Biocatalysis@TUDelft

Nature, Published online: 18 March 2026; doi:10.1038/d41586-026-00891-4

New evidence reveals biochemical pathway behind quinine production.

Nature, Published online: 18 March 2026; doi:10.1038/s41586-026-10227-x

A combination of isotopic labelling, gene silencing, single-nucleus RNA sequencing and comparative transcriptomics reveal the genes that mediate the biosynthesis of cinchona alkaloids in plants.

Nature, Published online: 18 March 2026; doi:10.1038/d41586-026-00790-8

The cinchona alkaloids are a family of plant-derived compounds that include quinine, an antimalarial drug also used as the bittering ingredient in tonic water. The biosynthetic pathway in Cinchona plants that produces the scaffold for these important molecules has been mapped.

Nature, Published online: 18 March 2026; doi:10.1038/d41586-026-00632-7

MicroRNAs control gene expression by modulating the output and stability of messenger RNAs. How are these crucial regulators kept in check?

This review summarizes the biochemical properties, catalytic properties, and applications of phosphorylation class III (PPK2-III) in the synthesis and regeneration of natural nucleoside triphosphates (NTPs) and the synthesis of modified nucleoside triphosphate, highlighting their potentials for adenosine-5′-triphosphate (ATP)-dependent industrial biocatalytic process and nucleic acid synthesis.

Enzymatic synthesis of natural or modified nucleoside triphosphates (NTPs) with significant advantages has emerged as a promising alternative to chemical synthesis. Polyphosphate kinase (PPKs) are a class of enzymes responsible for reversible polyphosphate (polyP) synthesis (PPK1) and nucleotides phosphorylation (PPK2) by utilizing cost effective and stable polyP as phosphate donors. Recently, PPK2 class III (PPK2-III) has been increasingly utilized as a single bifunctional enzyme for nucleotide phosphorylation either from nucleoside monophosphate or diphosphate substrates. The applications of PPK2-III extend to widespread use in adenosine-5′-triphosphate (ATP) regeneration and modified NTP synthesis, which significantly facilitated the biosynthesis of high-value pharmaceuticals and nucleic acid synthesis. Herein, we summarized the properties, functions and well-established applications of currently reported PPK2-III enzymes.

A TAm-NCS cascade towards THIQs has been established, starting from amines with the in situ production of aldehydes. The cascade was used with a variety of nonfunctionalized and functionalized amines, and reaction conditions modified to enhance formation of the desired cross-products. This resulted in an efficient one-pot approach to THIQs starting from readily available amines.

Tetrahydroisoquinolines (THIQs) are an important group of alkaloids, and many of these natural products and non-natural analogues are biologically active. For this reason, concise stereochemical synthetic routes are of significant interest. One strategy has been to use the Pictet–Spenglerase enzyme norcoclaurine synthase (NCS) with an arylethylamine and aldehyde in a single step reaction, alternatively enzyme cascades have been developed. The use of a transaminase (TAm) potentially provides efficient access to the aldehyde component required in NCS cascades, but currently suffers from limited substrate tolerance, in part due to potential complexities with the formation of mixed products. Here we present the development of a TAm-NCS cascade using structurally diverse primary amines to form (1S)-6,7-dihydroxy-THIQs via the generation of, in particular, aliphatic aldehyde intermediates in situ. Application of the one-pot cascade with amines successfully generated the corresponding products in up to >99% enantiomeric excess and 83% isolated yields. The cascade was also extended with a tyrosinase to produce a 3-hydroxymethylene substituted THIQ.

We engineered thermo-alkali-stable D-hydantoinases via mutagenesis (M63A/F65H/C317T) to resolve Pregabalin's challenging chiral splitting, achieving ee value > 97% for key intermediate (R)-3-isobutylglutaric acid monoamide (R-IBM) synthesis under extreme conditions (pH 10, 70°C–80°C).

ABSTRACT

Pregabalin is a widely used clinical pharmaceutical agent for treatment of neuropathic pain and as an adjunctive therapy for epilepsy. The efficient synthesis of (R)-3-isobutylglutaric acid monoamide (R-IBM), a critical intermediate, is crucial for pregabalin manufacturing. This present study focused on identifying R-selective and robust D-hydantoinases with R-selectivity and robustness for the stereoselective synthesis of R-IBM, a key intermediate of pregabalin, from 3-isobutylglutarimide (IBI). Three D-hydantoinases, namely GsDHTase (GenBank No. PX317655), AcDHTase (GenBank No. PX317656) and BhDHTase (GenBank No. PX317657) with unique catalytic advantages were successfully isolated from a marine gene resource library. These enzymes exhibited exceptional robustness under extreme conditions (pH 10, 70°C or 80°C) and inherent high stereoselectivity for R-IBM. Wild-type and mutant forms of the three D-hydantoinases were heterologously expressed in E. coli BL21(DE3) using the pET-28a vector, followed by whole-cell catalysis experiments. The optimal IPTG induction temperature was determined to be 28°C. Maximum catalytic activity, corresponding to the highest conversion rate of IBI to R-IBM, was achieved at 50°C and pH 10.0. Notably, triple amino acid mutations (M63A, F65H and C317T) significantly enhanced stereoselectivity with only a slight reduction in enzymatic activity. The enantiomeric excess (ee%) of R-IBM improved from 73.74% to 97.55% for GsDHTase, 56.08% to 97.59% for AcDHTase and 78.32% to 96.85% for BhDHTase after mutation. Owing to their inherent robustness, these enzymes hold great potential for developing a theoretical 100% atom-economical route for the eco-friendly and cost-effective industrial production of pregabalin.

