The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer

Abstract

The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact, the most widely used oral bioavailability rules (such as the Lipinsky's rule-of-five and the Veber rules) make use of this molecular descriptor. It is generally assumed that hydrogen bond donors and acceptors impact on passive diffusion across cell membranes, a fundamental event during drug absorption and distribution. Although the relationship between the number of these motifs and the probability of having good oral bioavailability has been studied and described for more than 20 years, little attention has been given to their spatial distribution in the molecule. In this paper, we used molecular dynamics to describe the effect of intramolecular hydrogen bonding on the passive diffusion of a small drug (piracetam) through a lipid membrane. The results indicated that the formation of an intramolecular hydrogen bond decreases the barrier for translocation by ca. 4 kcal mol^-1 and increases the permeability of the tested molecule, partially compensating the desolvation penalty arising from the penetration of the drug into the biological membrane core. This effect was apparent in simulations where the formation of this interaction was prevented with the help of modified potentials, and in simulations with a similar compound to piracetam that was not able to form this intramolecular hydrogen bond due to a larger distance between the hydrogen bond donor and acceptor groups. These results were also supported by coarse-grained methods, which are becoming an important resource for sampling a larger chemical space of molecules, with reduced computational effort. Furthermore, entropy and enthalpy derived profiles were also obtained as the compounds translocated across the membrane, suggesting that, even though the process of formation of internal hydrogen bonds is entropically unfavorable, the enthalpic gain is such that the formation of these interactions is beneficial for the passive diffusion across cell membranes.

Fig. 1. Compounds evaluated in this study. (a) 2-oxo-1-pyrrolidine acetamide (PCT, piracetam); (b) 3-oxo-1-pyrrolidine acetamide (here labelled as PCM).

Fig. 2. Dihedral angle and conformational analysis of PCT as it translocated the bilayer. (a and b) representation of two conformers of piracetam – in the middle of the membrane and in water, respectively; (c and d) representation of the D1 and D2 dihedral angles populations along the axis perpendicular do the plane of the bilayer. The range of ca. −1 to 1 nm with respect to the y axis, contains only the hydrophobic lipid tails, and has the lowest density of the entire system. The dihedral angles, D1 and D2, and the IMHB that was formed in (a), were also represented (IMHB, dashed yellow line; D1 and D2, white circles and white dashed lines).

Fig. 3. Free energy and hydrogen bond profiles of PCT and PCM in a DOPC hydrated bilayer model system. (a) Representation of the hydrated bilayer system and partial density profiles for the different functional groups or molecules in the system. (b) Free energy profiles for the translocation of the two tested compounds (PCT, black and PCM, blue) and for the simulation of PCT where a flat-bottom potential was employed to hold the donor and acceptor groups at a distance that hinder the formation of the IMHB (PCT*, grey). (c) Number of hydrogen bonds (h-bonds) along the translocated distance. We have outlined the number of h-bonds established between the compounds and water (red) or membrane (green), and the number of intramolecular h-bonds considering both compounds (black). In the right (with a grey background), we show the results for PCT; and in the left (with a blue background), we show the results for PCM.

Fig. 4. Thermodynamic profiles of PCT and PCM in a DOPC hydrated bilayer model system. (a) Thermodynamic profiles derived from the CGMD simulations (ΔG, black and blue; −TΔS, red; ΔH, green). (b) Thermodynamic profiles derived from the all-atom MD simulations (ΔG, black and blue; −TΔS, red; ΔH, green). In the right panels (with a grey background), we show the energy profiles for PCT; and in the left panels (with a blue background), we show the results for PCM. Vertical bars represent the uncertainty of the estimates and were derived from the multiple determinations of entropy per system that were made (see Methods section for details).