Dynamics of conserved waters in human Hsp90: implications for drug design

WaterKit: Thermodynamic Profiling of Protein Hydration Sites

Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the most recent decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models) to more computationally expensive and accurate ones, mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show an unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well-suited to be integrated in high-throughput pipelines such as molecular docking.

Assay design and development strategies for finding Hsp90 inhibitors and their role in human diseases

Heat shock protein 90 (Hsp90) is a molecular chaperone that facilitates the maturation of its client proteins including protein kinases, transcription factors, and steroid hormone receptors which are structurally and functionally diverse. These client proteins are involved in various cellular signaling pathways, and Hsp90 is implicated in various human diseases including cancer, inflammation, and diseases associated with protein misfolding; thus making Hsp90 a promising target for drug discovery. Some of its client proteins are well-known cancer targets. Instead of targeting these client proteins individually, however, targeting Hsp90 is more practical for cancer drug development. Efforts have been invested in recognizing potential drugs for clinical use that inhibit Hsp90 activity and result in the prevention of Hsp90 client maturation and dampening of subsequent signaling cascades. Here, we discuss current assays and technologies used to find and characterize Hsp90 inhibitors that include biophysical, biochemical, cell-based assays and computational modeling. This review highlights recent discoveries that N-terminal isoform-selective compounds and inhibitors that target the Hsp90 C-terminus that may offer the potential to overcome some of the detriments observed with pan Hsp90 inhibitors. The tools and assays summarized in this review should be used to develop Hsp90-targeting drugs with high specificity, potency, and drug-like properties that may prove immensely useful in the clinic.

A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors

Molecular chaperone Heat Shock Protein 90 (Hsp90) represents an interesting chemotherapeutic target for cancer treatments as it plays a role in cancer proliferation. Thus, continued effort to identify novel inhibitors of this target is an important task. Drug design using computational approach has gained significant attention in recent years. This work aims to propose docking protocols to re-purpose FDA-approved drugs targeting Hsp90. Sensitivity of results to different docking protocols such apo, holo and receptor ensembles (relaxed complex) structures, the role of water and conformational changes of Hsp90, are described. We show that the protein conformation and water have effects on drug binding. Holo relaxed complex receptors ensembles improves the binding energy of ligands to the protein. We also compare and contrast structural stability of three drugs namely: ezetimibe, pitavastatin and vilazodon in the Hsp90 protein. The results obtained serves as a possible basis towards developing Hsp90 inhibitors.

Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015

Here is reported the development of a novel scoring function that performs remarkably well at identifying the native binding pose of a subset of HSP90 inhibitors containing aminopyrimidine or resorcinol based scaffolds. This scoring function is called PocketScore, and consists of the interaction energy between a ligand and three residues in the binding pocket: Asp93, Thr184 and a water molecule. We integrated PocketScore into a molecular docking workflow, and used it to participate in the Drug Design Data Resource (D3R) Grand Challenge 2015 (GC2015). PocketScore was able to rank 180 molecules of the GC2015 according to their binding affinity with satisfactory performance. These results indicate that the specific residues considered by PocketScore are determinant to properly model the interaction between HSP90 and its subset of inhibitors containing aminopyrimidine or resorcinol based scaffolds. Moreover, the development of PocketScore aimed at improving docking power while neglecting the prediction of binding affinities, suggesting that accurate identification of native binding poses is a determinant factor for the performance of virtual screens.

Computational polypharmacology analysis of the heat shock protein 90 interactome

The design of a single drug molecule that is able to simultaneously and specifically interact with multiple biological targets is gaining major consideration in drug discovery. However, the rational design of drugs with a desired polypharmacology profile is still a challenging task, especially when these targets are distantly related or unrelated. In this work, we present a computational approach aimed at the identification of suitable target combinations for multitarget drug design within an ensemble of biologically relevant proteins. The target selection relies on the analysis of activity annotations present in molecular databases and on ligand-based virtual screening. A few target combinations were also inspected with structure-based methods to demonstrate that the identified dual-activity compounds are able to bind target combinations characterized by remote binding site similarities. Our approach was applied to the heat shock protein 90 (Hsp90) interactome, which contains several targets of key importance in cancer. Promising target combinations were identified, providing a basis for the computational design of compounds with dual activity. The approach may be used on any ensemble of proteins of interest for which known inhibitors are available.

Molecular docking study, synthesis and biological evaluation of Schiff bases as Hsp90 inhibitors

Heat shock protein 90 (Hsp90) is an emerging attractive target for the discovery of novel cancer therapeutic agents. Docking methods are powerful in silico tools for lead generation and optimization. In our mission to rationally develop novel effective small molecules against Hsp90, we predicted the potency of our designed compounds by Sybyl surflex Geom X docking method. The results of the above studies revealed that Schiff bases derived from 2,4-dihydroxy benzaldehyde/5-chloro-2,4-dihydroxy benzaldehyde demonstrated effective binding with the protein. Subsequently, a few of them were synthesized (1-10) and characterized by IR, (1)HNMR and mass spectral analysis. The synthesized molecules were evaluated for their potential to suppress Hsp90 ATPase activity by Malachite green assay. The anticancer studies were performed by 3-(4,5-dimethythiazol- 2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay method. The software generated results was in satisfactory agreement with the evaluated biological activity.

Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.

