| Assay Method Information | |
| | The HTRF Assay |
| Description: | The HTRF assay confirmed that compound 4b has an IC50 of 339.9 nM (see Experimental Section for details) to inhibit PD-1/PD-L1 interaction (FIG. 5D). This is comparatively better than the IC50 of 521.5 nM for the BMS compound 4a that was synthesized and tested in our lab (BMS-1 molecule in the BMS patent WO 2015/034820 A1). It should be noted that the BMS-1 molecule was denoted with the IC50 of 6-100 nM with HTRF assay in the BMS patent' . However, multiple replicates of our experiments did not result in the IC50 value less than 100 nM to inhibit PD-1/PD-L1 interaction (see Calculation of IC50 values section and Supporting File HTRF_IC50_Data.xlsx). As mentioned previously, this result does not affect our machine learning method since we have classified molecules based on high and low potency rather than estimating the specific IC50 value. A possible explanation of this difference in experimental results between our work and the patent could be differences in protocols used to perform the HTRF assay and calculation of IC50 values. For this reason, we have included a detailed account of HTRF assay protocol, analysis of data for calculation of IC50 and supporting data files to be used by the scientific community (see Experimental Section). In order to test the validity of our bootstrapped EGNN model to correctly identify low potency predictions, we also tested compounds 4c, 4d and 4e resulting in no/poor inhibition to PD-1/PD-L1 interaction (Table 2). The IC50 plots for each compound tested (Figure S6) as well as the 13C and 1H NMR spectra are provided as Supporting Information. |
| Affinity data for this assay | |
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