R.B. Leveson-Gower

Nature, Published online: 22 February 2023; doi:10.1038/s41586-023-05696-3

A deep-learning-based strategy is used to design artificial luciferases that catalyse the oxidative chemiluminescence of diphenylterazine with high substrate specificity and catalytic efficiency.

The direct catalytic hydrocarbylation of readily available amino acids with halohydrocarbons is one of the most straightforward methods leading to disubstituted non-proteinogenic amino acid compounds. However, all the re-ported methodologies depend on N-protected amino acids as starting materials. Herein, we report on three highly efficient aldehyde-catalyzed direct hydrocarbylations of N-unprotected amino acid esters with aryl-, allyl-, and benzyl halides. By promoting a simple chiral BINOL-aldehyde catalyst or combining catalysts of a chiral aldehyde and Lewis acid ZnCl2, the asymmetric arylation, allylation, and benzylation of amino acid esters with the corresponding halohydrocarbons proceed smoothly, producing disubstituted amino acids in moderate-to-high yields and good-to-excellent enantioselectivities. The asymmetric arylation reaction can be applied in the formal synthesis of the clinical candidate compound (+)-AG-041R. Based on the results given by control experiments, three reaction models are proposed to illustrate the stereoselective-control outcomes.

Nature Chemical Biology, Published online: 16 February 2023; doi:10.1038/s41589-022-01251-9

Development of a generalized method for dual site-specific incorporation of nonnatural photocaged and photoreactive amino acids into proteins expressed in live cells enabled engineering of a photoreactive photoactive antibody fragment.

Nature Catalysis, Published online: 16 February 2023; doi:10.1038/s41929-022-00909-w

Retrobiosynthesis aims to create novel biosynthetic pathways for the beneficial production of molecules of interest. This Review outlines how machine learning can help to advance retrobiosynthesis by improving retrosynthesis planning, enzyme identification and selection, and the engineering of enzymes and pathways.

Nature Communications, Published online: 14 February 2023; doi:10.1038/s41467-023-36119-6

Half of all pregnancies are unintended; thus, existing family planning options are inadequate. This proof-of-concept study validates an on-demand contraception strategy for men, showing high effectiveness in quickly and temporarily reducing male fertility in mice.

An efficient catalyst of the Morita–Baylis–Hillman reaction was discovered using a graph-based genetic algorithm. The catalytic activity was experimentally verified by a kinetic study and the newly discovered catalyst outcompetes a widely used catalyst for this reaction.

Abstract

We present a de novo discovery of an efficient catalyst of the Morita–Baylis–Hillman (MBH) reaction by searching chemical space for molecules that lower the estimated barrier of the rate-determining step using a genetic algorithm (GA) starting from randomly selected tertiary amines. We identify 435 candidates, virtually all of which contain an azetidine N as the catalytically active site, which is discovered by the GA. Two molecules are selected for further study based on their predicted synthetic accessibility and have predicted rate-determining barriers that are lower than that of a known catalyst. Azetidines have not been used as catalysts for the MBH reaction. One suggested azetidine is successfully synthesized and showed an eightfold increase in activity over a commonly used catalyst. We believe this is the first experimentally verified de novo discovery of an efficient catalyst using a generative model.

Directed evolution is used to engineer variants of the dioxygenase SadX that catalyze site-selective azidation of succinylated amino acids and a succinylated amine as a result of mutations throughout the SadX structure. This result provides a promising starting point for evolving additional variants with activity on structurally distinct substrates and for enabling enzymatic C−H functionalization with other non-native functional groups.

Abstract

Fe^II- and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C−H bonds via a variety of C−X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C−H functionalization with other non-native functional groups.

A chiral iron(III) salen complex with a chiral photo-switchable phosphate counterion is reported for the sulfoxidation of alkenes in a stereoselective manner. Irradiation with light allows access to either enantiomer of the sulfoxide.

Abstract

Here we describe a photoswitchable iron(III) salen phosphate catalyst, which is able to catalyze the enantiodivergent oxidation of prochiral aryl alkyl sulfides to chiral aryl alkyl sulfoxides. The stable (S)-axial isomer of the catalyst produced enantioenriched sulfoxides with the (R)-configuration in up to 75 % e.e., whereas the photoisomerized metastable (R)-axial isomer of the catalyst favored the formation of (S)-sulfoxides in up to 43 % e.e. The maximum Δe.e. value obtained in the enantiodivergent sulfoxidation was 118 %, which is identical to the maximum Δe.e. value that was measured in the enantiodivergent epoxidation of alkenes by a related recently described Mn1 catalyst. This iron-based catalyst broadens the scope of photoswitchable enantiodivergent catalysts and may be used in the future to develop a photoswitchable catalytic system that can write digital information on a polymer chain in the form chiral sulfoxide functions.