Nature Chemical Biology, Published online: 18 March 2026; doi:10.1038/s41589-026-02176-3

Proteins are promising ligands for selective metal capture, but low-throughput assays limit their discovery and design. Now, a high-throughput platform for quantifying the rare earth selectivity of lanmodulin (LanM) proteins has been developed. The SpyCI-LAMBS platform enabled the identification of a set of LanMs capable of separating light rare-earth elements in a single step.

Nature Chemistry, Published online: 19 March 2026; doi:10.1038/s41557-026-02105-w

Expanding diversity in chemical space

Nature, Published online: 17 March 2026; doi:10.1038/d41586-026-00787-3

The database of 200 million protein-structure predictions now includes homodimers, adding new biological relevance.

Terpene biosynthesis typically relies on classical terpene cyclases to initiate carbocation cascades. This study provides structural insights into a distinct family of methyltransferases that generate the initiating carbocation through methyl transfer. These enzymes couple methylation and terpene cyclization within a single active site. X-ray structures define a pyrophosphate-gated transition between open and closed states, while mutagenesis identifies residue networks that shape cascade trajectories and product outcomes. These findings establish the mechanistic basis of methylation-triggered terpene cyclization.

The synthesis of the PARP inhibitor Niraparib has been achieved via a chemoenzymatic dearomatization strategy. Chemical reduction combined with a one-pot enzymatic cascade comprising an amine oxidase (AmOx) and an ene imine reductase (EneIRED) allowed for asymmetric reduction with high enantioselectivity. Subsequent transformations and a final N-dealkylation step led to the isolation of Niraparib.

A chemoenzymatic dearomatization strategy, involving initial reduction of a pyridinium with sodium borohydride followed by a biocatalytic amine oxidase/ene imine reductase (AmOx/EneIRED) cascade, has enabled the synthesis of the PARP inhibitor Niraparib. A variety of tetrahydropyridines with different N-alkyl and 3-(4′-aryl) substituents were screened, leading to the selection of N-ethyl 3-(4′-aminophenyl)-1,2,5,6-tetrahydropyridine as the preferred substrate for the synthesis of Niraparib. Using AmOx 6-HDNO_{E350L_E352D} and EneIRED361 yielded the (S)-3-(4′-aminophenyl)piperidine product in 66% yield and 93% enantiomeric excesses (ee) on 50 mL scale. Subsequent modifications and a final N-dealkylation step allowed for the isolation of Niraparib.

Amide bond formation is central to active pharmaceutical ingredient (API) synthesis. A bio-organocatalytic cascade is reported, merging stereoselective ω-transaminase (ω-TA) transamination in neat organic solvent with choline chloride-mediated amidation under solvent-free microwave conditions. The method delivers chiral amides in high yields and >99% ee, enabling efficient, green access to pharmaceutical intermediates such as those of Racecadotril and AVR-48.

Amide bond formation is a key transformation in organic synthesis, especially for the preparation of active pharmaceutical ingredients (APIs). In this work, we report the development of a bio-organocatalytic cascade, combining stereoselective transamination catalyzed by ω-transaminases (ω-TAs) in neat organic solvent and choline chloride (ChCl)-mediated direct amidation. This strategy enables the synthesis of chiral amides from prochiral carbonyl compounds and carboxylic acids under solvent-free microwave conditions. After optimizing the biocatalytic transamination in MTBE, we applied the method to the synthesis of key intermediates of Racecadotril and AVR-48, achieving full conversions and enantiomeric excess above 99%. The amidation step, promoted by ChCl without traditional activating agents, proved highly efficient for a wide range of aliphatic and aromatic carboxylic acids, affording the target amides in 60%–86% yields. Solvent evaporation after the transamination step was essential to remove interfering byproducts such as acetone, thus improving amidation yields. Overall, this integrated methodology provides a green, efficient, and scalable route to access amide-based building blocks in high optical purity, opening new avenues for sustainable pharmaceutical manufacturing.

Nature Communications, Published online: 16 March 2026; doi:10.1038/s41467-026-70929-8

Author Correction: Generalizable and scalable protein stability prediction with rewired protein generative models

Nature Communications, Published online: 17 March 2026; doi:10.1038/s41467-026-70512-1

Pyomelanin is resistant to UV light, and has antibacterial and anti-inflammatory effects, however, the yield of pyomelanin isolated from natural producers is low. Here the authors engineer Komagataella phaffii to produce 70.5 g/L and isolate the product.

Communications Chemistry, Published online: 17 March 2026; doi:10.1038/s42004-026-01977-w

Enzymes often function in crowded environments due to the high concentration of macromolecules and the formation of biomolecular condensates, but most insights into enzyme kinetics stem from dilute solution studies. Here, the authors present a residue-resolved dynamic energy landscape model that explicitly accounts for the crowding agent, reporting a crowding-induced allosteric regulation mechanism of enzymatic catalysis for a model enzyme, adenylate kinase, and providing a computational framework for understanding the diversity of existing experimental observations.