Mapping Water Thermodynamics on Drug Candidates via Molecular Building Blocks: a Strategy to Improve Ligand Design and Rationalize SAR.

The consideration of interactions involving water molecules in protein-ligand binding is widely appreciated in drug discovery nowadays. However, it is not ultimately clear how insights about these interactions translate into molecular design concepts. In this work, we introduce a computational strategy that, trained with high-precision experimental data, allows for the decomposition of water-related thermodynamic properties into chemically relevant building blocks (BBs) of a given ligand scaffold. For each of these BBs, a score based on solvation energy and entropy is computed, thus enabling the analysis of solvent-related affinity contributions for individual BBs. We find the nonvariable BB in a congeneric ligand pair to have a larger impact on the binding affinity than the variable part thus suggesting strong cooperative effects. Furthermore, we find enhanced solute-solvent interactions for a BB due to the presence of a C-F bond. Our investigation may be used to design drug molecules with tailored solvent thermodynamic properties.

Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms.

Water molecules and their impact on the enthalpy and entropy of protein-ligand binding are of considerable interest in drug discovery. In this contribution, we use multiobjective optimization to fit the solvent enthalpy and entropy scoring terms of grid inhomogeneous solvation theory (GIST)-based solvent functionals to measured isothermal titration calorimetry (ITC) data of protein-ligand-binding reactions for ligand pairs of the protein thrombin. For the investigated ligand pairs, the overwhelming contribution to the relative binding affinity difference is assumed to be attributed to the contribution of water molecules. We present different implementations of the solvent functionals and then proceed by analyzing the most successful one in more detail through error assessment and presentation of the scoring regions in the binding pocket and the unbound ligands of selected examples. We find overall good agreement between calculated and experimental data and, although physically not fully justified, the ligand-desolvation score increases binding affinity, thus suggesting that the solvent molecules on the surface of the unbound ligand constitute a proxy for interactions gained through the protein. Furthermore, we find limited transferability of the parameters even between similar protein targets, thus suggesting refitting for each new protein target. Possible reasons for the limited transferability may arise through the initial assumption of dominating water contributions to binding affinity. Nonetheless, overall our study demonstrates a consistent approach to assign thermodynamic quantities to water molecules that is sensible to measured thermodynamic signatures and enables bridging the gap between experimentally determined water positions in protein-ligand complexes and measured thermodynamic data.

Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT.

Fragment-based lead discovery was applied to tRNA-guanine transglycosylase, an enzyme modifying post-transcriptionally tRNAs in Shigella, the causative agent of shigellosis. TGT inhibition prevents translation of Shigella's virulence factor VirF, hence reducing pathogenicity. One discovered fragment opens a transient subpocket in the preQ1-recognition site by pushing back an aspartate residue. This step is associated with reorganization of further amino acids structurally transforming a loop adjacent to the recognition site by duplicating the volume of the preQ1-recognition pocket. We synthesized 6-carboxamido-, 6-hydrazido-, and 4-guanidino-benzimidazoles to target the opened pocket, including a dihydro-imidazoquinazoline with a propyn-1-yl exit vector pointing into the transient pocket and displacing a conserved water network. MD simulations and hydration-site analysis suggest water displacement to contribute favorably to ligand binding. A cysteine residue, exclusively present in bacterial TGTs, serves as gatekeeper of the transient subpocket. It becomes accessible upon pocket opening for selective covalent attachment of electrophilic ligands in eubacterial TGTs.

Conformational Changes in Alkyl Chains Determine the Thermodynamic and Kinetic Binding Profiles of Carbonic Anhydrase Inhibitors.

Thermodynamics and kinetics of protein-ligand binding are both important aspects for the design of novel drug molecules. Presently, thermodynamic data are collected with isothermal titration calorimetry, while kinetic data are mostly derived from surface plasmon resonance. The new method of kinITC provides both thermodynamic and kinetic data from calorimetric titration measurements. The present study demonstrates the convenient collection of calorimetric data suitable for both thermodynamic and kinetic analysis for two series of congeneric ligands of human carbonic anhydrase II and correlates these findings with structural data obtained by macromolecular crystallography to shed light on the importance of shape complementarity for thermodynamics and kinetics governing a protein-ligand binding event. The study shows how minute chemical alterations change preferred ligand conformation and can be used to manipulate thermodynamic and kinetic signatures of binding. They give rise to the observation that analogous n-alkyl and n-alkyloxy derivatives of identical chain length swap their binding kinetic properties at unchanged binding affinity.

Role of Water Molecules in Protein-Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics.

