Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data

Abstract

This work describes the development and testing of a method for the identification and classification of conserved water molecules and their networks from molecular dynamics (MD) simulations. The conserved waters in the active sites of proteins influence protein–ligand binding. Recently, several groups have argued that a water network formed from conserved waters can be used to interpret the thermodynamic signature of the binding site. We implemented a novel methodology in which we apply the complex approach to categorize water molecules extracted from the MD simulation trajectories using clustering approaches. The main advantage of our methodology as compared to current state of the art approaches is the inclusion of the information on the orientation of hydrogen atoms to further inform the clustering algorithm and to classify the conserved waters into different subtypes depending on how strongly certain orientations are preferred. This information is vital for assessing the stability of water networks. The newly developed approach is described in detail as well as validated against known results from the scientific literature including comparisons with the experimental data on thermolysin, thrombin, and Haemophilus influenzae virulence protein SiaP as well as with the previous computational results on thermolysin. We observed excellent agreement with the literature and were also able to provide additional insights into the orientations of the conserved water molecules, highlighting the key interactions which stabilize them. The source code of our approach, as well as the utility tools used for visualization, are freely available on GitHub.

In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development

“…The ligand C(7)O in the back of the pocket does not form any direct interactions but may have some water-bridging potential [ 31 ], possibly with Asp200 sidechain carboxylate. Water-bridging in protein–ligand complexes can play a significant role in drug design [ 32 ]. Elsewhere, there is potential for van der Waals contacts with the same non-polar residues as mentioned for compound 1 above; the phenylamino moiety (ring E) points more in the direction of Ile62, but is also in reasonable proximity to the sidechain of Tyr134 from the hinge region, as well as Phe67 and Val70.…”

Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach

“…In the future, data for density analysis could also be obtained by using theoretical approaches such as MD simulations ,− facilitating the applicability of the MADE approach to less-investigated systems. Such an extension has already been performed with good results for conserved water identification with MD simulations. , In the future, if structure prediction tools such as AlphaFold evolve to include cofactors, they may also provide a means for our approach to obtain additional structural data. We also advocate the use of MD simulations on identified conserved water molecules for further structural optimization and for a critical study of dynamic water networks.…”

Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory

“…The enthalpic and entropic parameters of binding of water molecules are essential in understanding the role of water within a protein structure and its impact on the drug design process 45 . However, it is currently impossible to perform thermodynamic measurements for a single water molecule within a protein structure by experimental method because the effects cannot be isolated from all other water molecules 46 . The advanced computational tools and techniques (e.g., GIST, 47 WATCLUST, 48 WaterMap, 49,50 AquaMMapS, 51 ProBiS H 2 O, 52 and WATsite 53–55 ) represent an alternative approach for predicting the binding site of water molecules with a complete structural, dynamical, and thermodynamic picture of the protein system.…”

“…45 However, it is currently impossible to perform thermodynamic measurements for a single water molecule within a protein structure by experimental method because the effects cannot be isolated from all other water molecules. 46 The advanced computational tools and techniques (e.g., GIST, 47 WATCLUST, 48 WaterMap, 49,50 AquaMMapS, 51 ProBiS H 2 O, 52 and WATsite [53][54][55] represent an alternative approach for predicting the binding site of water molecules with a complete structural, dynamical, and thermodynamic picture of the protein system. Hence, applying the theory to calculate the binding free energy of a specific individual water molecule will only be a viable option for this purpose, as experimental methods cannot directly measure the binding energy of a single water molecule in a protein system.…”