Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids

Fungal meroterpenoids are a diverse group of hybrid natural products with impressive structural complexity and high potential as drug candidates. In this work, we evaluate the promiscuity of the early structure diversity-generating step in fungal meroterpenoid biosynthetic pathways: the multibond-forming polyene cyclizations catalyzed by the yet poorly understood family of fungal meroterpenoid cyclases. In total, 12 unnatural meroterpenoids were accessed chemoenzymatically using synthetic substrates. Their complex structures were determined by 2D NMR studies as well as crystalline-sponge-based X-ray diffraction analyses. The results obtained revealed a high degree of enzyme promiscuity and experimental results which together with quantum chemical calculations provided a deeper insight into the catalytic activity of this new family of non-canonical, terpene cyclases. The knowledge obtained paves the way to design and engineer artificial pathways towards second generation meroterpenoids with valuable bioactivities based on combinatorial biosynthetic strategies.     

A method of identifying the blood contributor in mixture stains through detecting blood-specific mRNA polymorphism

In the past decades, messenger RNA (mRNA) biomarkers have been employed to identify the origin of body fluids in forensic medicine. We hypothesized that the polymorphism of mRNA could be applied to identify individuals in mixture samples composed of two body fluids. In this study, we selected five blood-specific mRNA biomarkers of venous blood (SPTB, CD3G, AMICA1, ANK1, and GYPA) that encompass 16 SNPs to identify the mixture contributor(s). Five specific gene markers for menstrual blood, semen, skin, saliva, and vaginal secretions were amplified and typed as body-fluid positive controls. We established the system of multiplex PCR and single base extension (SBE) reaction followed by CE. The amplicon size was between 90bp and 294bp. The peripheral blood specificity was examined against other human body fluids, including saliva, semen, skin, menstrual blood, and vaginal secretion. The 16 SNPs were peripheral blood specific and could be successfully typed in homemade mixtures which are composed of different body fluids with 1 ng peripheral blood mRNA added. This system showed a supersensitivity (1:100) in detecting the trace amount of peripheral blood mixed in other body fluids and a combined discrimination power (CDP) of 0.99929 in Chinese population. It was the first time to establish a method for identifying the blood donors and deconvoluting mixtures through detecting mRNA polymorphism with SNaPshot assay. This peripheral blood specific SNP typing system showed high sensitivity to the typing of blood source specific markers regardless of other body fluids in the mixture.     

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins

Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.     

Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge

A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>_max) between bound and unbound states. The correlation coefficient (R²) between the <PMF>_max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R² = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.     

PyCDFT: A Python package for constrained density functional theory

We present PyCDFT, a Python package to compute diabatic states using constrained density functional theory (CDFT). PyCDFT provides an object-oriented, customizable implementation of CDFT, and allows for both single-point self-consistent-field calculations and geometry optimizations. PyCDFT is designed to interface with existing density functional theory (DFT) codes to perform CDFT calculations where constraint potentials are added to the Kohn–Sham Hamiltonian. Here, we demonstrate the use of PyCDFT by performing calculations with a massively parallel first-principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules. We show that PyCDFT yields results in agreement with existing implementations and is a robust and flexible package for performing CDFT calculations. The program is available at https://dx.doi.org/10.5281/zenodo.3821097 .     

烯醇-酮互变异构型亚胺衍生物对Co2+的高选择性识别

设计合成了新型烯醇-酮互变异构型亚胺衍生物R, 考察了受体R对18种阳离子的紫外光谱及裸眼识别性能. 结果表明, 该受体对Co²⁺, Fe²⁺和Ni²⁺表现出良好的紫外光谱识别能力, 且可实现对Co²⁺相对明显的裸眼单一识别. Job曲线表明, 受体R与Co²⁺形成了1:1型金属配合物, 且检出限可达4.14×10^-7 mol/L. 制备了受体R裸眼比色识别试纸; 根据理论计算及核磁滴定实验结果阐述了Co²⁺离子识别过程中烯醇-酮互变异构机理.     

Tertiary amines as vinyl source for the formations of aryl or pyrrole ring on amido-substitued 1,4-quinone with the assistance of palladium salt

The one-pot synthesis of 3-isopropyl-6-methyl-1H-benzo[f]indole-4,9-dione ( 3e ), N-(4-[isopentylamino]-3,6-dioxocyclohexa-1,4-dien-1-yl)acetamide ( 4d ), 2-(isopentylamino)-6-methylnaphthalene-1,4-dione ( 5b ), and 2-(4-acetamido-3,6-dioxocyclohexa-1,4-dien-1-yl)-N,N-diisopentyl-3-methylbutanamide ( 6a ) has been achieved via either pyrrol/aryl ring formations or amination reactions from the Pd(II)-catalyzed reaction of N-(3,6-dioxocyclohexa-1,4-dien-1-yl)acetamide ( 2a_BQ ) and in the presence of triisopentylamine. More 3 -, 4 -, 5 -, and 6 -like derivatives were obtained while other trialkylamines were used. Crystal structures of 3d_O , 3e , 4b , 4c , 4d , 5b, and 6a were determined by single-crystal X-ray diffraction methods. The 3 - and 5 -like products reveal the formations of newly generated benzene rings with/without substitutions. The formation of 6a also implies an unusual reaction pathway of its generation. Based on the structural conformations of various 3 -like products, as well as 6a , mechanisms were proposed to account for the formations of these compounds. Various fascinating conformations of products observed in this work demonstrate the diversities of this type of reactions.     

Indandione-Terminated Quinoids: Facile Synthesis by Alkoxide-Mediated Rearrangement Reaction and Semiconducting Properties

A series of 1,3-indandione-terminated π-conjugated quinoids were synthesized by alkoxide-mediated rearrangement reaction of the respective alkene precursors, followed by air oxidation. This new protocol allows access to quinoidal compounds with variable termini and cores. The resulting quinoids all show LUMO levels below −4.0 eV and molar extinction coefficients above 10⁵ L mol⁻¹ cm⁻¹. The optoelectronic properties of these compounds can be regulated by tuning the central cores as well as the aryl termini ascribed to the delocalized frontier molecular orbitals over the entire molecular skeleton involving aryl termini. n-Channel organic thin-film transistors with electron mobility of up to 0.38 cm² V⁻¹ s⁻¹ were fabricated, showing the potential of this new class of quinoids as organic semiconductors.     

Strong-Base-Assisted Synthesis of a Crystalline Covalent Triazine Framework with High Hydrophilicity via Benzylamine Monomer for Photocatalytic Water Splitting

Methods to synthesize crystalline covalent triazine frameworks (CTFs) are limited and little attention has been paid to development of hydrophilic CTFs and photocatalytic overall water splitting. A route to synthesize crystalline and hydrophilic CTF-HUST-A1 with a benzylamine-functionalized monomer is presented. The base reagent used plays an important role in the enhancement of crystallinity and hydrophilicity. CTF-HUST-A1 exhibits good crystallinity, excellent hydrophilicity, and excellent photocatalytic activity in sacrificial photocatalytic hydrogen evolution (hydrogen evolution rate up to 9200 μmol g⁻¹ h⁻¹). Photocatalytic overall water splitting is achieved by depositing dual co-catalysts in CTF-HUST-A1, with H₂ evolution and O₂ evolution rates of 25.4 μmol g⁻¹ h⁻¹ and 12.9 μmol g⁻¹ h⁻¹ in pure water without using sacrificial agent.