Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice?

Abstract

Predicting from first-principles the rate of passive permeation of small molecules across the biological membrane represents a promising strategy for screening lead compounds upstream in the drug-discovery and development pipeline. One popular avenue for the estimation of permeation rates rests on computer simulations in conjunction with the inhomogeneous solubility–diffusion model, which requires the determination of the free-energy change and position-dependent diffusivity of the substrate along the translocation pathway through the lipid bilayer. In this Perspective, we will clarify the physical meaning of the membrane permeability inferred from such computer simulations, and how theoretical predictions actually relate to what is commonly measured experimentally. We will also examine why these calculations remain both technically challenging and overly computationally expensive, which has hitherto precluded their routine use in nonacademic settings. We finally synopsize possible research directions to meet these challenges, increase the predictive power of physics-based rates of passive permeation, and, by ricochet, improve their practical usefulness.

How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?

“…In addition, significant regions of each neutral PMF are below zero, corresponding to higher equilibrium probability in the POPC bilayer than in the aqueous phase. This property of neutral organic small molecules in lipid membranes has been observed before, for instance, in the case of propranolol (PPL), ,, cocaine, short-chain alcohols, and ibuprofen . The protonated states of nicotine (Figure A, black and red) and state of varenicline (Figure B, black) face significant barriers against permeation, as would be expected considering the more stable solvation of a charged species in the aqueous phase compared to the hydrophobic interior of a membrane, especially in the context of an additive force field .…”

“…Reconciling computational permeability values with experimental measurements in the case of ionizable molecules remains challenging. ,,,,− Measurement of the apparent specific permeability of lipophilic small molecules, such as the neutral forms of many ionizable drugs, is confounded by additional rate-controlling barriers that are distinct from the permeability of the membrane. ,− In the common experimental setup of imposing a steady-state flux across a layer of cells (such as Caco-2), , the apparent permeability, P app , will be upper-bounded by the aqueous boundary layer (ABL) and lower-bounded by paracellular pathways, each with their own respective permeability, P ABL and P para . The P ABL term combines in series with the membrane permeability, while P para combines in parallel, such that the apparent permeability is given by 1 P a p p = 1 P + P normalp normala normalr normala + 1 P A B L …”

“…The membrane thickness L in eq should be chosen such that the PMF, W ( z ), is equal to a constant when | z | > L /2 in the bulk region (the constant can be set to zero for convenience). This theoretical framework, commonly referred to as “inhomogeneous solubility-diffusion” (ISD) since the pioneering work of Diamond and Katz, has been applied to a variety of molecules. − The simplest form of the ISD framework needs to be extended in the case of ionizable molecules. In the pH-partition mechanism mentioned above, it is assumed that the interconversion protonation/deprotonation rates have a negligible impact on the effective permeability.…”

“…In the present work, we use the enhanced-sampling algorithm well-tempered metadynamics with extended adaptive biasing force (WTM-eABF) , to compute the specific permeability of each of the ionization states of two small ionizable molecules, nicotine and varenicline. This approach has been previously applied to two protonation states of ibuprofen . Enhanced sampling is employed first for computing the PMF underlying permeation along the membrane normal and then for determining the position-dependent diffusivity by running trajectories on the flattened free energy surface.…”

Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs

“…Therefore, depending on the experiment being compared to (stirred or unstirred in vitro or in vivo assay), the reference UWL thickness should be chosen accordingly. The only exception to the above is in the case of liposomal assays, where the P m * is directly determined, and comparable to the differential solvation free energy calculated from MD simulations, avoiding the need for approximating δ UWL .…”