Fig. 1: Our library of compounds, experimental data, and molecular descriptors. | Communications Chemistry

Fig. 1: Our library of compounds, experimental data, and molecular descriptors.

From: Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

Fig. 1

a Computational representation of the outer membrane environment (OM) of P. aeruginosa detailing the seven sub-regions where MD simulations where the 35 descriptors listed in E were computed for each molecule. b Experimental structure of the tripartite efflux system MexAB-OprM (PDB ID: 6TA6 [10.1038/s41467-020-18770-5]). On the right: focus on the two MexB major binding pockets, AP and DP. c Assembled library of 1260 antimicrobial molecules classified into 16 distinct structural chemotypes as listed (top left), and some examples are shown in the bottom panel. d Each compound is characterized by its antimicrobial activity in three strains of P. aeruginosa by means of the 50% inhibitory concentration (IC50). e Molecules in c are further characterized by 174 computationally-derived mechanistic descriptors classified as either docking (D), permeation (P), or physicochemical (PC). These are computed using QSAR methods, density functional calculations, ensemble docking and MD simulations in water and in the OM of P. aeruginosa. f Principal components third degree decomposition of the molecules following the color code shown in c.

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