Systematic placement of structural water molecules for improved scoring of protein-ligand interactions

Structural water molecules are found in many protein-ligand complexes. They are known to be vital in mediating hydrogen-bonding interactions and, in some cases, key for facilitating tight binding. It is thus very important to consider water molecules when attempting to model protein-ligand interactions for cognate ligand identification, virtual screening and drug design. While the rigid treatment of water molecules present in structures is feasible, the more relevant task of treating all possible positions and orientations of water molecules with each possible ligand pose is computationally daunting. Current methods in molecular docking provide partial treatment for such water molecules, with modest success. Here we describe a new method employing dead-end elimination to place water molecules within a binding site, bridging interactions between protein and ligand. Dead-end elimination permits a thorough, though still incomplete, treatment of water placement. The results show that this method is able to place water molecules correctly within known complexes and to create physically reasonable hydrogen bonds. The approach has also been incorporated within an inverse molecular design approach, to model a variety of compounds in the process of de novo ligand design. The inclusion of structural water molecules, combined with ranking based on the electrostatic contribution to binding affinity, improves a number of otherwise poor energetic predictions.

Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies

The role of water molecules is increasingly gaining interest in drug design, and several studies have highlighted their paramount contributions to the specificity and the affinity of ligand binding. In this study, we employ the two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations, molecular dynamics (MD) simulations, and molecular docking studies to investigate the effect of bridging water molecules at the GSK3β-inhibitors interfaces. The results obtained from the ONIOM geometry optimization and AIM analysis corroborated the presence of bridging water molecules that form hydrogen bonds with protein side chain of Thr138 and/or backbone of Gln185, and mediate interactions with inhibitors in the 10 selected GSK3β-inhibitor complexes. Subsequently, MD simulations carried out on a representative system of 1R0E demonstrated that the bridging water molecule is stable at the GSK3β-inhibitor interface and appears to contribute to the stability of the protein-inhibitor interactions. Furthermore, molecular docking studies of GSK3β-inhibitor complexes indicated that the inhibitors can increase binding affinities and the better docked conformation of inhibitors can be obtained by inclusion of the bridging water molecules, especially for the flexible inhibitors, in docking experiments into individual protein conformations. Our results elucidate the importance of bridging water molecules at the GSK3β-inhibitor interfaces and suggest that they might prove useful in rational drug design.

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

Conventional molecular dynamics simulations on 50 ns to 1 μs time scales were used to study the effects of explicit solvent models on the conformational behavior and solvation of two oligopeptide solutes: α-helical EK-peptide (14 amino acids) and a β-hairpin chignolin (10 amino acids). The widely used AMBER force fields (ff99, ff99SB, and ff03) were combined with four of the most commonly used explicit solvent models (TIP3P, TIP4P, TIP5P, and SPC/E). Significant differences in the specific solvation of chignolin among the studied water models were identified. Chignolin was highly solvated in TIP5P, whereas reduced specific solvation was found in the TIP4P, SPC/E, and TIP3P models for kinetic, thermodynamic, and both kinetic and thermodynamic reasons, respectively. The differences in specific solvation did not influence the dynamics of structured parts of the folded peptide. However, substantial differences between TIP5P and the other models were observed in the dynamics of unfolded chignolin, stability of salt bridges, and specific solvation of the backbone carbonyls of EK-peptide. Thus, we conclude that the choice of water model may affect the dynamics of flexible parts of proteins that are solvent-exposed. On the other hand, all water models should perform similarly for well-structured folded protein regions. The merits of the TIP3P model include its high and overestimated mobility, which accelerates simulation processes and thus effectively increases sampling.

Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation

The Polo-Like Kinase 1 (PLK1) acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis. PLK1 comprises two structural elements, a kinase domain and a polo-box domain (PBD). The PBD binds phosphorylated substrates to control substrate phosphorylation by the kinase domain. Although the PBD preferentially binds to phosphopeptides, it has a relatively broad sequence specificity in comparison with other phosphopeptide binding domains. We analysed the molecular determinants of recognition by performing molecular dynamics simulations of the PBD with one of its natural substrates, CDC25c. Predicted binding free energies were calculated using a molecular mechanics, Poisson-Boltzmann surface area approach. We calculated the per-residue contributions to the binding free energy change, showing that the phosphothreonine residue and the mainchain account for the vast majority of the interaction energy. This explains the very broad sequence specificity with respect to other sidechain residues. Finally, we considered the key role of bridging water molecules at the binding interface. We employed inhomogeneous fluid solvation theory to consider the free energy of water molecules on the protein surface with respect to bulk water molecules. Such an analysis highlights binding hotspots created by elimination of water molecules from hydrophobic surfaces. It also predicts that a number of water molecules are stabilized by the presence of the charged phosphate group, and that this will have a significant effect on the binding affinity. Our findings suggest a molecular rationale for the promiscuous binding of the PBD and highlight a role for bridging water molecules at the interface. We expect that this method of analysis will be very useful for probing other protein surfaces to identify binding hotspots for natural binding partners and small molecule inhibitors.

Introduction. Biomolecular simulation

'Everything that living things do can be understood in terms of the jigglings and wigglings of atoms' as Richard Feynman provocatively stated nearly 50 years ago. But how can we 'see' this wiggling and jiggling and understand how it drives biology? Increasingly, computer simulations of biological macromolecules are helping to meet this challenge.