Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin

Abstract

Dedicated to Professor Jack D. Dunitz on the occasion of his 90th birthdayThe hydrophobic effect is viewed as the driving force for the aggregation of nonpolar substances with extended lipophilic molecular surfaces in aqueous solution through the exclusion of water molecules from the formed interfaces. [1,2] It is usually quoted to explain why an oil/water mixture spontaneously separates, why soluble proteins fold with a hydrophobic core and a hydrophilic outer surface, [3,4] why membrane components assemble as lipid bilayers and micelles, why membrane proteins are accommodated in membrane segments, and why small molecules associate in protein binding pockets with mutual burial of hydrophobic surfaces. [5] In the latter instance, it is a general strategy in medicinal chemistry to improve protein-ligand binding by increasing the ligands hydrophobic surface which becomes buried in hydrophobic pockets of the target protein. In all cases, the hydrophobic effect is considered to be the major force of association. On the molecular level, this phenomenon is commonly attributed to the displacement of water molecules arranged around the hydrophobic surfaces, and entropic effects are made responsible to drive this association. The entropic profile is related to changes in the degree of ordering and the dynamic properties of the water molecules, which are assumed to be more disordered in the bulk water phase relative to where they were located prior to being displaced upon hydrophobic association. Recent studies have demonstrated, however, that hydrophobic interactions can originate either from enthalpyor entropy-driven binding, making simple explanations often presented for the hydrophobic effect insufficient. [6][7][8][9][10][11][12] Also in computational design tools the handling of explicit water molecules has received increasing recognition. Tools such as WaterMap and Szmap [13,14] try to take into account water structures in drug design and the properties of individual water molecules are discussed in terms of enthalpy and entropy.In order to obtain a better understanding of the hydrophobic effect on the molecular level and its role in proteinligand binding, we embarked on a systematic study using thermolysin (TLN) as a model system. [6] This thermostable bacterial zinc metalloprotease from Bacillus thermoproteolyticus exhibits three specificity pockets of predominantly hydrophobic nature (Scheme 1). It has been considered a prototype for the entire class of enzymes [15] owing to its highly conserved active-site architecture, despite remarkable sequence differences to other zinc proteases. Potent TLN inhibitors are often designed as transition-state analogues. [16][17][18] The enzyme has been frequently used as a surrogate [19][20][21][22][23] for other metalloenzymes against which new drugs are developed, and served as a model system to test ideas [24,25] and new methodological concepts. [26] TLN was one of the first crystallographically investigated metalloproteases [27,28] and its catalytic zinc ion is coordinated ...

Nonclassical Hydrophobic Effect in Micellization: Molecular Arrangement of Non‐Amphiphilic Structures

“…ITC measurements indicate that metallacarborane aggregation is enthalpy driven which can be related to dehydration of the cluster upon aggregation and, more generally, with so-called nonclassical hydrophobic effect. [37,41,42] It is in line with bulkiness of Figure 9. Probability distribution of the number of observed B-HࢫࢫࢫH-C dihydrogen bonds as measured in the simulated potential of mean force minima for gauche, cisoid, and transoid rotamers of COSAN pairs (see Figure 6).…”

Synthesis, experimental evaluation and molecular modelling of hydroxamate derivatives as zinc metalloproteinase inhibitors

“…However, the S2'-subpocket is more easily accessible for water molecules than the S1-subpocket [32]. Docking LM2 and ML25 into thermolysin showed docking poses both with the aromatic ring system in the S2 ' -and the S1-subpocket, and we could not rank the poses relative to each other based on scoring.…”

Stealth Amphiphiles: Self-Assembly of Polyhedral Boron Clusters

“…Two types of hydrophobic effect are known in the literature: classical and nonclassical one. [25][26][27][28][29]68 The former is closely related with entropy of water molecules, while the latter is explained by the enthalpy contribution of water (heat of hydration). Further, it is known that the water structure in the vicinity of hydrophobic objects 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 ACS Paragon Plus Environment …”