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.

Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis

“…5 ). Interestingly, previous MD studies probing the effect of RES on membrane properties concluded a less perturbing effect while experimental assays even point to a fluidizing effect, in line with the general action of related phytochemicals 23 , 42 , 43 . We attribute this apparent discrepancy to the lower concentrations of RES (typically ~10 mol%) compared to our study (50 mol%), together with the difference in membrane composition.…”

Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function

“…Bilayer-active molecules, however, are likely to masquerade as hits in cell-based screens because changes in bilayer properties, measured as changes in the gramicidin monomer↔dimer equilibrium, will produce changes in the function of many, diverse membrane proteins ( Lundbaek et al, 2010a ; Ingólfsson et al, 2014 ), which may alter overall cell function, thereby making the molecule appear to be a hit. Bilayer-active molecules thus can be considered as cell-based assay interference compounds (CAINS; see also Sun et al, 2020 ) or membrane PAINS ( Magalhães et al, 2022 ).…”

Unraveling the Aquaporin-3 Inhibitory Effect of Rottlerin by Experimental and Computational Approaches

“…In the end, a series of alternating steps of compression and energy minimization brings the system back to its natural dimensions. In the end, the AQP3 tetrameric structure was assembled in a membrane bilayer previously equilibrated with 382 POPC lipids [ 60 ]. Once the protein was fully embedded in the bilayer membrane, the system was solvated with 36,237 SPC water molecules [ 61 ].…”

“…MD simulations of the AQP3 protein complexed with RoT were also performed to evaluate the dynamics of the interaction of the compound with AQP3. The topology of RoT was obtained from the Automated Topology Builder and Repository [ 73 , 74 ], and manually curated to include the complete 1–4 exclusions in rings as previously done in other works [ 60 , 75 ]. The starting conformations for this set of simulations were obtained from the Molecular Docking calculations as explained in the next section.…”