Untangling Dual-Targeting Therapeutic Mechanism of Epidermal Growth Factor Receptor (EGFR) Based on Reversed Allosteric Communication

Abstract

Dual-targeting therapeutics by coadministration of allosteric and orthosteric drugs is drawing increased attention as a revolutionary strategy for overcoming the drug-resistance problems. It was further observed that the occupation of orthosteric sites by therapeutics agents has the potential to enhance allosteric ligand binding, which leads to improved potency of allosteric drugs. Epidermal growth factor receptor (EGFR), as one of the most critical anti-cancer targets belonging to the receptor tyrosine kinase family, represents a quintessential example. It was revealed that osimertinib, an ATP-competitive covalent EGFR inhibitor, remarkably enhanced the affinity of a recently developed allosteric inhibitor JBJ-04-125-02 for EGFRL858R/T790M. Here, we utilized extensive large-scale molecular dynamics simulations and the reversed allosteric communication to untangle the detailed molecular underpinning, in which occupation of osimertinib at the orthosteric site altered the overall conformational ensemble of EGFR mutant and reshaped the allosteric site via long-distance signaling. A unique intermediate state resembling the active conformation was identified, which was further stabilized by osimertinib loading. Based on the allosteric communication pathway, we predicted a novel allosteric site positioned around K867, E868, H893, and K960 within the intermediate state. Its correlation with the orthosteric site was validated by both structural and energetic analysis, and its low sequence conservation indicated the potential for selective targeting across the human kinome. Together, these findings not only provided a mechanistic basis for future clinical application of the dual-targeting therapeutics, but also explored an innovative perception of allosteric inhibition of tyrosine kinase signaling.

Deciphering the Mechanism of Gilteritinib Overcoming Lorlatinib Resistance to the Double Mutant I1171N/F1174I in Anaplastic Lymphoma Kinase

“…However, in both the wild-type lorlatinib- and gilteritinib-bound states, the N-lobe (residues 1,093–1,203) showed enhanced anti-correlated motions with the C-lobe (resdues 1,204–1,401) compared to both the double mutant states ( Supplementary Figure S4 ). This pattern of the anti-correlated motions between the N- and C-lobes has been previously reported in MD simulations of other protein kinases such as protein kinase A ( Masterson et al, 2011 ), glycogen synthase kinase 3β ( Lu et al, 2011 ), and EGFR ( Qiu et al, 2021 ). Collectively, the CC ij analysis indicated that the double mutations I1171N/F1174I decreased the anti-correlated motions between the N- and C-lobes of ALK kinase domain.…”

“…The gilteritinib was extracted from the 4JQR structure, and we then employed molecular docking method to dock gilteritinib into the ALK active site using the crystal structure of ALK–lorlatinib complex (PDB ID: 4CLI) ( Johnson et al, 2014 ). Molecular docking method has been widely used to model previously unknown protein kinase/enzyme–ligand interactions such as epidermal growth factor receptor (EFGR)–osimertinib ( Qiu et al, 2021 ), angiotension-converting 2 (ACE2)–puerarin/quercetin ( Pan et al, 2020 ), proliferator activated receptor γ (PPARγ)–bavachinin ( Feng et al, 2021 ), and sirtuin 6 (SIRT6)–JYQ-42 interactions ( Zhang et al, 2021 ).…”

Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells

“…With the significant progresses in biophysics and bioinformatics, computational exploration of allosteric sites has prominently boosted rational allosteric drug design 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 . The reversed allosteric communication, namely orthosteric perturbations induce the emergence of allosteric sites, has been exemplified in the exchange protein activated by cAMP isoform 1 (EPAC1), 15-lipoxygenase and phosphoinositide-dependent protein kinase 1 (PDK1).…”

Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6

“…To describe and investigate residue-residue interactions within biomolecular systems, we employed concepts from network theories [108] , [109] , [110] , [111] . The whole ribonucleotide protein complex was defined as a set of nodes, which were assigned to the Cα atom within each amino acid residue or P atom in the nucleotide backbone for each nucleotide.…”