Mirror-image biological systems have the potential for broad-reaching impact in health and diagnostics, but their study has been greatly limited by the lack of routine access to synthetic D-proteins. We demonstrate that automated fast flow peptide synthesis (AFPS) can reliably produce novel mirror-image protein targets without prior sequence engineering. We synthesized 12 D-proteins, along with their L-counterparts. All 24 synthetic proteins were folded into active structures in vitro, and characterized using biochemical and biophysical techniques. From these chiral protein pairs, we chose MDM2 and CHIP to carry forward into mirror-image phage display screens, and identified macrocyclic D-peptides that bind the recombinant targets. We report 6 mirror-image peptide ligands with unique binding modes: three to MDM2, and three to CHIP, each confirmed with X-ray co-crystal structures. Reliable production of mirror-image proteins with AFPS stands to enable not only the discovery of D-peptide drug leads, but to the study of mirror-image biological systems more broadly.

Nanozymes mimic enzyme functions for use in periodontology and implantology, as illustrated on the cover. Periodontal and peri-implant diseases are important diseases worldwide. As multifunctional nanomaterials with enzyme-mimicking activities, nanozymes have made great contributions to maintaining periodontal health and improving the success rate of implantation. Herein, this review describes how nanozymes demonstrate antibacterial, anti-inflammatory, regenerative, and synergistic effects by mimicking properties similar to natural enzymes and exploiting the advantages of nanomaterials. More information can be found in the Review by J. Wu et al.

Proceedings of the National Academy of Sciences, Volume 120, Issue 4, January 2023.

Myoglobin combined with human serum albumin, Mb-HSA, was prepared using a yeast host cell with secretion into the culture medium. The heme of Mb-HSA was replaced with a zinc protoporphyrin IX, yielding ZnMb-HSA. This fluorescent fusion protein showed a superior activity of photodynamic cancer therapy in vitro. Its blood circulation half-life was 11-fold longer than free ZnMb in vivo.

Abstract

Myoglobin combined with human serum albumin (Mb-HSA) can be produced using yeast Pichia pastoris as a host strain, with secretion into the culture medium. This Mb-HSA fusion protein possesses identical O₂ binding affinity to that of naked Mb. The Mb unit is reconstituted with a zinc(II) protoporphyrin IX, yielding (zinc substituted Mb)-HSA, ZnMb-HSA. The photophysical property and singlet O₂ generation ability of ZnMb-HSA are equivalent to those of ZnMb. In vitro cell experiments revealed that ZnMb-HSA acts as a superior photosensitizer for photodynamic cancer therapy. It is noteworthy that ZnMb-HSA shows long circulation lifetime in vivo.

Nature Chemistry, Published online: 23 January 2023; doi:10.1038/s41557-022-01104-x

Cycloaddition reactions are among the most useful reactions in chemical synthesis, but biosynthetic enzymes with 2 + 2 cyclase activity have yet to be observed. Now it is shown that a β-barrel-fold protein catalyses competitive 2 + 2 and 4 + 2 cycloaddition reactions. This protein can be engineered to preferentially produce the exo-2 + 2, exo-4 + 2 or endo-4 + 2 product.

An efficient long-lived polymeric room-temperature phosphorescent material was achieved based on the rigid structure provided by aromatic and piperidine rings of mBPipQ and the dense molecular arrangement of an epoxy resin, which stabilized triplet excitons. More importantly, these materials exhibit stable yellow-green phosphorescence emission after being immersed in strong acid or alkali solutions for 10 days.

