Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds

Abstract

Membrane pan-assay interference compounds (PAINS) are a class of molecules that interact nonspecifically with lipid bilayers and alter their physicochemical properties. An early identification of these compounds avoids chasing false leads and the needless waste of time and resources in drug discovery campaigns. In this work, we optimized an in silico protocol on the basis of umbrella sampling (US)/molecular dynamics (MD) simulations to discriminate between compounds with different membrane PAINS behavior. We showed that the method is quite sensitive to membrane thickness fluctuations, which was mitigated by changing the US reference position to the phosphate atoms of the closest interacting monolayer. The computational efficiency was improved further by decreasing the number of umbrellas and adjusting their strength and position in our US scheme. The inhomogeneous solubility-diffusion model (ISDM) used to calculate the membrane permeability coefficients confirmed that resveratrol and curcumin have distinct membrane PAINS characteristics and indicated a misclassification of nothofagin in a previous work. Overall, we have presented here a promising in silico protocol that can be adopted as a future reference method to identify membrane PAINS.

Figure 1

PMF of translocating a probe across a POPC bilayer using either the center of the membrane as the reference (A) or the closest P-layer (B). The thicker colored lines include all replicates, whereas the thinner gray lines correspond to individual replicates. The gray area is half the average bilayer thickness. Cartoons of the relative positions of the probe in the z-axis using the membrane as a reference (C) or the closest P-layer (D).

Figure 2

(A) Population histograms for POPC 22U^M including all replicates and the corresponding K_f values (shown in kJ mol^–1 nm^–2). (B) PMF of translocating a probe across a POPC bilayer using the closest P-layer as reference using either 22 umbrellas (yellow) or 37 umbrellas (orange). The thicker lines include all replicates, whereas the thinner ones correspond to individual replicates in the 22U^M system.

Figure 3

PMF profiles of translocating a probe across a POPC bilayer in the absence or presence of the tested compounds: resveratrol (RES), nothofagin (NOT), curcumin 10% (CUR), and curcumin 20% (CUR24). The thicker lines include all replicates (average), whereas the thinner ones correspond to individual replicates of the system with PAINS compounds. The orange profile corresponds to the compound-free control.