R.B. Leveson-Gower

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.

Controlling histidine-containing proteins: The addition of photocaged histidine to the genetic code enables light-based control of protein function in bacteria and mammalian cells.

Abstract

The use of light to control protein function is a critical tool in chemical biology. Here we describe the addition of a photocaged histidine to the genetic code. This unnatural amino acid becomes histidine upon exposure to light and allows for the optical control of enzymes that utilize active-site histidine residues. We demonstrate light-induced activation of a blue fluorescent protein and a chloramphenicol transferase. Further, we genetically encoded photocaged histidine in mammalian cells. We then used this approach in live cells for optical control of firefly luciferase and, Renilla luciferase. This tool should have utility in manipulating and controlling a wide range of biological processes.

Proceedings of the National Academy of Sciences, Volume 120, Issue 3, January 2023.

Nature Reviews Chemistry, Published online: 15 January 2023; doi:10.1038/s41570-022-00459-6

To write this article, Emily Draper and Jennifer Leigh from the International Women in Supramolecular Chemistry (WISC) network again joined forces with David Smith and asked dads working within the field of supramolecular chemistry to share experiences around parental leave.

Nature Chemistry, Published online: 12 January 2023; doi:10.1038/s41557-022-01117-6

A Diels–Alderase that catalyses the inherently disfavoured cycloaddition and forms a bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity has now been discovered. This Diels–Alderase, called CtdP, is an NmrA-like protein. Isotopic labelling, structural biology and computational studies reveal that the CtdP-catalysed Diels–Alder reaction involves a NADP+/NADPH-dependent redox mechanism.

Nature Catalysis, Published online: 12 January 2023; doi:10.1038/s41929-022-00899-9

Insights on the mechanistic differences between artificial metalloenzymes (ArMs) with non-native metal centres and the free cofactor or natural enzymes are scarce. Now, a detailed mechanistic analysis of a cyclopropanation reaction catalysed by such an ArM is provided, revealing intriguing differences to the natural system.

In an exciting case of catalytic promiscuity, peroxidases and laccases participate in C−N bond-forming reactions through the generation of reactive nitroso intermediates from acylated hydroxylamines. The formal allylic C−H bond activation proceeds with air as the terminal oxidant and provides high yields both in intramolecular and intermolecular amination reactions through this unprecedented biocatalytic nitroso-ene-type reaction pathway.

Abstract

The biocatalytic oxidation of acylated hydroxylamines enables the direct and selective introduction of nitrogen functionalities by activation of allylic C−H bonds. Utilizing either laccases or an oxidase/peroxidase couple for the formal dehydrogenation of N-hydroxycarbamates and hydroxamic acids with air as the terminal oxidant, acylnitroso species are generated under particularly mild aqueous conditions. The reactive intermediates undergo C−N bond formation through an ene-type mechanism and provide high yields both in intramolecular and intermolecular enzymatic aminations. Investigations on different pathways of the two biocatalytic systems and labelling studies provide more insight into this unprecedented promiscuity of classical oxidoreductases as catalysts for nitroso-based transformations.

The high-resolution crystal structure of C−N bond forming diketopiperazine dimerase, AspB, was solved. However, the near complete superposition of active site residues and bound substrates in AspB/NzeB masked the molecular basis for their orthogonal chemoselectivities. Molecular dynamics simulations guided rational chimeragenesis to reprogram NzeB dimerase selectivity. Substrate mimics further validated differential substrate binding by the chemodivergent dimerases.

Abstract

In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp²−N bond forming dimerase, AspB. Overlay of the AspB structure onto C−C and C−N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C−N bond formation. MD simulations also suggest that intermolecular C−C or C−N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.

Proceedings of the National Academy of Sciences, Volume 120, Issue 1, January 2023.

Simulation datasets of proteins (e.g., those generated by molecular dynamics simulations) are filled with information about how the non-covalent interaction network within a protein regulates the conformation and thus function of said protein. Most proteins contain thousands of non-covalent interactions, with most of these being largely irrelevant to any single conformational change. The ability to automatically process any protein simulation dataset to identify the non-covalent interactions that are strongly associated with a single, defined conformational change would be a highly valuable tool for the community. Furthermore, the insights generated from this tool could be applied to both basic research, in order to improve understanding of a mechanism of action, or for protein engineering, to identify candidate mutations to improve/alter the functionality of any given protein. The open-source Python package Key Interactions Finder (KIF) enables users to identify those non-covalent interactions that are strongly associated with any conformational change of interest for any protein simulated. KIF gives the user full control to define the conformational change of interest as either a continuous or categorical variable, and methods from statistics or machine learning can be applied to identify and rank the interactions and residues distributed throughout the protein which are relevant to the conformational change. Finally, KIF has been applied to three diverse model systems (protein tyrosine phosphatase 1B, the PDZ3 domain, and the KE07 series of Kemp eliminases) in order to showcase its power to identify key features that regulate functionally important conformational dynamics.

We made a metagenome library and discovered urethanases that can hydrolyse a broad range of industrially relevant dicarbamates resulting from glycolysis of polyether-polyurethanes. This enables a two-step chemo-enzymatic recycling procedure consisting of glycolysis followed by enzymatic hydrolysis, allowing both the polyether polyols and the aromatic diamines to be recovered from polyether-polyurethane foams.

Abstract

Enzymatic degradation and recycling can reduce the environmental impact of plastics. Despite decades of research, no enzymes for the efficient hydrolysis of polyurethanes have been reported. Whereas the hydrolysis of the ester bonds in polyester-polyurethanes by cutinases is known, the urethane bonds in polyether-polyurethanes have remained inaccessible to biocatalytic hydrolysis. Here we report the discovery of urethanases from a metagenome library constructed from soil that had been exposed to polyurethane waste for many years. We then demonstrate the use of a urethanase in a chemoenzymatic process for polyurethane foam recycling. The urethanase hydrolyses low molecular weight dicarbamates resulting from chemical glycolysis of polyether-polyurethane foam, making this strategy broadly applicable to diverse polyether-polyurethane wastes.

Nature Catalysis, Published online: 02 January 2023; doi:10.1038/s41929-022-00895-z

Renilla luciferase is a popular bioluminescent enzyme, but the molecular details of its mechanism of action on luciferins such as coelenterazine remained elusive. Now, protein crystal structures and biochemical analyses provide an atomistic description of its catalytic mechanism.

A triazole-containing amino acid (ApmTri) was established as a mimic of acetyllysine for bromodomains of the BET family. Biochemical and structural investigations showed that ApmTri binds with similar affinity to bromodomains as acetyllysine and reflects the binding mode of the native modification at the atomic level. Genetic encoding enables ApmTri incorporation into proteins allowing investigations of bromodomain binding properties and inhibition.

Abstract

Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.