Antihydrophobic solvent effects: an experimental probe for the hydrophobic contribution to enzyme-inhibitor binding

Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics

Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed Zn‐dependent protease, which plays an important role in regulating endogenous peptide hormones, such as enkephalins or angiotensins. In previous biophysical studies, it could be shown that substrate binding is driven by a large entropic contribution due to the release of water molecules from the closing binding cleft. Here, the design, synthesis and biophysical characterization of peptidomimetic inhibitors is reported, using for the first time an hydroxyethylene transition‐state mimetic for a metalloprotease. Efficient routes for the synthesis of both stereoisomers of the pseudopeptide core were developed, which allowed the synthesis of peptidomimetic inhibitors mimicking the VVYPW‐motif of tynorphin. The best inhibitors inhibit DPP3 in the low μM range. Biophysical characterization by means of ITC measurement and X‐ray crystallography confirm the unusual entropy‐driven mode of binding. Stability assays demonstrated the desired stability of these inhibitors, which efficiently inhibited DPP3 in mouse brain homogenate.

Modelling drug adsorption in metal-organic frameworks: the role of solvent

Solvent plays a key role in biological functions, catalysis, and drug delivery. Metal-organic frameworks (MOFs) due to their tunable functionalities, porosities and surface areas have been recently used as drug delivery vehicles. To investigate the effect of solvent on drug adsorption in MOFs, we have performed integrated computational and experimental studies in selected biocompatible MOFs, specifically, UiO-AZB, HKUST-1 (or CuBTC) and NH2-MIL-53(Al). The adsorption of three drugs, namely, 5-fluorouracil (5-FU), ibuprofen (IBU), and hydroxyurea (HU) were performed in the presence and absence of the ethanol. Our computational predictions, at 1 atmospheric pressure, showed a reasonable agreement with experimental studies performed in the presence of ethanol. We find that in the presence of ethanol the drug molecules were adsorbed at the interface of solvent and MOFs. Moreover, the computationally calculated adsorption isotherms suggested that the drug adsorption was driven by electrostatic interactions at lower pressures (<10-4 Pa). Our computational predictions in the absence of ethanol were higher compared to those in the presence of ethanol. The MOF-adsorbate interaction (U HA) energy decreased with decrease in the size of a drug molecule in all three MOFs at all simulated pressures. At high pressure the interaction energy increases with increase in the MOFs pore size as the number of molecules adsorbed increases. Thus, our research shows the important role played by solvent in drug adsorption and suggests that it is critical to consider solvent while performing computational studies.

Key factors for successful generation of protein-fragment structures requirement on protein, crystals, and technology

In the past two decades, fragment-based approaches have evolved as a predominant strategy in lead discovery. The availability of structural information on the interaction geometries of binding fragments is key to successful structure-guided fragment-to-lead evolution. In this chapter, we illustrate methodological advances for protein-fragment crystal structure generation in order to offer general lessons on the importance of fragment properties and the most appropriate crystallographic setup to evaluate them. We analyze elaborate protocols, methods, and clues applied to challenging complex formation projects. The results should assist medicinal chemists to select the most promising targets and strategies for fragment-based crystallography as well as provide a tutorial to structural biologists who attempt to determine protein-fragment structures.

Probing the high energy states in proteins by proteolysis

Unless the native conformation has an unstructured region, proteases cannot effectively digest a protein under native conditions. Digestion must occur from a higher energy form, when at least some part of the protein is exposed to solvent and becomes accessible by proteases. Monitoring the kinetics and denaturant dependence of proteolysis under native conditions yields insight into the mechanism of proteolysis as well as these high-energy conformations. We propose here a generalized approach to exploit proteolysis as a tool to probe high-energy states in proteins. This "native state proteolysis" experiment was carried out on Escherichia coli ribonuclease HI. Mass spectrometry and N-terminal sequencing showed that thermolysin cleaves the peptide bond between Thr92 and Ala93 in an extended loop region of the protein. By comparing the proteolysis rate of the folded protein and a peptidic substrate mimicking the sequence at the cleavage site, the energy required to reach the susceptible state (Delta G(proteolysis)) was determined. From the denaturant dependence of Delta G(proteolysis), we determined that thermolysin digests this protein through a local fluctuation, i.e. localized unfolding with minimal change in solvent assessable surface area. Proteolytic susceptibilities of proteins are discussed based on the finding of this local fluctuation mechanism for proteolysis under native conditions.