De novo design of luciferases using deep learning.

De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein structures and the complexity of native protein sequence-structure relationships. Here we describe a deep-learning-based 'family-wide hallucination' approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine3 and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (kcat/Km = 106 M-1 s-1) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.

Computational Studies of Reactions of 1,2,4,5-Tetrazines with Enamines in MeOH and HFIP.

The reaction between 1,2,4,5-tetrazines and alkenes in polar solvents proceeds through a Diels-Alder cycloaddition along the C-C axis (C3/C6 cycloaddition) of the tetrazine, followed by dinitrogen loss. By contrast, the reactions of 1,2,4,5-tetrazines with enamines in hexafluoroisopropanol (HFIP) give 1,2,4-triazine products stemming from a formal Diels-Alder addition across the N-N axis (N1/N4 cycloaddition). We explored the mechanism of this interesting solvent effect through DFT calculations in detail and revealed a novel reaction pathway characterized by C-N bond formation, deprotonation, and a 3,3-sigmatropic rearrangement. The participation of an HFIP molecule was found to be crucial to the N1/N4 selectivity over C3/C6 due to the more favored initial C-N bond formation than C-C bond formation.

Chemiexcitation Acceleration of 1,2-Dioxetanes by Spiro-Fused Six-Member Rings with Electron-Withdrawing Motifs.

The chemiluminescent light-emission pathway of phenoxy-1,2-dioxetane luminophores attracts growing interest within the scientific community. Dioxetane probes undergoing rapid flash-type chemiexcitation exhibit higher detection sensitivity than those with a slow glow-type chemiexcitation rate. We discovered that dioxetanes fused to non-strained six-member rings, with hetero atoms or inductive electron-withdrawing groups, present both accelerated chemiexcitation rates and elevated chemical stability compared to dioxetanes fused to four-member strained rings. DFT computational simulations supported the chemiexcitation acceleration observed by spiro-fused six-member rings with inductive electron-withdrawing groups of dioxetanes. Specifically, a spiro-dioxetane with a six-member sulfone ring exhibited a chemiexcitation rate 293-fold faster than that of spiro-adamantyl-dioxetane. A turn-ON dioxetane probe for the detection of the enzyme ß-galactosidase, containing the six-member sulfone unit, exhibited a S/N value of 108 in LB cell growth media. This probe demonstrated a substantial increase in detection sensitivity towards E. coli bacterial cells expressing ß-galactosidase, with an LOD value that is 44-fold more sensitive than that obtained by the adamantyl counterpart. The accelerated chemiexcitation and the elevated chemical stability presented by dioxetane containing a spiro-fused six-member ring with a sulfone inductive electron-withdrawing group, make it an ideal candidate for designing efficient turn-on chemiluminescent probes with exceptionally high detection sensitivity.

Valence-Inverted States of Nickel(II) Complexes Perform Facile C-H Bond Activation.

Valence-inverted reactivity (VIR) is discovered here through high-level computations of excited states of Ni(II) complexes that are generated by triplet energy transfer. For example, the so-generated 3[(Ar)(bpy)NiII(Br)] species possesses a valence-inverted occupancy, dxy1dxz1dx2-y22, wherein the uppermost dx2-y2 orbital is metal-ligand antibonding. This state promotes C-H bond activation of THF and its cross-coupling to the aryl ligand. Thus, due to the metal-ligand antibonding character of dx2-y2, the dxy1dx2-y22 subshell opens a Ni-coordination site by shifting the bidentate bipyridine ligand to monodentate plus a dangling pyridine. The tricoordinate Ni(II) intermediate inserts into a C-H bond of THF, transfers a proton to the dangling pyridine moiety, and eventually generates an arylated THF by reductive-coupling. The calculated high kinetic isotope effect is in accord with experiment, both revealing C-H activation. The VIR pattern is novel, its cross-coupling reaction is highly useful, and it is generally expected to occur in other d8 complexes.

Computational Exploration of Ambiphilic Reactivity of Azides and Sustmann's Paradigmatic Parabola.

We examine the theoretical underpinnings of the seminal discoveries by Reiner Sustmann about the ambiphilic nature of Huisgen's phenyl azide cycloadditions. Density functional calculations with ωB97X-D and B2PLYP-D3 reproduce the experimental data and provide insights into ambiphilic control of reactivity. Distortion/interaction-activation strain and energy decomposition analyses show why Sustmann's use of dipolarophile ionization potential is such a powerful predictor of reactivity. We add to Sustmann's data set several modern distortion-accelerated dipolarophiles used in bioorthogonal chemistry to show how these fit into the orbital energy criteria that are often used to understand cycloaddition reactivity. We show why such a simple indicator of reactivity is a powerful predictor of reaction rates that are actually controlled by a combination of distortion energies, charge transfer, closed-shell repulsion, polarization, and electrostatic effects.

Chromium- and Cobalt-Catalyzed, Regiocontrolled Hydrogenation of Polycyclic Aromatic Hydrocarbons: A Combined Experimental and Theoretical Study.

