Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae

Abstract

The development of compounds able to modify biological functions largely took advantage of parallel synthesis to generate a broad chemical variance of compounds to be tested for the desired effect(s). The budding yeast Saccharomyces cerevisiae is a model for pharmacological studies since a long time as it represents a relatively simple system to explore the relations among chemical variance and bioactivity. To identify relations between the chemical features of the molecules and their activity, we delved into the effects of a library of small compounds on the viability of a set of S. cerevisiae strains. Thanks to the high degree of chemical diversity of the tested compounds and to the measured effect on the yeast growth rate, we were able to scale-down the chemical library and to gain information on the most effective structures at the substituent level. Our results represent a valuable source for the selection, rational design, and optimization of bioactive compounds.

Keywords: Saccharomyces cerevisiae; drug development; drug screening; high-throughput screening (HTS); phenotypic screening; principal component analysis; small compounds; stepwise regression analysis.

Figure 1

Two classifications of the scaffolds the chemical library is built on. (A) BTA(O), BTA and BTA(S); (B) BTK, BTF, and BTG. When a compound bore a cyclic residue at position R4′ and R4″, it was annotated as R4′.

Figure 2

Relationship among chemical features of selected compounds and their activity. Duality diagram for the first two principal components obtained by analyzing correspondence between the ΔODst %and the chemical features of the molecules selected at the first-level. The cases for analysis were the molecules selected in the first level assay as able to induce a W303 ODst decrease higher than the 20% with respect to the ODst of the untreated culture. The variables are both the ΔODst % induced by the molecules on the tested strains and the molecule chemical features (substituent types, scaffold types); black-boxes labels: effects on the tested strains, white-boxes labels: molecules classification as shown in Figure 1A, gray-boxes labels: molecules classification as shown in Figure 1B. PCA1, First Principal Component; PCA2, Second Principal Component.

Figure 3

Highlights of the effects of the selected molecules and their chemical characteristics. (A) Direct comparison of the molecules effect on BY4742 and W303 strains, each dot indicate a different molecule; (B) boxplot showing the effects on the BY4742Δsnq2 strain culture ODst caused by the molecules grouped according to the scaffold classification showed in Figure 1A; (C–E) relationship between the effects induced by the molecules classified accordingly to Figure 1B on the wild-type BY4742 and on the Δerg6, Δpdr3, and Δsnq2 strains, respectively.

Figure 4

Relationship between steric hindrance or polarizability and the phenotypic effects. (A) First two explanatory components identified with the Redundancy Analysis (RDA) on ΔODst % values and steric hindrances. RDA1, First RDA constrained axis; RDA2, Second RDA constrained axis. The ΔODst % calculated for every strain treatment were used as constraining variables; as explanatory variables we used the steric hindrance values (A3) calculated with the Marvin Sketch software (5.10.0). (B) First two explanatory components identified with RDA on ΔODst % values and molecule/substituent polarizability. The ΔODst % calculated for every strain treatment were used as constraining variables; as explanatory variables we used the polarizability indexes (A3) calculated with the Marvin Sketch software (5.10.0).

Figure 5

Results of the analysis on the complete library of molecules. (A) Duality diagram for the first two principal components obtained by analyzing the ΔODst % and the chemical features of the complete library of molecules. The cases for analysis were the molecules composing the library. The variables are the ΔODst % induced by the molecules on the W303 strain and the molecule chemical features (substituent types, scaffold types); black-box labels: effects on the tested strains, bold labels: molecules classification as shown in Figure 1A, gray-box labels: molecules classification as shown in Figure 1B. (B) Boxplots representing the influence of the presence of a secondary or tertiary amine in position R4″ in the effects induced on the W303 wild-type strain ODst by the molecules classified in three groups as described in Figure 1A.

Figure 6

Comparison of the effects induced on the W303 wild-type by the most fungicide molecule with respect to molecules almost identical to it but for small chemical features. Numbers correspond to compound names.