Communications Chemistry最新文献

Lactacystin is an irreversible proteasome inhibitor isolated from Streptomyces lactacystinicus. Despite its importance for its biological activity, the biosynthesis of lactacystin remains unknown. In this study, we identified the lactacystin biosynthetic gene cluster by gene disruption and heterologous expression experiments. We also examined the functions of the genes encoding a PKS/NRPS hybrid protein (LctA), NRPS (LctB), ketosynthase-like cyclase (LctC), cytochrome P450 (LctD), MbtH-like protein (LctE), and formyltransferase (LctF) by in vivo and in vitro experiments. In particular, we demonstrated that LctF directly transferred the formyl group of 10-N-formyl tetrahydrofolate to CoA. The formyl group of formyl-CoA was then transferred to ACP1 by LctA_AT1 to form formyl-ACP1. This is the first example of an AT domain recognizing a formyl group. The formyl group is perhaps transferred to methylmalonate tethered on LctA_ACP2 to yield methylmalonyl-semialdehyde-ACP2. Then, it would be condensed with leucine bound to PCP in LctB by the C domain in LctA. Using a mimic compound, we confirmed that LctC catalyzed the formation of the cyclic α,α-disubstituted amino acid structure with concomitant release of the product from PCP. Thus, we figured out the overall biosynthesis of lactacystin including a novel role of a formyl group in a secondary metabolite.

Various photoactive molecules contain motifs built on aza-aromatic heterocycles, although a detailed understanding of the excited state photophysics and photochemistry in such systems is not fully developed. To help address this issue, the non-adiabatic dynamics operating in azanaphthalenes under hexane solvation was studied following 267 nm excitation using ultrafast transient absorption spectroscopy. Specifically, the species quinoline, isoquinoline, quinazoline, quinoxaline, 1,6-naphthyridine, and 1,8-naphthyridine were investigated, providing a systematic variation in the relative positioning of nitrogen heteroatom centres within a bicyclic aromatic structure. Our results indicate considerable differences in excited state lifetimes, and in the propensity for intersystem crossing vs internal conversion across the molecular series. The overall pattern of behaviour can be explained in terms of potential energy barriers and spin-orbit coupling effects, as demonstrated by extensive quantum chemistry calculations undertaken at the SCS-ADC(2) level of theory. The fact that quantum chemistry calculations can achieve such detailed and nuanced agreement with experimental data across a full set of six molecules exhibiting subtle variations in their composition provides an excellent example of the current state-of-the-art and is indicative of future opportunities for rational design of photoactive molecules.

Liquid cell transmission electron microscopy (LCTEM) is a powerful technique for investigating crystallisation dynamics with nanometre spatial resolution. However, probing phenomena occurring in liquids while mixing two precursor solutions has proven extremely challenging, requiring sophisticated liquid cell designs. Here, we demonstrate that introducing and withdrawing solvents in sequence makes it possible to maintain optimal imaging conditions while mixing liquids in a commercial liquid cell. We succeeded in visualising a fast nanoscale crystallisation mechanism when an organic molecule of R-BINOL-CN dissolved in chloroform interacts with methanol. The scanning transmission electron microscopy images recorded in real-time during the interaction of the two volatile solvents reveal the formation of chain-like structures of R-BINOL-CN particles, whereas they coalesce to form single large particles when methanol is absent. Our approach of mixing liquids establishes a platform for novel LCTEM studies of a wide range of electron-beam-sensitive materials, including drug molecules, polymers and molecular amphiphiles.

Serial macromolecular crystallography has become a powerful method to reveal room temperature structures of biological macromolecules and perform time-resolved studies. ID29, a flagship beamline of the ESRF 4th generation synchrotron, is the first synchrotron beamline in the world capable of delivering high brilliance microsecond X-ray pulses at high repetition rate for the structure determination of biological macromolecules at room temperature. The cardinal combination of microsecond exposure times, innovative beam characteristics and adaptable sample environment provides high quality complete data, even from an exceptionally small amount of crystalline material, enabling what we collectively term serial microsecond crystallography (SµX). After validating the use of different sample delivery methods with various model systems, we applied SµX to an integral membrane receptor, where only a few thousands diffraction images were sufficient to obtain a fully interpretable electron density map for the antagonist istradefylline-bound A_2A receptor conformation, providing access to the antagonist binding mode. SµX, as demonstrated at ID29, will quickly find its broad applicability at upcoming 4th generation synchrotron sources worldwide and opens a new frontier in time-resolved SµX.

Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is a key regulator of cell detoxification, which maintains homoeostasis in healthy cells and promotes chemoresistance in cancer cells. Controlling the expression of this transcription factor is therefore of great interest. There are many compounds that have been shown to induce Nrf2 expression, but ligands that can inhibit Nrf2 are scant. Herein we characterise an i-motif-forming sequence downstream of the Nrf2 promoter, which we hypothesised may regulate the expression of the gene. The Nrf2 i-motif was found to be stable at near-physiological conditions. We identified small molecule ligands that interact with this i-motif structure and one significantly upregulated Nrf2 mRNA expression, and one ligand reduced Nrf2 mRNA expression in human cancer cells. This is the first example of controlling the promoter of Nrf2 by targeting DNA structures and offers an alternative mode of action for the development of compounds to improve the chemotherapeutic responsiveness of existing treatments for cancer.

While the abilities of language models are thoroughly evaluated in areas like general domains and biomedicine, academic chemistry remains less explored. Chemical QA tools also play a crucial role in both education and research by effectively translating complex chemical information into an understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. Specifically, the questions are from paper titles with a question mark, and the multi-choice answers are reasoned out based on the corresponding abstracts. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a ChemMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. Experiments show that Large Language Models (LLMs) still have significant room for improvement in the field of chemistry. Moreover, ChemMatch significantly outperforms recent similar-scale baselines: https://github.com/iriscxy/chemmatch .

Time-resolved coherent Raman spectroscopy (CRS) is a powerful non-linear optical technique for quantitative, in-situ analysis of chemically reacting flows, offering unparalleled accuracy and exceptional spatiotemporal resolution. Its application to large polyatomic molecules, crucial for understanding reaction dynamics, has thus far been limited by the complexity of their rotational-vibrational Raman spectra. Progress in developing comprehensive spectral codes for these molecules, a longstanding goal, has been hindered by prohibitively long computation times required for their spectral synthesis. Here, we present an algorithm that achieves a million-fold improvement in computation time compared to existing methods. The algorithm demonstrates remarkable accuracy, with an approximation error below 0.1% across all tested probe delays, at both room temperature (296 K) and elevated temperatures (1500 K). This result could greatly expand the application of time-resolved CRS, particularly in plasma research, as well as in broader atmospheric and astrophysical sciences.

Protein-RNA interactions play important biological roles and hence reactive RNA probes for cross-linking with proteins are important tools in their identification and study. To this end, we designed and synthesized 5'-O-triphosphates bearing a reactive squaramate group attached to position 5 of cytidine or position 7 of 7-deazaadenosine and used them as substrates for polymerase synthesis of modified RNA. In vitro transcription with T7 RNA polymerase or primer extension using TGK polymerase was used for synthesis of squaramate-modified RNA probes which underwent covalent bioconjugations with amine-linked fluorophore and lysine-containing peptides and proteins including several viral RNA polymerases or HIV reverse transcriptase. Inhibition of RNA-depending RNA polymerases from Japanese Encephalitis virus was observed through formation of covalent cross-link which was partially identified by MS/MS analysis. Thus, the squaramate-linked NTP analogs are useful building blocks for the synthesis of reactive RNA probes for bioconjugations with primary amines and cross-linking with lysine residues.