Polycyclic aromatic hydrocarbons are difficult substrates for hydrogenation because of the thermodynamic stability caused by aromaticity. We report here the first chromium- and cobalt-catalyzed, regiocontrolled hydrogenation of polycyclic aromatic hydrocarbons at ambient temperature. These reactions were promoted by low-cost chromium or cobalt salts combined with diimino/carbene ligand and methylmagnesium bromide and are characterized by high regioselectivity and expanded substrate scope that includes tetracene, tetraphene, pentacene, and perylene, which have rarely been reduced. The approach provides a cost-effective catalytic protocol for hydrogenation, is scalable, and can be utilized in the synthesis of tetrabromo- and carboxyl-substituted motifs through functionalization of the hydrogenation product. The systematic theoretical mechanistic modelings suggest that low-valent Cr and Co monohydride species, most likely from zerovalent transition metals, are capable of mediating these hydrogenations of fused PAHs.

Low-Valent, High-Spin Chromium-Catalyzed Cleavage of Aromatic Carbon-Nitrogen Bonds at Room Temperature: A Combined Experimental and Theoretical Study.

The cleavage of aromatic carbon-nitrogen bonds catalyzed by transition metals is of high synthetic interest because such bonds are common in organic chemistry. However, few metal catalysts can be used to selectively break C(aryl)-N bonds in electronically neutral molecules. We report here the first low-valent, high-spin chromium-catalyzed cleavage of C(aryl)-N bonds in electronically neutral aniline derivatives at room temperature. By using simple and inexpensive chromium(II) chloride as precatalyst, accompanied by an imino auxiliary, the selective arylative and alkylative C-C coupling of C(aryl)-N bonds can be achieved. Crossover experiments indicate that a low-valent chromium species, formed in situ by reduction of CrCl2 with Grignard reagent, is responsible for the catalytic cleavage of C(aryl)-N bonds. DFT calculations show that facile insertion of the C(aryl)-N bond by chromium(0) can take place in a high-spin quintet (S = 2) ground state, whereas the lower-spin singlet (S = 0) and triplet (S = 1) states are inaccessible in energy. It was found that both donation of the sole paired d electrons in the d6 shell of high-spin chromium(0) to the antibonding orbital of the C(aryl)-N bond and the nitrogen ligating interaction to the metal center with its lone pair play important roles in the cleavage of the C(aryl)-N bond by the zerovalent chromium species.

Merging of Palladium and Organocatalysis Enabled Asymmetric Decarboxylative (2+1) Cycloadditions toward Cyclopropanes.

A cascade reaction enabling enantio- and diastereoselective construction of strained cyclopropanes is described. This asymmetric (2+1) annulation process uses vinyl methylene carbonate and 2-cyanoacrylate as reaction partners in the presence of Pd(PPh3)4 as a precatalyst and an enantioenriched phosphoramidite ligand featuring a morpholine functionality. Mechanistic investigations unveil that the PPh3 derived from the Pd(PPh3)4 and the morpholine-containing phosphoramidite work as cooperative phosphorus and Brønsted base catalysts to promote the reaction.

Stereoselective Construction of ß-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation.

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Methods for the asymmetric synthesis of these molecules are therefore highly desirable, particularly through the selective functionalization of unreactive aliphatic C-H bonds. Here we show the development of a strategy for the asymmetric synthesis of ß-, γ-, and δ-lactams via hemoprotein-catalysed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation yielding the desired lactam products in high yields, high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Additionally, an alkaloid natural product and a drug molecule were synthesized chemoenzymatically in much fewer steps (7-8 vs. 11-12) than previously reported, further demonstrating the power of biosynthetic strategy for the preparation of complex bioactive molecules.

Metal-free, photoredox-catalyzed aromatization-driven deconstructive functionalization of spiro-dihydroquinazolinones with α-CF3 alkenes.

Metal-free, photoredox-catalyzed aromatization-driven deconstructive functionalization of spiro-dihydroquinazolinones with α-CF3 alkenes is presented. The readily available spiro-dihydroquinazolinones reacted efficiently with α-CF3 alkenes during photocatalysis to give the gem-difluoroallylated and the CF3-containing quinazolin-4(3H)-ones in good yields with excellent chemoselectivity. The selectivity depends on the electron effect of substituents in α-CF3 alkenes. A wide range of four-, five-, six-, seven-, eight- and twelve-membered spiro-dihydroquinazolinones were compatible with this transformation. The protocol is also characterized by the mild and redox-neutral reaction conditions, good functional group compatibility and excellent atom economy. Mechanistic studies revealed that the reaction proceeds via a radical pathway.

Spirostrain-Accelerated Chemiexcitation of Dioxetanes Yields Unprecedented Detection Sensitivity in Chemiluminescence Bioassays.

