Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non‐heme Iron BesD Enzyme

Abstract

Selective halogenation is important in synthetic chemistry. BesD, a new member of the non‐heme Fe(II)/α‐ketoglutarate (αKG)‐dependent halogenase family, can activate the sp3 C−H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl−Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl−Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate‐limiting. The isomerization of Cl−Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD‐catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly‐changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X‐introduced reactions catalyzed by BesD may be extended to other X anions.

Why Nonheme Iron Halogenases Do Not Fluorinate C–H Bonds: A Computational Investigation

“…30 kcal/mol observed for BesD in prior work owing to additional constraints used in that study. In comparison to another study, we find that the HAT barriers we observe are higher by ca. 5 kcal/mol likely because we evaluate HAT reaction energetics using first coordination sphere residues and a model substrate, whereas first and second coordination sphere residues along with the complete substrate are used to compute the HAT barrier in this other work.…”

“…Because fluorination by nonheme halogenases is not observed in nature, re-engineering of biological systems to enable C−F bond formation would be of great use. C−H chlorination by nonheme iron halogenases has been extensively studied through experiments 27,56,57 and computation 58−61 with fewer studies of C−H bromination 32,45,62 and fluorination 50,51 having been carried out. The only enzyme with fluorinase activity characterized to date uses a mechanism entirely distinct from the radical rebound mechanism 63 from nonheme iron halogenases.…”

“…C–H chlorination by nonheme iron halogenases has been extensively studied through experiments ,, and computation − with fewer studies of C–H bromination ,, and fluorination , having been carried out. The only enzyme with fluorinase activity characterized to date uses a mechanism entirely distinct from the radical rebound mechanism from nonheme iron halogenases.…”

Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases

“…It is worth noting that fixing the backbone atoms of the QM cluster models to the coordinates of their respective MD centroids expectedly introduces additional energetic cost into the potential energy scan calculations. When the restraints are removed, we obtain barrier heights closer to those previously reported , but at the cost of not controlling the acute vs obtuse approach at all (Supporting Information, Figure S28). The energy barriers reported here should be considered upper bounds but are necessary to compare acute and obtuse energetics.…”

How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases?

“…C–H activation is difficult to achieve synthetically , owing to the high C–H bond dissociation energy and its inertness due to low polarity . These nonheme iron enzymes are studied widely and are known to catalyze a variety of reactions such as C–H hydroxylation, − halogenation, − epoxidation, − desaturation, and ring cleavage. , These reactions play important roles in several biosynthetic processes − such as primary and secondary metabolism in plants, generation of clinically relevant natural products, − DNA repair, − and transcription. − …”