Non-covalent bonds play a crucial role in chemistry, biochemistry, and biology. H-bonds, and hydrophobic bonds at the core of protein folding, and govern reversible interactions between biomolecules and their ligands. In drug discovery, H-bonding and hydrophobic interactions define the affinity and selectivity of small molecules for their biological targets.
With the intent to better understand these interactions and their relevance in the design of small molecule modulators of biological function, several computational solvent-mapping methods have been developed over the past few years. Schrodinger introduced WaterMap, a method that allows understanding the locations and thermodynamics of water molecules that solvate binding sites, and guiding the optimization of small molecule hits; conserved, strongly bound water molecules are costly to displace but can be useful bridges. An alternative method for understanding the role of water in ligand binding, which uses all-atom molecular dynamics (MD), and that can be accessed through this company, was developed by De Fabritiis et al. in 2011. Mapping of other solvents like ACN, propane, benzene, and IPA has also been demonstrated with MD simulations of binary mixtures, and been put in the context of target druggability assessment.
A new category of substrate to study: organohalogens
Halogens are common substituents in drugs as halogen bonding interactions can offer key boosts in selectivity and potency. Initially attributed to van der Waals forces, this is now explained in terms of the halogen bond, another type of non-covalent interaction that in recent years has been exploited for many applications in synthetic, supramolecular and medicinal chemistry.
Anisotropy in halogen electron charge distribution allows halogens to interact with donors such as Lewis base centers and π-surfaces, something that, if one is to consider electron density alone, can be rather counter intuitive. Halogen-donor interactions increase with the polarizability of the halogen’s surrounding electron cloud, and with the withdrawing power of adjacent atoms. These observations are now explained using the sigma hole concept, which defines a region of positive charge at the surface of the halogen, along the covalent bond axis.
Within the complex structure of a protein, there are many atoms to which a halogen-containing substrate can form a halogen bond. Halogen – usually chlorine – interactions with backbone and side chain carbonyls, as well as with side chain alcohols, thiols and thioethers, amines and the surfaces of aromatic rings can affect the conformation of the protein as well as the affinity that other binding sites on the protein have for other substrates, such as water. This is however difficult to predict even though doing so could be highly beneficial in guiding structure-based drug design. Experimental techniques that allow solvent mapping such as the multiple solvent crystal structure (MCSC), can be effective but are time intensive and expensive to run, and lack of an ideal strategy and/or representative force fields have limited computational approaches.
Computational halogen bond mapping with molecular dynamics simulations
Recently, Verma and collaborators proposed a molecular dynamics based method for halogen bond mapping. This study aimed to observe the effect of a chosen probe, in this case chlorobenzene, on the binding sites of four different proteins using molecular dynamics. Chlorobenzene is potentially a bifunctional substrate; the sp2 bonded chlorine can probe for halogen bonds while the aromatic ring can probe for π-stacking, or hydrophobic sites. For proof-of-concept, MDM2(Pdb:1YCR), MCL-1(Pdb:3kJ0), interleukin-2(Pdb:1Z92), and Bcl-xL(Pdb:1BXL) were selected because of their involvement in protein-protein interactions, the availability of structural data, and the well reported structural changes they endure upon substrate binding, which can present unexposed halogen bonding sites. All-atom MD simulations were selected for the development of protein-small molecule interaction maps because other computational methods considered could not capture the protein’s dynamics sufficiently, and Lexa and Carlson showed this to be crucial for effective solvent interaction mapping.
For chlorobenzene preparation the authors used GAFF. Atomic charges were derived using the R.E.D. Server by fitting restrained electrostatic potential charges to a molecular electrostatic potential computed with Gaussian. One peculiarity of chlorobenzene when compared to benzene, a molecule the authors also used for mapping in a previous study, was found to be the propensity of the halogenated compound to aggregate at lower concentrations, which forced to reduce the substrate concentration by 25% to 0.15M, and to increase the sampling time during the simulation experiments to 10ns per trajectory.
Using molecular dynamics simulations to construct halogen affinity maps
For MDM2, all of the six halogen bonding sites found in the Pdb were recovered by the proposed method. Three of these, known to be occupied by a halogenated benzodiazepine inhibitor, and two others, occupied by Nutlin-2, were recovered on first instance by the mapping protocol. The sixth was recovered after modification of the Pdb structure, as the initial structure lacked an important sequence of residues at the N- terminus. In addition, four cryptic hydrophobic binding sites were detected that were not present in the initial input conformation of the protein. The existence of these sites could also be validated by matching with results available in the literature. For the other three targets the authors report similar results.
All-atom MD simulation with chlorobenzene can be used to map halogen and hydrophobic binding sites
Using molecular dynamics simulations, and the chlorobenzene parameters shown above, the authors could map halogen and hydrophobic binding sites on all four tested proteins. The results were consistent with available experimental data, and show the potential of this method in structure based drug design. As we have come to see in our own work at Acellera probing libraries of fragments using all-atom MD simulations, the choice of force field is difficult for halogenated molecules. The ability of the force fields used in this paper to reproduce the binding sites was remarkable, and could potentially be harnessed for a broader use in computer aided drug design.