Integration of Enhanced Sampling Methods with Saturation Transfer Difference Experiments to Identify Protein Druggable Pockets

Abstract

Saturation transfer difference (STD) is an NMR technique conventionally applied in drug discovery to identify ligand moieties relevant for binding to protein cavities. This is important to direct medicinal chemistry efforts in small-molecule optimization processes. However, STD does not provide any structural details about the ligand-target complex under investigation. Herein, we report the application of a new integrated approach, which combines enhanced sampling methods with STD experiments, for the characterization of ligand-target complexes that are instrumental for drug design purposes. As an example, we have studied the interaction between StOASS-A, a potential antibacterial target, and an inhibitor previously reported. This approach allowed us to consider the ligand-target complex from a dynamic point of view, revealing the presence of an accessory subpocket which can be exploited to design novel StOASS-A inhibitors. As a proof of concept, a small library of derivatives was designed and evaluated in vitro, displaying the expected activity.

Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand–based drug design

“…Despite the range of activity allowed only a rough SAR, these results somehow confirmed the presence of a lipophilic pocket in the proximity of the enzyme active site where the pyrazole substituent can locate, as previously noticed by us 27 , 36 , 37 . In addition, the activity shown by compounds 4e and 5f demonstrated that the size of the molecule may have some influence on the binding to the enzyme pocket.…”

“…This is due to several considerations. First of all, the analysis of the key interactions established by compound 4a with OASS backbone ( Figure 4 ) anticipates a similar binding pattern as for our previously reported hits 25 , 27 , 36 .…”

“…A scaffold hopping using a hit compound previously identified by us was performed in order to identify a novel inhibitor of OASS to be further investigated. Our group has already made use of computational tools in order to broaden the body of SAR of these derivatives 36 . Among the several scaffolds suggested by the program ( Figure 3 ), we deemed of particular interest to further investigate hit compound 4a , which was characterised by an N -substituted pyrazole central spacer.…”

Refining the structure−activity relationships of 2-phenylcyclopropane carboxylic acids as inhibitors of O-acetylserine sulfhydrylase isoforms

“…While the sulphonamide group is a nonplanar isoster of the carboxylic acid, the tetrazole is planar and presents a similar acidity. On a similar vein, substituted amides were prepared because it is well known that the nature of the substituents might affect the selectivity of action toward different bacterial strains, either Gram-positive or Gram-negative 29 , 30 . For instance, in the case of sulphonamide drugs, potency and selectivity are modulated by the substituent at the amidic nitrogen 31 .…”

Strategies to Overcome Antimicrobial Resistance (AMR) Making Use of Non-Essential Target Inhibitors: A Review

“…In 2016, Pieroni et al [115,116], starting from the evidence that SAT competitively inhibits OASS-A, developed a rational design of the first sulfydrylase inhibitors based on the structural features of the OASS–SAT interaction. Taking into account the data from their previous studies [117], and combining computational [118,119] and spectroscopic approaches, such as saturation transfer difference (STD) and nuclear magnetic resonance (NMR), they rationally designed and synthesized a series of 2-phenylcyclopropane carboxylic acid derivatives tested against both isoforms of St -OASS [120]. Indeed, they demonstrated that the compounds binding to the enzyme active sites efficiently inhibit both OASS-A and B isoforms by competing with SAT.…”