Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility

Abstract

We present a new molecular dynamics methodology to assist in structure-based drug design and other studies that seek to predict protein deformability. Termed Active Site Pressurization (ASP), the new methodology simply injects a resin into the ligand binding-site of a protein during the course of a molecular dynamics simulation such that novel, energetically reasonable protein conformations are generated in an unbiased way that may be better representations of the ligand binding conformation than are currently available. Here we apply two different versions of the ASP methodology to three proteins, cytochrome P450cam, PcrA helicase, and glycogen synthase kinase 3beta (GSK3beta), and show that the method is capable of inducing significant conformational changes when compared to the X-ray crystal structures. Application of the ASP methodology therefore provides a view of binding site flexibility that is a rich source of data for inclusion in a variety of further investigations, including high-throughput virtual screening, lead hopping, revealing alternative modes of deformation, and revealing hidden exit and entrance tunnels.

Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1

“…[3][4][5][6] Consequently, binding sites may not be apparent in experimental structures of the unliganded protein. As a prototypical example, we focus here on the polo-box domain (PBD) of polo-like kinase 1 (Plk1), a serine/ threonine kinase that is overexpressed in a wide range of cancers, [7,8] and is a known anticancer target due to its critical role in mitotic progression.…”

Description and assessment of a model for GSK-3β database virtual screening

“…Moreover, it has been previously reported that kinases are subject to conformational changes during activation 23 , and several methods have been presented to overcome this phenomenon 24 . A new method based on molecular dynamics was recently proposed to simulate the flexibility of the active site, and it might also be an alternative to our proposed protocol 25 . We devised a new way to obtain several models from a PDB structure (see "Materials and methods") that presents the advantage of being inexpensive in terms of computational time and very easy to perform.…”

GPCRs through the keyhole: the role of protein flexibility in ligand binding to β-adrenoceptors

“…ASP was performed using the approach described by Withers et al, (Withers et al, 2008) re-implemented in code written in the modelling language NAB. (Macke & Case, 2009) Grids for the insertion of the Lennard-Jones (LJ) particles were built, with a 1.1 Å spacing, to encompass the region occupied by the carbazole group present in carazolol (1), plus a 7.0 Å margin along all axes beyond it.…”

“…We envisaged that our Active Site Pressurization (ASP) method (Withers, Mazanetz, Wang, Fischer, & Laughton, 2008) would be ideal for this investigation. ASP simulates the process of injecting particles into a protein cavity rather like injecting a resin into a mould.…”