Covalent inhibition is a reemerging paradigm in kinase drug design, but the roles of inhibitor binding affinity and chemical reactivity in overall potency are not well-understood. To characterize the underlying molecular processes at a microscopic level and determine the appropriate kinetic constants, specialized experimental design and advanced numerical integration of differential equations are developed. Previously uncharacterized investigational covalent drugs reported here are shown to be extremely effective epidermal growth factor receptor (EGFR) inhibitors (k inact /K i in the range 10), despite their low specific reactivity (k inact ≤ 2.1 × 10), which is compensated for by high binding affinities (K i < 1 nM). For inhibitors relying on reactivity to achieve potency, noncovalent enzyme-inhibitor complex partitioning between inhibitor dissociation and bond formation is central. Interestingly, reversible binding affinity of EGFR covalent inhibitors is highly correlated with antitumor cell potency. Furthermore, cellular potency for a subset of covalent inhibitors can be accounted for solely through reversible interactions. One reversible interaction is between EGFRCys 797 nucleophile and the inhibitor's reactive group, which may also contribute to drug resistance. Because covalent inhibitors target a cysteine residue, the effects of its oxidation on enzyme catalysis and inhibitor pharmacology are characterized. Oxidation of the EGFR cysteine nucleophile does not alter catalysis but has widely varied effects on inhibitor potency depending on the EGFR context (e.g., oncogenic mutations), type of oxidation (sulfinylation or glutathiolation), and inhibitor architecture. These methods, parameters, and insights provide a rational framework for assessing and designing effective covalent inhibitors.cysteine oxidation | protein kinase | signaling | capture period | warhead interactions R eceptor tyrosine kinases, such as the epidermal growth factor receptor (EGFR) tyrosine kinase, catalyze protein phosphorylation reactions to trigger signaling networks. Oncogenic activating mutations of EGFR lead to aberrant signaling for a subpopulation (10-30%) of nonsmall cell lung cancer patients (1). These mutations reside primarily in two regions of the EGFR catalytic domain [namely, the in-frame deletion mutations (e.g., Del746-750) preceding the N-terminal Cα-helix (exon 19) and the C-terminal activation loop L858R mutation (exon 21)] (2). Patients harboring these activating mutations usually respond to reversible ATP competitive drugs (e.g., erlotinib and gefitinib), but their effectiveness is limited by the emergence of drug resistance, in part, through an additional active site mutation (T790M and gatekeeper residue) in 50% of the responsive patients (3).A second generation of drug discovery dating back to the 1990s resulted in inhibitors that incorporate a chemically reactive Michael Acceptor (MA) electrophile (warhead) to target a cysteine nucleophile (EGFR-Cys 797 ) in the hinge region of the ATP binding cleft (4). The ...

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Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′-14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′-3H]-, [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 Å at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo confirmation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction

The photolysis of adenosylcobalamin (coenzyme B 12 ) results in homolytic cleavage of the Co-C5′ bond, forming cob(II)alamin and the 5′-deoxyadenosyl radical. In the presence of molecular oxygen, it has been proposed that the primary reaction is interception of the 5′-deoxyadenosyl radical by O 2 to form adenosine-5′-aldehyde as the product (Hogenkamp, H. P. C., Ladd, J. N., and Barker, H. A. (1962) J. Biol. Chem. 237, 1950-1952. 5′-Peroxyadenosine is here found to be the initial nucleoside product of this reaction and that it decomposes to adenosine-5′-aldehyde. Evidence indicates that 5′-peroxyadenosine arises from the hydrolysis of 5′-peroxyadenosylcobalamin, with the formation of cob(III)alamin. 5′-Peroxyadenosine undergoes further decomposition to adenosine-5′-aldehyde as the major final product of aerobic photolysis, as well as to adenosine and adenine as minor products. In a cobalamin-dependent process, 5′-peroxyadenosine becomes religated to cob(III)alamin to form 5′-peroxyadenosylcobalamin, which quickly decomposes to adenosine-5′-aldehyde and cob(III)alamin. This is supported by spectrophotometric observations of both rapidly photolyzed adenosylcobalamin and of the reaction of cob(III)alamin with excess 5′-peroxyadenosine. 5′-Peroxyadenosine also slowly undergoes cobalamin-independent decomposition to adenosine-5′-aldehyde and the minor products adenosine and adenine. The present study provides a detailed description of the products initially formed when aqueous, homolytically cleaved adenosylcobalamin reacts with molecular oxygen and of the behavior of those products subsequent to photolysis.Enzymes dependent upon the vitamin B 12 -coenzyme adenosylcobalamin 1 catalyze intriguingly diverse chemical reactions, including carbon-skeleton rearrangements, reductive heteroatom eliminations, and intramolecular 1,2-migrations of heteroatomic substituents; and they proceed by mechanisms involving organic free radicals as intermediates (1,2). Adenosylcobalamin incorporates a cobalt ion in an octahedral arrangement with the pyrroline and pyrrolidine groups of a corrin ring system making up the equatorial ligands, the nitrogen from a dimethylbenzimidazole moiety as the lower axial ligand, and a 5′-deoxadenosyl moiety forming a cobalt-carbon (Co-C5′) bond in the sixth, upper axial ligand position (3).The key to the function of adenosylcobalamin in enzymatic catalysis is the reversible homolytic scission of the Co-C5′ bond, generating cob(II)alamin and a transiently formed 5′- †

Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis, promotes angiogenesis, and is involved in metabolic inactivation of antiproliferative agents that inhibit thymidylate synthase. Understanding its transition state structure is on the path to design transition state analogues. Arsenolysis of dT by hTP permits kinetic isotope effect (KIE) analysis of the reaction by forming thymine and the chemically unstable 2-deoxyribose 1-arsenate. The transition state for the arsenolytic reaction was characterized using multiple KIEs and computational analysis. Transition state analysis revealed a concerted bimolecular (A N D N ) mechanism. A transition state constrained to match the intrinsic KIE values was found using density functional theory [B3LYP/6-31+G*]. An active site histidine is implicated as the catalytic base responsible for activation of the arsenate nucleophile and stabilization of the thymine leaving group during the isotopically sensitive step. At the transition state, the deoxyribose ring exhibits significant oxocarbenium ion character with bond-breaking (r C-N = 2.45 Å) nearly complete but no significant bond-making to the attacking nucleophile (r C-O = 2.95 Å). The transition state model predicts a deoxyribose conformation with a 2′-endo ring geometry. Transition state structure for the slow hydrolytic reaction of hTP involves a stepwise mechanism (Schwartz, P.A., Vetticatt, M.J., Schramm, V.L. (2010) J. Am. Chem. Soc. 132, 13425-13433), in contrast to the concerted mechanism described here for arsenolysis.Human thymidine phosphorylase (hTP) 1 catalyzes the reversible phosphorolytic depyrimidination of thymidine (dT) (1,2):Arsenate is a substrate analogue of phosphate and reduces the reverse reaction to permit transition state analysis by kinetic isotope effects (KIEs) (see commitments to catalysis). The hTP-catalyzed arsenolytic depyrimidination of dT forms an unstable 2-deoxy-α-D-ribose 1-arsenate which undergoes spontaneous hydrolysis (Fig. 1). hTP is involved in dT homeostasis by participating in pyrimidine salvage (3,4).