R.B. Leveson-Gower

Proceedings of the National Academy of Sciences, Volume 120, Issue 9, February 2023.

Here we report functionalized peptides that can participate in disulfide and acyl-hydrazone chemistry. DCLs of such molecules yield self-assembling fibres. We incorporated cell adhesion-promoting sequences into the scaffold that can undergo hydrogelation to obtain materials that present biologically relevant ligands. The importance of this work lies in the methodology for fabricating tailor-made materials through a modular approach.

Abstract

Dynamic covalent chemistry (DCC) has proven to be a valuable tool in creating fascinating molecules, structures, and emergent properties in fully synthetic systems. Here we report a system that uses two dynamic covalent bonds in tandem, namely disulfides and hydrazones, for the formation of hydrogels containing biologically relevant ligands. The reversibility of disulfide bonds allows fiber formation upon oxidation of dithiol-peptide building block, while the reaction between NH−NH₂ functionalized C-terminus and aldehyde cross-linkers results in a gel. The same bond-forming reaction was exploited for the “decoration” of the supramolecular assemblies by cell-adhesion-promoting sequences (RGD and LDV). Fast triggered gelation, cytocompatibility and ability to “on-demand” chemically customize fibrillar scaffold offer potential for applying these systems as a bioactive platform for cell culture and tissue engineering.

Biased esterification of nucleosides with borate preferentially removes those reactants from biocatalytic equilibrium systems, with the resulting cyclic borate esters acting as reversible enzyme inhibitors. This effect can be used to manipulate glycosylation equilibria and facilitate biocatalytic access to nucleoside analogues.

Abstract

Biocatalytic nucleoside (trans-)glycosylations catalyzed by nucleoside phosphorylases have evolved into a practical and convenient approach to the preparation of modified nucleosides, which are important pharmaceuticals for the treatment of various cancers and viral infections. However, the obtained yields in these reactions are generally determined exclusively by the innate thermodynamic properties of the nucleosides involved, hampering the biocatalytic access to many sought-after target nucleosides. We herein report an additional means for reaction engineering of these systems. We show how apparent equilibrium shifts in phosphorolysis and glycosylation reactions can be effected through entropically driven, biased esterification of nucleosides and ribosyl phosphates with inorganic borate. Our multifaceted analysis further describes the kinetic implications of this in situ reactant esterification for a model phosphorylase.

A general one-pot in vivo biocatalytic cascade for the production of α,ω-diamines as important nylon monomers was developed, starting from cheap and readily available cycloalkanes. The desired α,ω-diamines were successfully produced with the highest biosynthesis productivity to date, thus providing an ecologically viable alternative to the current industrial process for manufacturing α,ω-diamines.

Abstract

Aliphatic α,ω-diamines (DAs) are important monomer precursors that are industrially produced by energy-intensive, multistage chemical reactions that are harmful to the environment. Therefore, the development of sustainable green DA synthetic routes is highly desired. Herein, we report an efficient one-pot in vivo biocatalytic cascade for the transformation of cycloalkanes into DAs with the aid of advanced techniques, including the RetroBioCat tool for biocatalytic route design, enzyme mining for finding appropriate enzymes and microbial consortia construction for efficient pathway assembly. As a result, DAs were successfully produced by the designed microbial consortia-based biocatalytic system. In particular, the highest biosynthesis productivity record of 1,6-hexanediamine was achieved when using either cyclohexanol or cyclohexane as a substrate. Thus, the developed biocatalytic process provides a promising alternative to the dominant industrial process for manufacturing DAs.

An efficient organocatalytic method to synthetically versatile chiral triflones with two non-adjacent stereogenic centers was developed. The work uses, for the first time, α-aryl vinyl triflones as Michael acceptors in stereoselective catalysis. Control over the absolute configuration is achieved by a catalyst-controlled stereoselective C−C bond formation-protonation sequence.

Abstract

Trifluoromethylsulfones (triflones) are useful compounds for synthesis and beyond. Yet, methods to access chiral triflones are scarce. Here, we present a mild and efficient organocatalytic method for the stereoselective synthesis of chiral triflones using α-aryl vinyl triflones, building blocks previously unexplored in asymmetric synthesis. The peptide-catalyzed reaction gives rise to a broad range of γ-triflylaldehydes with two non-adjacent stereogenic centers in high yields and stereoselectivities. A catalyst-controlled stereoselective protonation following a C−C bond formation is key to control over the absolute and relative configuration. Straightforward derivatization of the products into, e.g., disubstituted δ-sultones, γ-lactones, and pyrrolidine heterocycles highlights the synthetic versatility of the products.

Nature Communications, Published online: 24 February 2023; doi:10.1038/s41467-023-36756-x

Detoxification enzymes are crucial for the survival of animals in new environments. Here, the authors study the molecular mechanism behind the catalytic diversification of a major family of tetrapod detoxification enzymes—the FMOs—during evolution.

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.