Ian Bakanas

De novo design of catalytic metalloproteins has the potential to generate enzymes that combine the efficiency of natural proteins with the reactivity of synthetic organometallic catalysts. Here, we develop a computational strategy to design enzymes with novel tertiary structures that bind metal salen complexes, classic small-molecule catalysts not found in biology. Six proteins were designed and screened for function; five of six express well, bind a Co-salen cofactor, and catalyze a transition metal hydrogen atom transfer (MHAT)-mediated deallylation reaction, representing the first de novo proteins to catalyze this class of transformation. The spectroscopic properties and crystal structure of the most active sequence were in excellent agreement with the design, and the holoprotein retained its structure and activity over a broad range of pH (2–12), temperatures up to 95 °C, and aqueous/organic solvent mixtures. We suggest that the combinatorial space provided by metal ion identity, ligand substitution, and active site structure can be used to generate artificial metalloenzymes that catalyze many chemical transformations.

Proton-coupled electron transfer (PCET) reactions mediate essential biological energy-conversion processes, yet dynamical experiments that distinguish concerted electron/proton motion from sequential electron-transfer/proton-transfer pathways are unprecedented on ultrafast time scales. Here we report a tightly coupled donor–spacer–acceptor assembly, NDI-Sp-PhOH/BI, that enables direct interrogation of light-triggered and ultrafast PCET dynamics. Photoexcitation of the naphthalene diimide chromophore drives charge separation forming NDI radical anion and benzimidazolium phenoxy radical (PhO•/BIH+) products with a 440 fs time constant, followed by thermal charge recombination on a 5 ps time scale. Transient visible/near-infrared and mid-infrared spectroscopies independently track electron and proton motion and reveal coincident formation and decay of the charge-separated PCET products, excluding detectable phenol radical cation or phenoxide intermediates expected for sequential electron transfer-proton transfer (ET-PT) pathways. Surface-hopping quasiclassical trajectory simulations demonstrate rapid proton relocation coupled to evolution from locally excited to charge-transfer states, congruent with a concerted mechanism. These combined spectroscopic and computational results establish NDI-Sp-PhOH/BI as an archetype for ultrafast, concerted PCET occurring with unit quantum yield; further, because this platform provides distinct electronic and vibrational spectroscopic handles in its ground, electronically excited, and charge-separated states, it provides new opportunities to characterize mechanistic crossover in biomimetic PCET systems.

The de novo design of proteins that bind chemically complex small molecules has broad chemical and biological implications, but strategies typically rely on a small set of protein scaffolds and require extensive experimental screening. Here, we computationally designed proteins around a minimal aromatic π-stacking motif to bind the anthracycline anticancer drug doxorubicin. Experimental characterization of twelve proteins revealed a µM doxorubicin binder; two additional design cycles improved scaffold stability and binding affinity to yield an 85-residue protein that binds doxorubicin with a dissociation constant of 85 nM. An X-ray crystal structure of the protein-drug complex confirmed the accuracy of the designed π-π stacking interactions. The designed protein could act to protect cultured cells from doxorubicin-induced cytotoxicity. Unlike previous ligand-binding protein designs based on repeat proteins or naturally occurring folds, the designed protein adopts a previously unobserved 5-helix globular fold, indicating that a broader space of folded, functional proteins exists even for compact tertiary structures smaller than 100 residues. These results demonstrate that motif-guided generative protein design can discover compact de novo protein folds capable of high-affinity recognition of chemically complex small molecules.

De novo protein design provides a framework to test our understanding of protein function and to build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small molecule reactive species for applications in proximity labeling. Because excited state dynamics are influenced by the dynamics and hydration of a photo-oxidant’s environment, it was important to not only design a binding site, but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP ( N DI B inding P rotein) that held a naphthalenediimide (NDI), a powerful photooxidant, in a programable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein, using ultra-fast pump-probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein proximity labeling.

Divergent and enantiospecific total syntheses of the indolosesquiterpenoids xiamycins A, C, F, H and oridamycin A have been accomplished. The syntheses, which commence from (R)‐carvone, employ a key photoinduced benzannulation sequence to forge the carbazole moiety characteristic of these natural products. Late‐stage diversification from a common intermediate enabled the first syntheses of xiamycins C and F, and an unexpected one‐pot oxidative decarboxylation, which may prove general, led to xiamycin H. All synthetic intermediates and the natural products were tested for anti‐fungal activity. Xiamycin H emerged as an inhibitor of three agriculturally relevant fungal pathogens.

Herein we report the synthesis of tetrasubstituted pyrazoles from simple hydrazines and β‐keto esters under mild, basic conditions. This reaction enables the selective synthesis of pyrazolones, alkoxypyrazoles, and tetrasubstituted pyrazoles for a large variety of aromatic hydrazines and substituted β‐keto esters with high yields and selectivities. This method permits access to highly complex pyrazole scaffolds with four orthogonal diversification groups.

Novel eco-friendly tetramethylguanidinium propanesulfonic acid trifluoromethylacetate ([TMGHPS][TFA]) ionic liquid was developed as catalyst and medium for the Fischer indole synthesis of a wide variety of hydrazines and ketones. The indole products were isolated in high yields and with minimal amounts of organic solvent. This reaction showed that [TMGHPS][TFA] can be regenerated and reused with reproducible yields without eroding the integrity of the ionic liquid. GRAPHICAL ABSTRACT