Promiscuity of in Vitro Secondary Pharmacology Assays and Implications for Lead Optimization Strategies

Abstract

We conducted an analysis on screening data generated from 1445 compounds against a panel of 130 enzymes, ion channels, and receptors to assess secondary pharmacological risks. Hit rates of these targets as well as physicochemical properties for those hits were evaluated. A majority of targets yielded hits with higher clogP, molecular weight, and more basic character than inactive compounds. Although most targets favored lipophilic hits, the average clogP of hits at a given target did not correlate with its hit rate. Furthermore, a matched pair analysis was completed to determine structural changes that impacted off-target activities. A correlation of binding assays used in this analysis illustrated that some pharmacologically related binding assays are highly correlative and may be substituted for a smaller set of surrogate assays.

Target-Based Evaluation of “Drug-Like” Properties and Ligand Efficiencies

“…For example, values of PSA < 75 Å 2 in combination with LogP > 3 have been shown in several studies from large pharmaceutical companies to increase the risk of in vivo toxicity. − Drug candidates that fail due to clinical toxicity are more lipophilic on average than those that do not . Lipophilicity ,,− will remain a key driver of ADMET properties and strategies to assess and control , it are growing. Measurement of LogD 7.4 and LogP is essential, and chromatographic methods have greater measurement bandwidth than the traditional shake flask method. , Lipophilicity associated with high aromatic ring count has been highlighted as significant developability risk, , with carboaromatic compounds carrying greater risks than heteroaromatics .…”

Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data

“…Within the scope of the Ro5 it is interesting to consider the generosity of the 90th percentile clog P of 5 in this context; the Pfizer 3/75 analysis was based on an increased risk of promiscuity with clog P > 3 . The impact of lipophilicity on attrition risk is well documented, − and the additional impact of aromaticity is evident. , To illustrate this point, analysis of data from the GSK expanded cross screening panel (eXP), a consensus set of 52 assays, showed an increasing propensity for promiscuity and off-target risks as lipophilicity and aromaticity increased (intrinsic PFI or iPFI, the summation of measured Chrom log P + #Ar appeared a better differentiator) . In these assays, promiscuity is expressed by the number of assays where an IC 50 curve could be fitted (Figure a), and off-target risks are defined by the number of assays with activity levels above defined thresholds (Figure b).…”

Into the Fray! A Beginner's Guide to Medicinal Chemistry

“…[12] These additional orthogonal methods are particularly useful in reducing the impact of promiscuous compounds and false positives, which plague screening campaigns. [13] Furthermore, the challenges associated with traditional assay formats in the face of the expansion of druggable targets into the protein-protein interaction (PPI) space, [14][15][16] and the growing prominence of using weakly interacting low molecular weight chemical probes in fragment-based drug discovery, [17][18][19] requires the increased application of sensitive orthogonal biophysical techniques for biological assessments. Following the development of a suitable assay, the next phase involves compound screening with the intention of identifying promising chemical starting points for optimization.…”

“…Figure13. Overlay of the binding positions of camptothecin (green, PDB ID: 1T8I) and topotecan (lilac, PDB ID: 1 K4T) at the active site of the topoisomerase-DNA complex.…”