Managing Experimental 3D Structures in the Beyond‐Rule‐of‐5 Chemical Space: The Case of Rifampicin

Abstract

The beyond-Rule-of-5 (bRo5) chemical space is a source of new oral drugs and includes large and flexible compounds. Because of their size and conformational variability, bRo5 molecules assume different privileged conformations in the compartments of human body, i. e., they can exhibit chameleonic properties. The elucidation of the ensemble of 3D structures explored by such molecules under different conditions is therefore critical to check the role played by chameleonicity to modulate cell permeability. Here we characterized the conformational ensembles of rifampicin, a bRo5 drug, in polar and nonpolar solvents and in the solid state. We performed NMR experiments, analyzed their results with a novel algorithm and set-up a pool of ad hoc in silico strategies to investigate crystallographic structures retrieved from the CSD. Moreover, a polarity descriptor often related to permeability (SA-3D-PSA) was calculated for all the conformers and its variation with the environment analyzed. Results showed that the conformational behavior of rifampicin in solution and in the solid state is not superposable. The identification of dynamic intramolecular hydrogen bonds can be assessed by NMR spectroscopy but not by X-ray structures. Moreover, SA-3D-PSA revealed that dynamic IMHBs do not provide rifampicin with chameleonic properties. Overall, this study highlights that the peculiarity of rifampicin, which is cell permeable probably because of the presence of static IMHBs but is devoid of any chameleonic behavior, can be assessed by a proper analysis of experimental 3D structures.

Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader

“…Indeed, molecules above a certain molecular weight have a risk of being either too polar, resulting in adequate solubility and poor membrane permeability, or the opposite, if too lipophilic [ 10 , 11 , 12 , 13 ]. This is verified for some bRo5 failed drug candidates, but it is widely known that many successful drugs lie in the bRo5 chemical space [ 8 , 12 , 14 , 15 ].…”

Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape

“…Rifampicin is an interesting type 6 bRo5 compound that is believed to exhibit static IMHB formation reduction. 29 This compound is very polar with moderate lipophilicity and was found to be highly dependent on its polarity reducing behavior (ETR = 0.38) to achieve absorption.…”

“…36,38,72,73 This behavior, evident in simulations 40,73,74 and column-based studies, 35 facilitates solubility and permeability. Some compounds, such as rifampicin, leverage static IMHB for polarity reduction, 29 whereas molecules like paritaprevir 22 and cyclosporin A 75 combine both shielding and IMHBs.…”

Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs

“…In this case, the solvent can be ad hoc chosen to mimic different polarities accounting for the in vivo situations. Using this technique, two macrocycles, telithromycin and roxithromycin, , were identified as true chameleons, whereas rifampicin , was revealed to be a weak chameleon. Indeed, NMR showed that the orientation of the side chains of telithromycin and roxithromycin varied between nonpolar and polar environments, confirming the crucial effect of macrocyclic side chains on chameleonicity .…”