Designed Local Electric Fields-Promising Tools for Enzyme Engineering.

Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.

A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient.

The present work outlines a general methodology for designing efficient catalytic machineries that can easily be tweaked to meet the demands of the target reactions. This work utilizes a principle of the designed local electric field (LEF) as the driver for an efficient catalyst. It is demonstrated that by tweaking the LEF, we can catalyze the desired hydroxylation products with enantioselectivity that can be changed at will. Using computation tools, we caged a synthetic analog of heme porphyrin (HM1) and investigated the pharmaceutically relevant conversion of tetralin to tetralol, inside the modified supramolecular cage. The QM/MM calculations demonstrate a resulting catalytic efficiency with virtually absolute R-selectivity for the tetralin hydroxylation. Our calculations show that the LEF of the supramolecular cage and HM1 exert a strong electric field along the Fe-O reaction axis, which is the main driving force for enhanced reactivity. At the same time, the supramolecular cage applies a lateral LEF that regulates the enantioselectivity. We further demonstrate that swapping the charged/polar substitution in the supramolecular cage switches the lateral LEF which changes the enantioselectivity of hydroxylation from R to S.

Design and Synthesis of Co-initiators via Base-Catalysed Sequential Conjugate Addition: Application in Photoinduced Radical Polymerisation Reaction.

Applications of photochemistry are becoming very popular in modern-day life due to its operational simplicity, environmentally friendly and economically sustainable nature in comparison to thermochemistry. In particular photoinduced radical polymerisation (PRP) reactions are finding more biological applications and especially in the areas of dental restoration processes, tissue engineering and artificial bone generation. A type-II photoinitiator and co-initiator-promoted PRP turned out to be a cost-effective protocol, and herein we report the design and synthesis of a new efficient co-initiator for a PRP reaction via a barrierless sequential conjugate addition reaction. Experimental mechanistic observations have been further complemented by computational data. Time for newly synthesised 1,2-benzenedithiol (DTH) based co-initiator promoted polymerisation of urethane dimethacrylate (UDMA, 70 %) and triethylene glycol dimethacrylate (TEGDMA, 30 %) in presence of 450 nm LED (15 W) under the aerobic conditions is 38 seconds. Polymeric material has high glass transition temperature, improved mechanical strength (860 BHN) and longer in-depth polymerisation (3 cm).

Unraveling key interactions and the mechanism of demethylation during hAGT-mediated DNA repair via simulations.

Alkylating agents pose the biggest threat to the genomic integrity of cells by damaging DNA bases through regular alkylation. Such damages are repaired by several automated types of machinery inside the cell. O6-alkylguanine-DNA alkyltransferase (AGT) is an enzyme that performs the direct repair of an alkylated guanine base by transferring the alkyl group to a cysteine residue. In the present study, using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of the damaged base as a three-step process in a thermodynamically feasible and irreversible manner. Our calculations show that the final product forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.

Local Electric Fields Dictate Function: The Different Product Selectivities Observed for Fatty Acid Oxidation by Two Deceptively Very Similar P450-Peroxygenases OleT and BSß.

Cytochrome P450 peroxygenases use hydrogen peroxide to hydroxylate long-chain fatty acids by bypassing the use of O2 and a redox partner. Among the peroxygenases, P450OleT uniquely performs decarboxylation of fatty acids and production of terminal olefins. This route taken by P450OleT is intriguing, and its importance is augmented by the practical importance of olefin production. As such, this mechanistic choice merits elucidation. To address this puzzle, we use hybrid QM/MM calculations and MD simulations for the OleT enzyme as well as for the structurally analogous enzyme, P450BSß. The study of P450OleT reveals that the protonated His85 in the wild-type P450OleT plays a crucial role in steering decarboxylation activity by stabilizing the corresponding hydroxoiron(IV) intermediate (Cpd II). In contrast, for P450BSß in which Q85 replaces H85, the respective Cpd II species is unstable and it reacts readily with the substrate radical by rebound, producing hydroxylation products. As shown, this single-site difference creates in P450OleT a local electric field (LEF), which is significantly higher than that in P450BSß. In turn, these LEF differences are responsible for the different stabilities of the respective Cpd II/radical intermediates and hence for different functions of the two enzymes. P450BSß uses the common rebound mechanism and leads to hydroxylation, whereas P450OleT proceeds via decarboxylation and generates terminal olefins. Olefin production projects the power of a single residue to alter the LEF and the enzyme's function.

Can the local electric field be a descriptor of catalytic activity? A case study on chorismate mutase.

The current theoretical perception of enzymatic activity is highly reliant on the determination of the activation energy of the reactions, which is often calculated using computationally demanding quantum mechanical calculations. With the ever-increasing use of bioengineering techniques that produce too many variants of the same enzyme, a fast and accurate way to study the relative efficiency of enzymes is currently in high demand. Here, we propose the local electric field (LEF) of the enzyme along the reaction axis as a descriptor for the enzymatic activity using the example of chorismate mutase in its native form and several variants (R90A, R90G, and R90K/C88S). The study shows a direct correlation between the calculated enzymatic EF and the enzymatic activity for all the complexes. MD simulations of the Michaelis complex and the transition state analog (TSA) show a stabilizing force on the TSA due to the enzymatic EF. QM/MM and QM-only DFT calculations in the presence of an external electric field (EEF) oriented along the reaction axis show that the electric field can interact with the dipole moment of the TS, thereby stabilizing it and thus lowering the activation energy.