Exploring QSAR models for activity-cliff prediction.
J Cheminform
; 15(1): 47, 2023 Apr 17.
Article
in English
| MEDLINE | ID: covidwho-2293809
ABSTRACT
INTRODUCTION AND METHODOLOGY:
Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that QSAR models struggle to predict ACs and that ACs thus form a major source of prediction error. However, the AC-prediction power of modern QSAR methods and its quantitative relationship to general QSAR-prediction performance is still underexplored. We systematically construct nine distinct QSAR models by combining three molecular representation methods (extended-connectivity fingerprints, physicochemical-descriptor vectors and graph isomorphism networks) with three regression techniques (random forests, k-nearest neighbours and multilayer perceptrons); we then use each resulting model to classify pairs of similar compounds as ACs or non-ACs and to predict the activities of individual molecules in three case studies dopamine receptor D2, factor Xa, and SARS-CoV-2 main protease. RESULTS ANDCONCLUSIONS:
Our results provide strong support for the hypothesis that indeed QSAR models frequently fail to predict ACs. We observe low AC-sensitivity amongst the evaluated models when the activities of both compounds are unknown, but a substantial increase in AC-sensitivity when the actual activity of one of the compounds is given. Graph isomorphism features are found to be competitive with or superior to classical molecular representations for AC-classification and can thus be employed as baseline AC-prediction models or simple compound-optimisation tools. For general QSAR-prediction, however, extended-connectivity fingerprints still consistently deliver the best performance amongs the tested input representations. A potential future pathway to improve QSAR-modelling performance might be the development of techniques to increase AC-sensitivity.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Type of study:
Experimental Studies
/
Prognostic study
/
Randomized controlled trials
Language:
English
Journal:
J Cheminform
Year:
2023
Document Type:
Article
Affiliation country:
S13321-023-00708-w
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