The mechanism by which water molecules modulate biomolecular interactions and the time scale of microscopic solvation processes are usually not known. This is particularly problematic as it prevents the incorporation of effects of water molecules into the design of drug molecules with optimal binding kinetics and selectivity. We investigated this crucial problem of drug discovery using trypsin and thrombin in complex with benzamidine and N-amidinopiperidine. For these systems, we studied the mechanism and time scale of solvation using molecular dynamics and umbrella sampling calculations. In thrombin, water molecules are seemingly stable in the apo binding pocket and have an exchange rate on the nanosecond time scale. On the contrary, water molecules in apo trypsin exchange approximately one order of magnitude faster than in thrombin. This difference in the exchange rate is due to internal water channels that are only found in thrombin linking the interior of the binding pocket with bulk solvent. These cause the exchange rate of water molecules to be independent of the ligand molecule. However, in the case of trypsin, the solvent exchange rate greatly varies between the two complexes, indicating a strong dependence on the ligand molecule. Furthermore, the binding mechanism of the ligand molecules critically depends on water molecules that intercalate between key amino acids and the ligand, leading to enhanced water residence times in intermediate dissociation steps. Our findings strongly indicate a selectivity discriminating role of water molecules for these two proteins and underline the functional interplay between water channels and binding affinity of ligand molecules.

Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals.

In drug design, the importance of molecular solvation and desolvation is increasingly appreciated and water molecules are recognized as active contributors to protein-ligand binding. However, despite a number of theoretical approaches, computational tools are still far from routinely integrating solvation features into rational structure-affinity relationships (SARs). In this contribution, we present a set of solvent functional-based models, which calculate the relative binding free energy contributions resulting from solvation for a diverse set of 53 thrombin protein-ligand complexes. These protein-ligand complexes were further matched into chemically similar pairs of ligand molecules. Our solvent functionals are based on molecular dynamics simulations in conjunction with grid inhomogeneous solvation theory (GIST) processing, and they are calibrated using accurate experimental data from isothermal titration calorimetry (ITC) measurements. We found that excellent agreement with experimental measurements can be achieved by considering either the desolvation of the protein-binding pocket or the ligand in solution prior to binding. The incorporation of contributions from the protein-ligand complexes generally results in good agreement with experimental measurements but require additional adjustment of spatial cutoff parameters. In addition, we investigated the transfer of the trained solvent functionals to another protein target, which revealed deviating performance results, indicating a target-specific treatment of solvation features within the model. Together with our tool GIST-based processing of solvent functionals (Gips), we provide a way to automatically generate solvent functional parameters from GIST data and allow for the design of compounds with favorable solvation properties given the chemical similarity and affinity range of the matching pairs in the training set. Finally, we reflect on the resemblance with the popular three-dimensional quantitative SAR (3D-QSAR) method, as our study allows for (retrospective) insights on the high predictive power of this well-established method.

Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.

Structural fixation of a ligand in its bioactive conformation may, due to entropic reasons, improve affinity. We present a congeneric series of thrombin ligands with a variety of functional groups triggering preorganization prior to binding. Fixation in solution and complex formation have been characterized by crystallography, isothermal titration calorimetry (ITC), and molecular dynamics (MD) simulations. First, we show why these preorganizing modifications do not affect the overall binding mode and how key interactions are preserved. Next, we demonstrate how preorganization thermodynamics can be largely dominated by enthalpy rather than entropy because of the significant population of low-energy conformations. Furthermore, a salt bridge is shielded by actively reducing its surface exposure, thus leading to an enhanced enthalpic binding profile. Our results suggest that the consideration of the ligand solution ensemble by MD simulation is necessary to predict preorganizing modifications that enhance the binding behavior of already promising binders.

Diamondoid Amino Acid-Based Peptide Kinase†A Inhibitor Analogues.

The incorporation of diamondoid amino acids (DAAs) into peptide-like drugs is a general strategy to improve lipophilicity, membrane permeability, and metabolic stability of peptidomimetic pharmaceuticals. We designed and synthesized five novel peptidic DAA-containing kinase inhibitors of protein kinase A using a sophisticated molecular dynamics protocol and solid-phase peptide synthesis. By means of a thermophoresis binding assay, NMR, and crystal structure analysis, we determined the influence of the DAAs on the secondary structure and binding affinity in comparison to the native protein kinase inhibitor, which is purely composed of proteinogenic amino acids. Affinity and binding pose are largely conserved. One variant showed 6.5-fold potency improvement, most likely related to its increased side chain lipophilicity. A second variant exhibited slightly decreased affinity presumably due to loss of hydrogen-bond contacts to surrounding water molecules of the first solvation shell.

Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.

Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 Å in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.

On the Implication of Water on Fragment-to-Ligand Growth in Kinase Binding Thermodynamics.

A ligand-binding study is presented focusing on thermodynamics of fragment expansion. The binding of four compounds with increasing molecular weight to protein kinase A (PKA) was analyzed. The ligands display affinities between low-micromolar to nanomolar potency despite their low molecular weight. Binding free energies were measured by isothermal titration calorimetry, revealing a trend toward more entropic and less enthalpic binding with increase in molecular weight. All protein-ligand complexes were analyzed by crystallography and solution NMR spectroscopy. Crystal structures and solution NMR data are highly consistent, and no major differences in complex dynamics across the series are observed that would explain the differences in the thermodynamic profiles. Instead, the thermodynamic trends result either from differences in the solvation patterns of the conformationally more flexible ligand in aqueous solution prior to protein binding as molecular dynamics simulations suggest, or from local shifts of the water structure in the ligand-bound state. Our data thus provide evidence that changes in the solvation pattern constitute an important parameter for the understanding of thermodynamic data in protein-ligand complex formation.

Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug-Kinase Binding.

Biophysical parameters can accelerate drug development; e.g., rigid ligands may reduce entropic penalty and improve binding affinity. We studied systematically the impact of ligand rigidification on thermodynamics using a series of fasudil derivatives inhibiting protein kinase A by crystallography, isothermal titration calorimetry, nuclear magnetic resonance, and molecular dynamics simulations. The ligands varied in their internal degrees of freedom but conserve the number of heteroatoms. Counterintuitively, the most flexible ligand displays the entropically most favored binding. As experiment shows, this cannot be explained by higher residual flexibility of ligand, protein, or formed complex nor by a deviating or increased release of water molecules upon complex formation. NMR and crystal structures show no differences in flexibility and water release, although strong ligand-induced adaptations are observed. Instead, the flexible ligand entraps more efficiently water molecules in solution prior to protein binding, and by release of these waters, the favored entropic binding is observed.

Price for Opening the Transient Specificity Pocket in Human Aldose Reductase upon Ligand Binding: Structural, Thermodynamic, Kinetic, and Computational Analysis.

Insights into the thermodynamic and kinetic signature of the transient opening of a protein-binding pocket resulting from accommodation of suitable substituents attached to a given parent ligand scaffold are presented. As a target, we selected human aldose reductase, an enzyme involved in the development of late-stage diabetic complications. To recognize a large scope of substrate molecules, this reductase opens a transient specificity pocket. The pocket-opening step was studied by X-ray crystallography, microcalorimetry, and surface plasmon resonance using a narrow series of 2-carbamoyl-phenoxy-acetic acid derivatives. Molecular dynamics simulations suggest that pocket opening occurs only once an appropriate substituent is attached to the parent scaffold. Transient pocket opening of the uncomplexed protein is hardly recorded. Hydration-site analysis suggests that up to five water molecules entering the opened pocket cannot stabilize this state. Sole substitution with a benzyl group stabilizes the opened state, and the energetic barrier for opening is estimated to be ∼5 kJ/mol. Additional decoration of the pocket-opening benzyl substituent with a nitro group results in a huge enthalpy-driven potency increase; on the other hand, an isosteric carboxylic acid group reduces the potency 1000-fold, and binding occurs without pocket opening. We suggest a ligand induced-fit mechanism for the pocket-opening step, which, however, does not represent the rate-determining step in binding kinetics.

A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring.

With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.

Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin.

Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a ß-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFPLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74 000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.

Impact of Surface Water Layers on Protein--Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?

Drug binding involves changes of the local water structure around proteins including water rearrangements across surface-solvation layers around protein and ligand portions exposed to the newly formed complex surface. For a series of thermolysin-binding phosphonamidates, we discovered that variations of the partly exposed P2'-substituents modulate binding affinity up to 10 kJ mol(-1) with even larger enthalpy/entropy partitioning of the binding signature. The observed profiles cannot be completely explained by desolvation effects. Instead, the quality and completeness of the surface water network wrapping around the formed complexes provide an explanation for the observed structure-activity relationship. We used molecular dynamics to compute surface water networks and predict solvation sites around the complexes. A fairly good correspondence with experimental difference electron densities in high-resolution crystal structures is achieved; in detail some problems with the potentials were discovered. Charge-assisted contacts to waters appeared as exaggerated by AMBER, and stabilizing contributions of water-to-methyl contacts were underestimated.