title: Quantum mechanics/molecular mechanics modeling of covalent addition between EGFR-cysteine 797 and N-(4-anilinoquinazolin-6-yl) acrylamide.
abstract: Irreversible epidermal growth factor receptor (EGFR) inhibitors can circumvent resistance to first-generation ATP-competitive inhibitors in the treatment of nonsmall-cell lung cancer. They covalently bind a noncatalytic cysteine (Cys797) at the surface of EGFR active site by an acrylamide warhead. Herein, we used a hybrid quantum mechanics/molecular mechanics (QM/MM) potential in combination with umbrella sampling in the path-collective variable space to investigate the mechanism of alkylation of Cys797 by the prototypical covalent inhibitor N-(4-anilinoquinazolin-6-yl) acrylamide. Calculations show that Cys797 reacts with the acrylamide group of the inhibitor through a direct addition mechanism, with Asp800 acting as a general base/general acid in distinct steps of the reaction. The obtained reaction free energy is negative (ΔA = -12 kcal/mol) consistent with the spontaneous and irreversible alkylation of Cys797 by N-(4-anilinoquinazolin-6-yl) acrylamide. Our calculations identify desolvation of Cys797 thiolate anion as a key step of the alkylation process, indicating that changes in the intrinsic reactivity of the acrylamide would have only a minor impact on the inhibitor potency.
authors: Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy.
authors: Luigi
authors: L
authors: Capoferri
authors: Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy.
authors: Alessio
authors: A
authors: Lodola
authors: Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy.
authors: Silvia
authors: S
authors: Rivara
authors: Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze 27/A, I-43124, Parma, Italy.
authors: Marco
authors: M
authors: Mor
mesh_terms: D000178:Acrylamides / Q000737:chemistry* / Q000494:pharmacology; D001224:Aspartic Acid / Q000737:chemistry; D020134:Catalytic Domain; D003545:Cysteine / Q000737:chemistry*; D066246:ErbB Receptors / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011789:Quantum Theory; D011799:Quinazolines / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology
chemical_list: D000178:Acrylamides; C000607358:N-(4-anilinoquinazolin-6-yl)acrylamide; D011799:Quinazolines; D001224:Aspartic Acid; C512478:EGFR protein, human; D066246:ErbB Receptors; D003545:Cysteine