragment Descriptors

Abstract

ISIDA Property-Labelled Fragment Descriptors (IPLF) were introduced as a general framework to numerically encode molecular structures in chemoinformatics, as counts of specific subgraphs in which atom vertices are coloured with respect to some local property/feature. Combining various colouring strategies of the molecular graph - notably pH-dependent pharmacophore and electrostatic potential-based flagging - with several fragmentation schemes, the different subtypes of IPLFs may range from classical atom pair and sequence counts, to monitoring population levels of branched fragments or feature multiplets. The pH-dependent feature flagging, pursued at the level of each significantly populated microspecies involved in the proteolytic equilibrium, may furthermore add some competitive advantage over classical descriptors, even when the chosen fragmentation scheme is one of the state-of-the-art pattern extraction procedures (feature sequence or pair counts, etc.) in chemoinformatics. The implemented fragmentation schemes support counting (1) linear feature sequences, (2) feature pairs, (3) circular feature fragments a.k.a. "augmented atoms" or (4) feature trees. Fuzzy rendering - optionally allowing nonterminal fragment atoms to be counted as wildcards, ignoring their specific colours/features - ensures for a seamless transition between the "strict" counts (sequences or circular fragments) and the "fuzzy" multiplet counts (pairs or trees). Also, bond information may be represented or ignored, thus leaving the user a vast choice in terms of the level of resolution at which chemical information should be extracted into the descriptors. Selected IPLF subsets were - tree descriptors, in particular - successfully tested in both neighbourhood behaviour and QSAR modelling challenges, with very promising results. They showed excellent results in similarity-based virtual screening for analogue protease inhibitors, and generated highly predictive octanol-water partition coefficient and hERG channel inhibition models.

Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde?

“…Otherwise, the descriptor space found is robust but static. The introduction of in silico design and data analysis (ISIDA) propertylabeled fragment descriptors is a good example pointing in this direction [36].…”

Continuous indicator fields: a novel universal type of molecular fields

“…In this section, we demonstrate that CIFs can be considered as 3D analogues of 2D topological fragment descriptors [1][2][3][4][25][26][27][28]. Let's consider the fragment descriptor based on the simplest substructure-an atom.…”

“…Fragment (substructure) descriptors [1][2][3][4] and molecular fields [5] are two common ways of representing molecules in numerous applications in chemoinformatics and drug discovery [6,7]. Although both of them play an important role in building structure-property/activity models, visualizing chemical space, performing similarity search and virtual screening, they represent molecules in a totally different manner, and therefore they are used differently.…”

An Evolutionary Optimizer of libsvm Models

“…These DS include pharmacophore (PH)-and atom-symbol (SY) labeled sequences (seq) and circular fragment counts (tree,aab), as well as fuzzy pharmacophore triplets [9,10]. For each DS, a descriptor file encoding one molecule per line (in the order of the reference list) is provided: FPT1.svm, seqPH37.svm, seqSY37.svm, aabPH02.svm, treeSY03.svm, treePH03.svm in .svm format.…”