Chemiluminescence is a fascinating phenomenon that involves the generation of light through chemical reactions. The light emission from adamantyl-phenoxy-1,2-dioxetanes can glow from minutes to hours depending on the specific substituent present on the dioxetane molecule. In order to improve the light emission properties produced by these chemiluminescent luminophores, it is necessary to induce the chemiexcitation rate to a flash mode, wherein the bulk of light is emitted instantly rather than slowly over time. We report the realization of this goal through the incorporation of spirostrain release into the decomposition of 1,2-dioxetane luminophores. DFT computational simulations provided support for the hypothesis that the spiro-cyclobutyl substituent accelerates chemiexcitation as compared to the unstrained adamantyl substituent. Spiro-linking of cyclobutane and oxetane units led to greater than 100-fold and 1000-fold emission enhancement, respectively. This accelerated chemiexcitation rate increases the detection sensitivity for known chemiluminescent probes to the highest signal-to-noise ratio documented to date. A turn-ON probe, containing a spiro-cyclobutyl unit, for detecting the enzyme ß-galactosidase exhibited a limit of detection value that is 125-fold more sensitive than that for the previously described adamantyl analogue. This probe was also able to instantly detect and image ß-gal activity with enhanced sensitivity in E. coli bacterial assays.

Characterization and heterologous reconstitution of Taxus biosynthetic enzymes leading to baccatin III.

Paclitaxel is a well known anticancer compound. Its biosynthesis involves the formation of a highly functionalized diterpenoid core skeleton (baccatin III) and the subsequent assembly of a phenylisoserinoyl side chain. Despite intensive investigation for half a century, the complete biosynthetic pathway of baccatin III remains unknown. In this work, we identified a bifunctional cytochrome P450 enzyme [taxane oxetanase 1 (TOT1)] in Taxus mairei that catalyzes an oxidative rearrangement in paclitaxel oxetane formation, which represents a previously unknown enzyme mechanism for oxetane ring formation. We created a screening strategy based on the taxusin biosynthesis pathway and uncovered the enzyme responsible for the taxane oxidation of the C9 position (T9αH1). Finally, we artificially reconstituted a biosynthetic pathway for the production of baccatin III in tobacco.

Stereoselective Construction of ß-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation.

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Given their widespread presence in bioactive molecules, methods for the asymmetric synthesis of these molecules, in particular through the selective functionalization of ubiquitous yet unreactive aliphatic C-H bonds, are highly desirable. In this study, we report the development of a novel strategy for the asymmetric synthesis of 4-, 5-, and 6-membered lactams via an unprecedented hemoprotein-catalyzed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation producing an array of ß-, γ-, and δ-lactam molecules in high yields, with high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps in these reactions and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Using this system, it was possible to accomplish the chemoenzymatic total synthesis of an alkaloid natural product and a drug molecule in much fewer steps (7-8 vs. 11-12) than previously possible, which showcases the power of this biosynthetic strategy toward enabling the preparation of complex bioactive molecules.

A cheap metal catalyzed ring expansion/cross-coupling cascade: a new route to functionalized medium-sized and macrolactones.

An efficient alkoxyl radical-triggered ring expansion/cross-coupling cascade was developed under cheap metal catalysis. Through the metal-catalyzed radical relay strategy, a wide range of medium-sized lactones (9-11 membered) and macrolactones (12, 13, 15, 18, and 19-membered) were constructed in moderate to good yields, along with diverse functional groups including CN, N3, SCN, and X groups installed concurrently. Density functional theory (DFT) calculations revealed that reductive elimination of the cycloalkyl-Cu(iii) species is a more favorable reaction pathway for the cross-coupling step. Based on the results of experiments and DFT, a Cu(i)/Cu(ii)/Cu(iii) catalytic cycle is proposed for this tandem reaction.

Phosphine-catalyzed activation of cyclopropenones: a versatile C3 synthon for (3+2) annulations with unsaturated electrophiles.

We herein report a phosphine-catalyzed (3 + 2) annulation of cyclopropenones with a wide variety of electrophilic π systems, including aldehydes, ketoesters, imines, isocyanates, and carbodiimides, offering products of butenolides, butyrolactams, maleimides, and iminomaleimides, respectively, in high yields with broad substrate scope. An α-ketenyl phosphorous ylide is validated as the key intermediate, which undergoes preferential catalytic cyclization with aldehydes rather than stoichiometric Wittig olefinations. This phosphine-catalyzed activation of cyclopropenones thus supplies a versatile C3 synthon for formal cycloadditon reactions.

Ambiphilic Reactivity of Vinyl Pd-Oxyallyl for Expeditious Construction of Highly Functionalized Cyclooctanoids.

We report the catalytic generation of a vinyl Pd-oxyallyl that dimerizes regiospecifically to form highly functionalized nonbridged cyclooctanoids. Such compounds are otherwise synthetically challenging, but highly useful in synthesis. This vinyl Pd-oxyallyl species demonstrates both electrophilic and nucleophilic properties. DFT calculations elucidate the mechanism and the origins of the chemoselective cyclooctanoid formation.

Amine-accelerated manganese-catalyzed aromatic C-H conjugate addition to α,ß-unsaturated carbonyls.

Since 1987, the stoichiometric two-step C-H conjugate addition reactions have been developed. Herein we describe the first manganese-catalyzed one-step direct aromatic C-H conjugate addition to α,ß-unsaturated carbonyls, which is accelerated by a catalytic amount of dicyclohexylamine. Experimental and computational studies substantiated the validity of the proposed catalytic cycle.