R.B. Leveson-Gower

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.

Structural diversification of lead molecules is a key component of drug discovery to explore close-in chemical space. Late stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity of LSF is still an open challenge in the field. Numerous efforts from chemoinformatics and machine learning (ML) groups have made significant strides in this area. However, it is arduous to isolate and characterize the multitude of LSF products generated, limiting available data and hindering pure ML approaches. We report the development of an approach that combines message-passing neural network and an 13C NMR-based transfer learning to predict the atom-wise probabilities of functionalization. We validated our model retrospectively and with a series of prospective experiments, showing that it accurately predicts the outcomes of Minisci-type and P450 transformations, outperforming state-of-the-art Fukui-based reactivity indices.

In nature, flavin dependent halogenases (FDHs) catalyze site-selective chlorination and bromination of aromatic natural products. This ability has led to extensive efforts to engineer FDHs for selective chlorination, bromination, and iodination of electron rich aromatic compounds. On the other hand, FDHs are unique among halogenases and haloperoxidases that exhibit catalyst-controlled site selectivity in that no examples of enantioselective FDH catalysis in natural product biosynthesis have been characterized. Over the past several years, our group has established that FDHs can catalyze enantioselective reactions involving desymmetrization, atroposelective halogenation, and halocyclization. Achieving high activity and selectivity for these reactions has required extensive mutagenesis and mitigation of problems resulting from hypohalous acid generated during FDH catalysis. The single-component flavin reductase/FDH AetF is unique among the wild type enzyme, we have studied in that it provides high activity and selectivity toward several asymmetric transformations. These results highlight the ability of FDH active sites to tolerate different substrate topologies and suggest that they could be useful for a broad range of oxidative halogenations.

Nature Chemistry, Published online: 22 December 2022; doi:10.1038/s41557-022-01082-0

Macrocyclic peptides can be genetically encoded and synthesized in cells; however, the programmable diversity is limited. Now, macrocycles containing two non-canonical amino acids have been genetically encoded and synthesized in codon-reassigned Syn61Δ3 cells. Incorporating diverse hydroxy acids in Syn61Δ3 cells enables the synthesis of non-natural depsipeptides containing either one or two ester bonds.

Protoglobins were engineered to catalyze stereodivergent cyclopropanation to afford a variety of trifluoromethyl-substituted cyclopropanes using trifluorodiazoethane as the trifluoromethyl-carbene precursor.

Abstract

Trifluoromethyl-substituted cyclopropanes (CF₃-CPAs) constitute an important class of compounds for drug discovery. While several methods have been developed for synthesis of trans-CF₃-CPAs, stereoselective production of corresponding cis-diastereomers remains a formidable challenge. We report a biocatalyst for diastereo- and enantio-selective synthesis of cis-CF₃-CPAs with activity on a variety of alkenes. We found that an engineered protoglobin from Aeropyrnum pernix (ApePgb) can catalyze this unusual reaction at preparative scale with low-to-excellent yield (6–55 %) and enantioselectivity (17–99 % ee), depending on the substrate. Computational studies revealed that the steric environment in the active site of the protoglobin forced iron-carbenoid and substrates to adopt a pro-cis near-attack conformation. This work demonstrates the capability of enzyme catalysts to tackle challenging chemistry problems and provides a powerful means to expand the structural diversity of CF₃-CPAs for drug discovery.

Nature Communications, Published online: 19 December 2022; doi:10.1038/s41467-022-35468-y

Chiral heterocyclic compounds are privileged structures in medicinal chemistry. Here, the authors report an in silico strategy for the enzymatic synthesis of pharmaceutically significant chiral N- and O-heterocycles via Baldwin cyclization of hydroxy- and amino-substituted epoxides and oxetanes using epoxide hydrolase mutants.

A new cyclisation approach for peptides, derived from in vitro translation, is developed that is highly selective for N-terminal cysteines. This approach allows other cysteine residues to be exploited for further peptide diversification. A model peptide showed a large impact from this cyclisation on binding and biological activity, and molecular dynamics was used to illustrate how this cyclisation change can influence peptide conformation.

Abstract

Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.