New star-shaped ligands generated by evolutionary fitting the Omicron spike inner-cavity

25 April 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Predictions generated by evolutionary docking of star-shaped ligands targeting the prefusion state of Omicron variants are described here. For this, one selected star-shaped molecule previously identified with the seeSAR program, was used as parent to randomly generate made-on-demand large children libraries evolutionary selected for best fitting to the Omicron spike top-to-bottom inner-cavity with the DataWarrior subprogram. The generated children docking-scores were consensed by AutoDockVina ranks normalized by molecular size and hydrophobicity. These explorations identified one new main chemotype and variants with improved specificity and exceptional nanomolar affinities, predicting aqueous soluble molecules targeting the prefusion state of Omicron spike inner-cavity of trimeric alpha-helices.


star-shaped molecules
evolutionary libraries

Supplementary materials

Table S3- 107 children from 9990
Table S3 Table S3- 107 children from 9990.sdf Table containing the properties of all non-toxic children derived from the 9990, including 2D graphs, Molecular Name(Numbers), generation, DW docking-score, Molecular weight, ADV Vina Binding Affinity in Kcal/mol and nM, and LE, LLE and LELP ligand efficiency values derived from ADV nM.


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