Macrocyclization is a vital process in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), significantly enhancing their structural diversity and biological activity. Universally found in living organisms, cytochrome P450 enzymes (P450s) are versatile catalysts that facilitate a wide array of chemical transformations and have recently been discovered to contribute to the expansion and complexity of the chemical spectrum of RiPPs. Particularly, P450-catalyzed biaryl-bridged RiPPs, characterized by highly modified structures, represent an intriguing but underexplored class of natural products, as demonstrated by the recent discovery of tryptorubin A, biarylitide and cittilin. These P450 enzymes demonstrate their versatility by facilitating peptide macrocyclization through the formation of carbon–carbon (C–C), carbon–nitrogen (C–N) and ether bonds between the side chains of tyrosine (Tyr), tryptophan (Trp) and histidine (His). This Review briefly highlights the latest progress in P450-catalyzed macrocyclization within RiPP biosynthesis, resulting in the generation of structurally complex RiPPs. These findings have expedited the discovery and detailed analysis of new P450s engaged in RiPP biosynthetic pathways.

The high throughput YESS 2.0 platform was used to screen a large library of SARS-CoV-2 M^pro variants in the presence of nirmatrelvir. Of the 100 individual most prevalent mutations identified in the screen and reported here, the most common were E166V, L27V, N142S, A173V, and Y154N, along with their various combinations. In vitro analysis revealed that resistance to nirmatrelvir for these individual mutations, as well as all of the combinations we analyzed, was accompanied by decreased catalytic activity with the native substrate. Importantly, the mutations we identified have not appeared as significantly enriched in SARS-CoV-2 M^pro sequences isolated from COVID-19 patients following the introduction of nirmatrelvir. We also analyzed three of the most common SARS-CoV-2 M^pro mutations that have been seen in patients recently, and only a measured increase in nirmatrelvir resistance was seen when the more recently appearing A285V is added to both P132H and K90R. Taken together, our results predict that resistance to nirmatrelvir will be slower to develop than expected based on experience with other viral protease inhibitors, perhaps due in part to the close structural correspondence between nirmatrelvir and SARS-CoV-2 M^pro’s preferred substrates.

Base modification and the use of lipid nanoparticles are thought to be essential for efficient in vivo delivery and expression of mRNA. However, for ex vivo immune cell engineering, the need for either of the two is unclear. Previous reports have suggested that nucleic acids may be efficiently delivered to immune cells ex vivo, through a nonendosomal delivery route, but the need for base modification has not been determined. Herein, we demonstrate that when a nonendosomal delivery method is used, unmodified mRNA performs equally well to the commonly used base-modified mRNA, including the N¹ methyl pseudouridine modification, in terms of protein expression and inflammatory response in cells. However, if an endosomal delivery route is used, then N¹ methyl pseudouridine modification is necessary for high expression and low inflammatory response, as demonstrated by others as well. Overall, we show that nonendosomal mRNA delivery renders nucleoside modifications nonessential and that unmodified mRNA combined with nonendosomal delivery route may be used for efficient ex vivo mRNA-based engineering of immune cells.

This study introduces novel cospray-dried (Co-SD) formulations of simvastatin, a Nrf2 activator ROCK inhibitor, with l-carnitine as molecular mixtures in various molar ratios for targeted pulmonary inhalation aerosol delivery in pulmonary hypertension, optimized for excipient-free dry powder inhalers (DPIs). The two components were spray-dried at various molar ratios by using different starting feed solution concentrations and process parameters. In addition to comprehensive physicochemical characterization, in vitro aerosol dispersion performance as DPIs using two FDA-approved DPI devices with different shear stress properties, in vitro viability as a function of dose on 2D human pulmonary cellular monolayers and on 3D small airway epithelia human primary cultures at the air–liquid interface (ALI), and in vitro transepithelial electrical resistance (TEER) at the ALI were conducted. Solid-state physicochemical characterization confirmed homogeneous molecular mixtures and the crystalline nature of the Co-SD formulations. In vitro aerosolization dispersion performance demonstrated that all Co-SD dual combination molecular mixtures aerosolized successfully with both human FDA-approved DPI devices, had ∼100% emitted dose, and good fine particle fraction values. The in vitro viability and TEER assays demonstrated that all formulations were safe to the human pulmonary cell as 2D and 3D cultures as a function of dose.

Cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes constitute a large subclass of radical SAM (RS) enzymes that use Cbl to catalyze various types of reactions, the most common of which are methylations. Most Cbl-dependent RS enzymes contain an N-terminal Rossmann fold that aids Cbl binding. Recently, it has been demonstrated that the methanogenesis marker protein 10 (Mmp10) requires Cbl to methylate an arginine residue in the α-subunit of methyl coenzyme M reductase. However, Mmp10 contains a Cbl-binding domain in the C-terminal region of its primary structure that does not share significant sequence similarity with canonical RS Cbl-binding domains. Bioinformatic analysis of Mmp10 identified DUF512 (Domain of Unknown Function 512) as a potential Cbl-binding domain in RS enzymes. In this paper, four randomly selected DUF512-containing proteins from various organisms were overexpressed, purified, and shown to bind Cbl. X-ray crystal structures of DUF512-containing proteins from Clostridium sporogenes and Pyrococcus furiosus were determined, confirming their C-terminal Cbl-binding domains. The structure of the DUF512-containing protein from C. sporogenes is the first of an RS enzyme containing a PDZ domain. Its RS domain has an unprecedented β₃α₄ core, whereas most RS enzymes adopt a (βα)₆ core. The DUF512-containing protein from P. furiosus has no PDZ domain, but its RS domain also has an uncommon (βα)₅ core.

Vesicle Amine Transport-1 (VAT1) is a protein that is overexpressed in many cancers, including breast cancer, glioblastoma, and angiosarcoma. High VAT1 expression correlates with poor overall survival, and genetic knockout models of VAT1 indicate potent antimigratory activity, suggesting that VAT1 is a promising antimetastasis target. Recently, the natural product neocarzilin A (NCA) from Streptomyces carzinostaticus was reported to be the first validated small-molecule inhibitor of VAT1, having strong activity in metastasis models of angiosarcoma and breast cancer. While knockdown of VAT1 has no effect on cell viability, NCA has significant cytotoxicity, suggesting that NCA is not selective for VAT1. Additionally, NCA has poor aqueous solubility, making in vivo administration of NCA challenging and thus limiting its therapeutic potential. Here, we report the design, synthesis, bioactivity, and pharmacokinetics of novel NCA derivatives with improved drug-like properties. Specifically, we have developed derivatives with altered warheads, replacing chlorines on the trichloroketone with fluorines. Using a modified synthetic route, we accessed NCA derivatives with greater than 25-fold improvements in solubility and 30-fold improvements in the antimigratory to antiproliferative bioactivity ratio. The two best derivatives, along with the parent, were analyzed for oral bioavailability, with the two more soluble derivatives showing greatly improved bioavailability. Overall, these studies have resulted in the development of VAT1 inhibitors with improved properties, which will enable further study of the pharmacological inhibition of VAT1 as an antimetastatic strategy. Additionally, these studies provide insights into novel trihalomethyl ketone warheads and identify chlorodifluoroketone as a potent and selective new warhead.

Glycan sulfation is a widespread postglycosylation modification crucial for modulating biological functions including cellular adhesion, signaling, and bacterial colonization. 6-Sulfo-β-GlcNAcases are a class of enzyme that alters sulfation patterns. Such changes in sulfation patterns are linked to diseases such as bowel inflammation, colitis, and cancer. Despite their significance, 6-sulfo-β-GlcNAcases, which cleave β-linked 6-sulfo-N-acetylglucosamine (6S-GlcNAc), have been but rarely identified. This scarcity results mainly from the short, diverse, and distinctive sulfate-binding motifs required for recognition of the 6-sulfate group in 6S-GlcNAc in addition to the conserved GH20 family features. In this study, we discovered 6-sulfo-β-GlcNAcases and assigned two novel sulfate-binding motifs by the use of comparative genomics, structural predictions, and activity-based screening. Our findings expand the known microbiota capable of degrading sulfated glycans and add significant enzymes to the tool kit for analysis and synthesis of sulfated oligosaccharides.

Chlorophyll (Chl) is one of Nature’s most complex pigments to biosynthesize and derivatize. This pigment is vital for survival and also paradoxically toxic if overproduced or released from a protective protein scaffold. Therefore, along with the mass production of Chl, organisms also invest in mechanisms to control its degradation and recycling. One important enzyme that is involved in these latter processes is chlorophyllase. This enzyme is employed by numerous photosynthetic organisms to hydrolyze the phytol tail of Chl. Although traditionally thought to catalyze the first step of Chl degradation, recent work suggests that chlorophyllase is instead employed during times of abiotic stress or conditions that produce reactive oxygen species. However, the molecular details regarding how chlorophyllases are regulated to function under such conditions remain enigmatic. Here, we investigate the Arabidopsis thaliana chlorophyllase isoform AtCLH2 using site-directed mutagenesis, mass spectrometry, dynamic light scattering, size-exclusion multiangle light scattering, and both steady-state enzyme kinetic and thermal stability measurements. Through these experiments, we show that AtCLH2 exists as a monomer in solution and contains two disulfide bonds. One disulfide bond putatively maps to the active site, whereas the other links two N-terminal Cys residues together. These disulfide bonds are cleaved by chemical or chemical and protein-based reductants, respectively, and are integral to maintaining the activity, stability, and substrate scope of the enzyme. This work suggests that Cys residue oxidation in chlorophyllases is an emerging regulatory strategy for controlling the hydrolysis of Chl pigments.