Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria

Abstract

Modern medicine relies upon antibiotics, but we have arrived to the point where our inability to come up with new effective molecules against resistant pathogens, together with the declining private investment, is resulting in the number of untreatable infections increasing worldwide at worrying pace. Among other pathogens, widely recognized institutions have indicated Gram-negative bacteria as particularly challenging, due to the presence of the outer membrane. The very first step in the action of every antibiotic or adjuvant is the permeation through this membrane, with small hydrophilic drugs usually crossing through protein channels. Thus, a detailed understanding of their properties at a molecular level is crucial. By making use of Molecular Dynamics simulations, we compared the two main porins of four members of the Enterobacteriaceae family, and, in this paper, we show their shared geometrical and electrostatic characteristics. Then, we used metadynamics simulations to reconstruct the free energy for permeation of selected diazobicyclooctans through OmpF. We demonstrate how porins features are coupled to those of the translocating species, modulating their passive permeation. In particular, we show that the minimal projection area of a molecule is a better descriptor than its molecular mass or the volume. Together with the magnitude and orientation of the electric dipole moment, these are the crucial parameters to gain an efficient compensation between the entropic and enthalpic contributions to the free energy barrier required for permeation. Our results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field.

The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway

“…However, as already observed [30], the dipole reaches its largest value at the lowest value of the minimum radius, or when the molecule is extended, an indication of a longitudinal dipole. This is confirmed by the analysis of the dipole moment components with respect to the MPA plane.…”

“…The latter is due to the presence of basic residues on one side (the basic ladder) facing the acidic loop L3 on the other, thus creating a large transversal electric field [ 36 ] to which molecules align when diffusing through [ 37 ]. For these reasons, two key molecular parameters for diffusion are the size of molecules and their dipole moment [ 30 ].…”

“…Here, we performed metadynamics simulations to observe and sample the diffusion of the BLIs through OmpF. As performed in the past [ 30 ], we biased two coordinates: (i) CV1 is related to the orientation of the boronate ring ( Figure 5 , left panel) with respect to the z diffusion axis; (ii) CV2 represents the position of BLIs boronate ring along the z diffusion axis. Thanks to these CVs, we can force the orientation of molecules to change at the entrance of the pore, thus sampling more efficiently the relative orientation also in the constricted region, where there is no space for reorienting.…”

“…Although the scoring function is based on general molecular properties [ 29 ], namely the size, the charge, and the electric dipole moment, the molecules selected for its fitting were all beta-lactam antibiotics, which are considered molecules with good permeation [ 28 ]. Investigations on diazobicyclooctan derivatives [ 30 ] confirmed, by molecular modeling, that the main contribution to an efficient permeation comes from the size, charge state, and electric dipole moment of molecules, irrespective of the chemical scaffold [ 28 ]. In addition, for the development of ETX0462 the molecular dipole moment was monitored to improve rationally its permeation through the OM [ 31 ].…”

Ab Initio Spectroscopic Investigation of Pharmacologically Relevant Chiral Molecules: The Cases of Avibactam, Cephems, and Idelalisib as Benchmarks for Antibiotics and Anticancer Drugs

“…Its inhibitory properties have been also measured across a large variety of enzymes considered for their clinical importance [8]. Through chemical modifications we have today diverse diazabicyclooctane derivatives [9].…”