title: Global connectivity of hub residues in Oncoprotein structures encodes genetic factors dictating personalized drug response to targeted Cancer therapy.
abstract: The efficacy and mechanisms of therapeutic action are largely described by atomic bonds and interactions local to drug binding sites. Here we introduce global connectivity analysis as a high-throughput computational assay of therapeutic action--inspired by the Google page rank algorithm that unearths most "globally connected" websites from the information-dense world wide web (WWW). We execute short timescale (30 ps) molecular dynamics simulations with high sampling frequency (0.01 ps), to identify amino acid residue hubs whose global connectivity dynamics are characteristic of the ligand or mutation associated with the target protein. We find that unexpected allosteric hubs--up to 20 Å from the ATP binding site, but within 5 Å of the phosphorylation site--encode the Gibbs free energy of inhibition (ΔG(inhibition)) for select protein kinase-targeted cancer therapeutics. We further find that clinically relevant somatic cancer mutations implicated in both drug resistance and personalized drug sensitivity can be predicted in a high-throughput fashion. Our results establish global connectivity analysis as a potent assay of protein functional modulation. This sets the stage for unearthing disease-causal exome mutations and motivates forecast of clinical drug response on a patient-by-patient basis. We suggest incorporation of structure-guided genetic inference assays into pharmaceutical and healthcare Oncology workflows.
authors.affiliation: Lumen Biomics Inc., 1 Broadway, Cambridge, Massachusetts 02142, USA.
authors.forename: Venky
authors.initials: V
authors.lastname: Soundararajan
authors.affiliation: Lumen Biomics Inc., 1 Broadway, Cambridge, Massachusetts 02142, USA.
authors.forename: Murali
authors.initials: M
authors.lastname: Aravamudan
mesh_terms: D001665:Binding Sites / Q000235:genetics; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D006801:Humans; D056004:Molecular Dynamics Simulation; D058990:Molecular Targeted Therapy / Q000379:methods; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D015513:Oncogene Proteins / Q000235:genetics*; D057285:Precision Medicine / Q000379:methods; D011485:Protein Binding / Q000235:genetics; D011494:Protein Kinases / Q000235:genetics
chemical_list: D015513:Oncogene Proteins; D011494:Protein Kinases