Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing

Abstract

Background: Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds.

Methodology: In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy.

Conclusions: The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy.

Figure 1. Conformational association of an energetically favored ligand and specific target.

The ligand is associated to the specific target with hydrogen bonds and hydrophobic interactions inferring the biological activity of compounds. (A) The hypothetical model where the ligand is forming hydrogen bonds to target. (B) The ligand is associated with hydrophobic interactions. (Ci) target is modified. (Cii) ligand is modified. (Ciii) ligand is allied with metal-associated hydrogen bonds for a specific target showing the interrelation between long-range hydrogen bonds and hydrophobic interactions.

Figure 2. Sequence and structural alignment of c-Src and c-Abl kinase.

(A) The sequence and secondary structure alignment of c-Src and c-Abl; sequence alignment of c-Src and c-Abl has been carried out using ClustalW. The secondary structure assigned with the SSEA server is depicted as orange cylindrical (alpha helices) and light-blue arrows (beta-strand). (B) Three-dimensional structural alignments of c-Src and c-Abl kinases; superimposed structure of c-Src (PDB ID 2H8H) and c-Abl (PDB ID 2FO0); color coding for the ribbon diagram of c-Src is sand yellow and for c-Abl is split-pea-green color. This figure was made using PyMOL program (www.pymol.org).

Figure 3. Ligand-associated amino acids of c-Src and c-Abl Kinase.

(A) A stick model of active inhibitors 1, 12, 19 and 28 docked in c-Src with conserved hydrophobic amino acids is shown. (B) Stick model of active inhibitors 1, 12, 19 and 28 docked in c-Abl with conserved hydrophobic amino acids is shown. (C) Alignment of hydrophobic amino acids observed at the interface of c-Src (PDB ID 1Y57), c-Abl (PDB ID 1M52) and functionally important inhibitors as listed in Table S1: (1, 12, 19 and 28). In figure (B) and (C), structure was aligned using COOT and figure was made by PyMOL program.

Figure 4. Correlation between crystallographically determined and computationally- generated modeled structure.

(A) Heavy atom was docked between the ligand and hydrophobic amino acid in c-Src. (B) The sulfate group was at the interface of the ligand and hydrophobic amino acid. (C) Superimposed of (A) and (B) structure. All three figures were made by PyMOL program.

Figure 5. Hydrophobic interactions and hydrogen bonding between ligands and target.

(A) Two-dimensional representations of interactions observed between c-Src and ligands listed in Table S1: (1, 12, 19 and 28). (B) Two-dimensional representations of interactions observed between c-Abl and ligands listed in Table S1: (1, 12, 19 and 28). Hydrogen bonds are depicted with dashed line and hydrophobic interactions are shown as arcs. Both the figures were made using LIGPLOT program.