Abstract

Long-lived polymeric room temperature phosphorescence (RTP) materials have drawn more attention due to their convenient preparation process and equally efficient phosphorescence performance in recent years. As the polymer matrix is sensitive to air and humidity, some non-covalent interactions in the matrix are easily decomposed in water or air, which means that it is difficult for this material to be stored stably for a long time in the atmospheric environment or under harsh conditions. In this work, polymer powder mBPipQ contains aromatic and piperidine rings that are designed and synthesized successfully. Then the polymer is uniformly dispersed into epoxy resin matrix to form long-lived polymeric RTP material with efficient afterglow properties. The stiff backbone structure of mBPip and dense molecular arrangement of epoxy resin provide a rigid environment to stabilize triplet excitons, the RTP performance is greatly enhanced. The lifetime of mBPipQ in epoxy resin is 2 times higher than that of small molecule chromophore in that one. Interestingly, after soaking in strong acid or alkali solution for 10 days, the material can still emit stable and efficient long-lived phosphorescence. It is thanks to the hard matrix after full curing, which can provide a protective layer to prevent external quenchers from interfering with phosphorescence emission. Utilizing the efficient phosphorescence emission and excellent abominable-solvent resistance of this RTP material, multilevel information encryption has been successfully demonstrated. This work broadens the application scope of polymeric RTP materials in harsh environments and provides a new idea for achieving efficient RTP emission.

The replacement of benzene rings with sp3-hybridized bioisosteres in drug candidates generally improves pharmacokinetic properties while retaining biological activity. Rigid, strained frameworks such as bicyclo[1.1.1]pentane and cubane are particularly well-suited since the ring strain imparts high bond strength and thus metabolic stability on its C–H bonds. Cubane is the ideal bioisostere since it provides the closest geometric match to benzene. At present, however, all cubanes in drug design, like almost all benzene bioisosteres, act solely as substitutes for mono- or para-substituted benzene rings. This is due to the difficulty of accessing 1,3- and 1,2-disubstituted cubane precursors. The adoption of cubane in drug design has been further hindered by the incompatibility of cross-coupling reactions with the cubane scaffold, owing to a competing metal-catalyzed valence isomerization. Herein, we disclose expedient routes to 1,3- and 1,2-disubstituted cubane building blocks using a convenient cyclobutadiene precursor and a photolytic C–H carboxylation reaction, respectively. Moreover, we leverage the slow oxidative addition and rapid reductive elimination of copper to develop C–N, C–C(sp3), C–C(sp2), and C–CF3 cross-coupling protocols. Our research enables facile elaboration of all cubane isomers into drug candidates thus enabling ideal bioisosteric replacement of ortho-, meta-, and para-substituted benzenes.

<p>Nature's way to construct highly complex molecular entities with virtue as part of biosynthetic pathways is unmatched by any chemical synthesis. Yet, relying on a cascade of native enzymatic transformations to achieve a certain target structure, biosynthesis is also significantly limited in its scope. In this work, non-natural biocatalytic modules are successfully implemented into an artificial metabolism, combining the benefits of traditional retrosynthesis with the elegance and efficacy of biosynthetic networks. In a highly streamlined process, a total synthesis of the tricyclic angiopterlactone B is achieved operating entirely in an aqueous environment while relying on enzymes as reaction mediators.</p>

Nature Catalysis, Published online: 19 January 2023; doi:10.1038/s41929-022-00908-x

The design of complementary catalysts to target different C–H bonds in a specific molecule is challenging. Now, a pair of P450-based carbene transferase enzymes is engineered, which can selectively cyanomethylate either a C(sp3)–H or arene C(sp2)–H bond present in the same substrate.

Multiple 2D H-bonded macrocycles are threaded onto a box-like cationic cyclophane, which further assembles into higher order dimeric shish-kebab-like structures. Such ring-in-ring(s) superstructures maximize their stability through the conformational adaptivity of both host and guest.

Abstract

Use of abiotic chemical systems for understanding higher order superstructures is challenging. Here we report a ring-in-ring(s) system comprising a hydrogen-bonded macrocycle and cyclobis(paraquat-o-phenylene) tetracation ( o -Box) or cyclobis(paraquat-p-phenylene) tetracation (CBPQT ⁴⁺, p -Box) that assembles to construct discrete higher order structures with adaptive conformation. As indicated by mass spectrometry, computational modeling, NMR spectroscopy, and single-crystal X-ray diffraction analysis, this ring-in-ring(s) system features the box-directed aggregation of multiple macrocycles, leading to generation of several stable species such as H4G (1 a/ o -Box) and H5G (1 a/ o -Box). Remarkably, a dimeric shish-kebab-like ring-in-rings superstructure H7G2 (1 a/ o -Box) or H8G2 (1 a/ p -Box) is formed from the coaxial stacking of two ring-in-rings units. The formation of such unique dimeric superstructures is attributed to the large π-surface of this 2D planar macrocycle and the conformational variation of both host and guest.