Title:Water Mapping and Scoring Approaches to Predict the Role of
Hydration Sites in the Binding Affinity of PAK1 Inhibitors
Volume: 25
Issue: 4
Author(s): Jayashree Biswal, Prajisha Jayaprakash, Suresh Kumar Rayala, Ganesh Venkatraman, Raghu Rangasamy, Saritha Poopandi and Jeyaraman Jeyakanthan*
Affiliation:
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu,India
Keywords:
PAK1, SP and XP docking, WaterMap, WM/MM scoring, SARs, MDS.
Abstract: Aim: This study aims to develop and establish a computational model that can identify
potent molecules for p21-activating kinase 1 (PAK1)
Background: PAK1 is a well-established drug target that has been explored for various therapeutic
interventions. Control of this protein requires an indispensable inhibitor to curb the structural
changes and subsequent activation of signalling effectors responsible for the progression of
diseases, such as cancer, inflammatory, viral, and neurological disorders.
Objective: The study aims to establish a computational model that could identify active molecules
which will further provide a platform for developing potential PAK1 inhibitors.
Methods: A congeneric series of 27 compounds were considered for this study, with Ki (nm)
covering a minimum of 3 log range. The compounds were developed based on a previously
reported Group-I PAK inhibitor, namely G-5555. The 27 compounds were subjected to the SP and
XP mode of docking to understand the binding mode, its conformation and interaction patterns. To
understand the relevance of biological activity from computational approaches, the compounds
were scored against generated water maps to obtain WM/MM ΔG binding energy. Moreover,
molecular dynamics analysis was performed for the highly active compound to understand the
conformational variability and stability of the complex. We then evaluated the predictable binding
pose obtained from the docking studies.
Results: From the SP and XP modes of docking, the common interaction pattern with the amino
acid residues Arg299 (cation-π), Glu345 (Aromatic hydrogen bond), hinge region Leu347, salt
bridges Asp393 and Asp407 was observed, among the congeneric compounds. The interaction
pattern was compared with the co-crystal inhibitor FRAX597 of the PAK1 crystal structure (PDB id:
4EQC). The correlation with different docking parameters in the SP and XP modes was insignificant
and thereby revealed that the SP and XP’s scoring functions could not predict the active compounds.
This was due to the limitations in the docking methodology that neglected the receptor flexibility and
desolvation parameters. Hence, to recognise the desolvation and explicit solvent effects, as well as to
study the Structure-Activity Relationships (SARs) extensively, WaterMap (WM) calculations were
performed on the congeneric compounds. Based on displaceable unfavourable hydration sites (HS)
and their associated thermodynamic properties, the WM calculations facilitated in understanding the
significance of correlation in the folds of activity of highly active (19 and 17), moderately active (16
and 21) and less active (26 and 25) compounds. Furthermore, the scoring function from WaterMap,
namely WM/MM, led to a significant R2 value of 0.72 due to a coupled conjunction with MM
treatment and displaced unfavourable waters at the binding site. To check the “optimal binding
conformation”, molecular dynamics simulation was carried out with the highly active compound 19 to
explain the binding mode, stability, interactions, solvent-accessible area, etc., which could support
the predicted conformation with bioactive conformation.
Conclusion: This study determined the best scoring function, established SARs and predicted
active molecules through a computational model. This will contribute to the development of the
most potent PAK1 inhibitors.
