Additional file 1 of Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism
Creators: name: Kant, Ravi
name: Tilford, Hannah
name: Freitas, Camila S.
name: Ferreira, Dayana A. Santos
name: Ng, James
name: Rucinski, Gwennan
name: Watkins, Joshua
name: Pemberton, Ryan
name: Abramyan, Tigran M.
name: Contreras, Stephanie C.
name: Vera, Alejandra
name: Christodoulides, Myron
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Figure S1. Minimum inhibitory concentration (MIC) titration curves for Ng-LdcA compounds. Compound 35 could not be titrated (MIC value &lt; 50 μM). S2. Minimum inhibitory concentration (MIC) titration curves for Ng-LtgD compounds. Compounds 68 and 74 could not be titrated (MIC values &lt; 50 μM). S3. Titration of compounds to determine minimum bactericidal concentrations (MBC) for Ng-LdcA and Ng-LtgD compounds. Data are representative of n = 2 experiments for the best-performing compounds with most active MICs. S4. Sequence alignment of Ng-LtgD with E. coli 1D0K at the C-terminus, highlighting the modelled regions and indicating the excluded parts. The position of the modelled region start is also shown. S5. Ramachandran plots. To assess model accuracy and stereo-chemical properties of Ng-LdcA and Ng-LtgD. S6. MIC and MBC titration curves for Ng-LdcA and Ng-LtgD compounds tested against P. aeruginosa PAO-1. Bacteria (105 CFU/well, n = 3) were treated with various concentrations of compounds Ng-LdcA-16, -37 and -69 and Ng-LtgD-45, -52 and -69 in the standard MIC and MBC assays. Data are representative of n = 2 experiments. S7. MIC and MBC titration curves for Ng-LdcA and Ng-LtgD compounds tested against Staphylococcus spp. Bacteria (105 CFU/well, n = 3) were treated with various concentrations of compounds Ng-LdcA-16, -37 and -69 and Ng-LtgD-45, -52 and -69 in the standard MIC and MBC assays. Data are representative of n = 2 experiments. MBC experiments were only done with compounds that showed detectable MIC50 values. S8. MIC and MBC titration curves for Ng-LdcA and Ng-LtgD compounds tested against Lactobacillus gasseri. Bacteria (105 CFU/well, n = 3) were treated with various concentrations of compounds Ng-LdcA-16, -37 and -69 and Ng-LtgD-45, -52 and -69 in the standard MIC and MBC assays. Data are representative of n = 2 experiments. MBC experiments were done only with 50 μM concentrations. S9. MIC and MBC titration curves for Ng-LdcA-16 tested against different gonococci belonging to the FDA/CDC AR gonococcal biobank. Bacteria (105 CFU/well, n = 3) were treated with various concentrations of compounds Ng-LdcA-16, in the standard MIC and MBC assays. Data curves are representative of n = 2 experiments. S10. MBC assays for Ng-LtgD-45 against strain P9-17 and other gonococci belonging to the FDA/CDC AR gonococcal biobank. Bacteria (105 CFU/well) were treated with various concentrations of compound Ng-LtgD-45 in the MBC assay in PBSB for 1h with variable counting. Symbols represent the mean and any error bars the standard error of the means from three independent experiments. S11. Clustal alignments of the Ng-LdcA and Ng-LtgD enzymes from three Neisseria spp. The green highlighted amino acids belong to the binding sites of the enzymes that interact with the compounds. S12. Alignment of active site amino acid residues for Ng-LdcA and Ng-LtgD, determined by AtomNet and our computational modelling. Yellow highlight denotes the shared amino acids identified by both algorithms.