Fernando R. Clemente

De Novo Computational Design of Retro-Aldol Enzymes

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.

Rate Limiting Step Precedes C–C Bond Formation in the Archetypical Proline-Catalyzed Intramolecular Aldol Reaction

The archetypical proline-catalyzed intramolecular aldol reaction, the Hajos-Parrish-Eder-Sauer-Wiechert reaction, has served as a model reaction for the mechanistic study of the ever-growing class of proline-catalyzed conversions. Experimental measurements of the (13)C kinetic isotope effects for this reaction show conclusively that carbon-carbon bond formation is not rate-limiting.

Quantum Mechanical Design of Enzyme Active Sites

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design

Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate‐determining transition state plus the catalytic groups modeled by side‐chain mimics was optimized using B3LYP/6–31G(d) or, in one case, HF/3–21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X‐ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate–active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 Å from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 Å. The implications for computational enzyme design are discussed.

Carbohydrates as chiral controllers: synthesis of dihydrothieno[2,3-c]furanones

Chiral dihydrothiophenes derived from carbohydrates can be transformed into a novel class of bicyclic and highly functionalized chirons by treatment with NaH. A mechanistic rationale is proposed which is consistent with experimental observations and demonstrates the stereodiscriminating properties exerted by carbohydrate chains with different configurations.

A cycloaddition strategy for the synthesis of thiirane-containing glycomimetics

Abstract This manuscript describes a one-pot, selective synthesis of optically active thiiranes by [3+2] cycloaddition of mesoionic dipoles with sugar aldehydes. Overall, the result is the formation of monosaccharide mimetics that display numerous functional groups for molecular recognition.