Combined use of computational chemistry, NMR screening, and X‐ray crystallography for identification and characterization of fluorophilic protein environments

Abstract

(19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description.

Design of gem‐Difluoro‐bis‐Tetrahydrofuran as P2 Ligand for HIV‐1 Protease Inhibitors to Improve Brain Penetration: Synthesis, X‐ray Studies, and Biological Evaluation

“…Similar interactions of fluorine atom with carbonyl oxygen of various amino acids have been previously observed in various protein structures with a frequency of over 9%. [31] Since Gly48 is located in the flap, for inhibitor 3 , these F….OC interactions with Gly48 may tend to stabilize the flexible flap region as well as improve the binding affinity for HIV-1 protease complex. The structure also shows hydrogen bonding interactions of urethane NH with the backbone carbonyl oxygen of Gly27.…”

“…We also presume that our structure-based fluorine substitution may improve molecular binding properties in the HIV-1 protease active site through noncovalent interactions involving fluorine. [17,18] This may result in potent antiviral activity against multi-drug resistant HIV-1 variants. Herein, we report an enantioselective synthesis of gem -difluoro- bis -THF ligands and their conversion to gem -difluoro- bis -THF containing HIV-1 protease inhibitors resembling darunavir.…”

Fluorine–Protein Interactions and 19F NMR Isotropic Chemical Shifts: An Empirical Correlation with Implications for Drug Design

“…All protein heteroatoms that are at a distance of 3.2 from the ligand fluorine atoms were selected using the previously described procedure. [15] This value is slightly larger than the sum of the van der Waals radii, to allow for uncertainty in measurements. The analysis was performed for all structures available in the PDB as of August 2009.…”

“…This LEF (Local Environment of Fluorine) library [14] has since been successfully used in 19 F NMR screening of different targets. [15] The aim of the current analysis is to demonstrate a correlation between the fluorine isotropic chemical shift measured in 19 F NMR spectra and the type of fluorine-protein interactions observed in crystal structures. It is envisaged that these findings will aid in the rational drug design process by providing guidance in the selection of fluorinated moieties to be judiciously incorporated into molecules in order to create favorable interactions with the receptor.…”

Harnessing Fluorine–Sulfur Contacts and Multipolar Interactions for the Design of p53 Mutant Y220C Rescue Drugs

“…13−16 Vulpetti et al identified fluorinated fragments binding to trypsin by 19 F NMR screening and crystal structure determination and described a general approach to identify fluorophilic hot-spots in proteins using crystal and computational analysis. 17 Recently, Pollock et al investigated the impact of fluorine–protein interactions on the binding affinity of a menin–MLL inhibitor and introduced their computational algorithm FMAP, which aims to facilitate the rational design of fluorine–protein interactions. 18 …”