Design, optimisation and validation of novel HSP-70 modulators

Abstract

Heat shock protein 70 (HSP70) has a cytoprotective role against tumour necrosis factor alpha apoptosis, enhancing cancer cell survival. Literature indicates that overexpression of HSP70 molecules in triple negative breast cancer (TNBC) results in a cytoprotective role preventing apoptosis (Lazarev et al., 2018). Molecular inhibitors targeting different parts of the HSP70 survival pathway are in clinical trial phases. TNBC manifests the poorest prognosis of breast cancer subtypes due to the lack of targeted therapy. VER-155008 (4(-{(2R,3S,4R)-5-[(R)-6- Amino-8-(3,4-dichloro-benzylamino)-purin-9-yl]3,4-dihydroxy-tetrahydro-furan-2- ylmethoxymethyl}-benzonitrile), an HSP70 molecular inhibitor, was used as a scaffold to design molecules with the potential to challenge the HSP70’s tumour protective role. Its bioactive coordinates were extracted from pdb crystallographic deposition 4IO8 (Bernstein et al., 1997; Schlecht et al., 2013) describing its co-crystallisation together with the HSP70 receptor. Virtual screening (VS – Ligand-based) and de novo (structure-based) drug design tools were used to identify structures capable of similar inhibitory roles. Using LigandScout®, a consensus pharmacophore was designed superimposing the extracted VER-155008 and ADP-486, an endogenous ligand, from pdb crystallographic deposition 3JXU (Wisniewska et al., 2010). A protomol was modelled using Sybyl-X ®. Using Lipinski rule of 5 and Rule of 3 filters for lead likeness, VS yielded 7 high affinity HSP70 modulators. When docked into the proposed protomol, the top 3 hits had calculated binding affinities of 5.24, 5.60 and 5.29 respectively expressed in terms of total score. In the de novo approach, 5 drawn seeds derived from the VER-155008 scaffold sustained novel growth to fit the ligand binding pocket (LBP). Topology maps of the highest affinity hits were mapped, with the highest affinity molecules being further optimised. From these hits, two superior hybrid molecules were modelled using LigandScout®. Conformational analysis of the hybrids complexed with the HSP70 LBP was performed, and graphs were drawn. This study was valuable in the modelling of an average pharmacophoric structure that predisposed to optimal small molecule interaction with the HSP70 ligand binding site. The de novo approach retained the critical VER-155008 moieties with novel side-chain incorporation to create novel high efficiency molecules capable of successful target modulation.