Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.

An ECD and NMR/DP4+ Computational Pipeline for Structure Revision and Elucidation of Diphenazine-Based Natural Products.

Discovery and structure elucidation of natural products available in infinitesimally small quantities are recognized challenge. This challenge is epitomized by the diphenazine class of molecules that contain three bridged stereocenters, several conformations, ring fusions, and multiple spatially isolated phenols. Because empirical NMR and spatial analyses using ROESY/NOESY were unsuccessful in tackling these challenges, we developed a computational pipeline to determine the relative and absolute configurations and phenol positions of diphenazines as inhibitors of eukaryotic translation initiation factor 4E (eIF4E) protein-protein interactions. In this pipeline, we incorporated ECD and GIAO NMR calculations coupled with a DP4+ probability measure, enabling the structure revision of phenazinolin D (4), izumiphenazine A (5), and baraphenazine G (7) and the structure characterization of two new diphenazines, baraphenazine H (3) and izumiphenazine E (6). Importantly, through these efforts, we demonstrate the feasibility of NMR/DP4+ analysis for the determination of phenol positions in phenazine-based molecules, further expanding the limits of computational methods for the structure elucidation of complex natural products.

Single-Atomic-Layer Stanene on Ferromagnetic Co Nanoislands with Topological Band Structures.

Introducing magnetism to two-dimensional topological insulators is a central issue in the pursuit of magnetic topological materials in low dimensionality. By means of low-temperature growth at 80 K, we succeeded in fabricating a monolayer stanene on Co/Cu(111) and resolving ferromagnetic spin contrast by field-dependent spin-polarized scanning tunneling microscopy (SP-STM). Increases of both remanence to saturation magnetization ratio (Mr/Ms) and coercive field (Hc) due to an enhanced perpendicular magnetic anisotropy (PMA) are further identified by out-of-plane magneto-optical Kerr effect (MOKE). In addition to ultraflat stanene fully relaxed on bilayer Co/Cu(111) from density functional theory (DFT), characteristic topological properties including an in-plane s-p band inversion and a spin-orbit coupling (SOC) induced gap about 0.25 eV at the Γ̅ point have also been verified in the Sn-projected band structure. Interfacial coupling of single-atomic-layer stanene with ferromagnetic Co biatomic layers allows topological band features to coexist with ferromagnetism, facilitating a conceptual design of atomically thin magnetic topological heterostructures.

Discovery of Surfactins as Inhibitors of MicroRNA Processing Using Cat-ELCCA.

MicroRNAs (miRNAs) are a family of small noncoding RNAs that regulate gene expression. Due to their important activity in the fine-tuning of protein translation, abnormal expression of miRNAs has been linked to many human diseases, making the targeting of miRNAs attractive as a novel therapeutic strategy. Accordingly, researchers have been heavily engaged in the discovery of small molecule modulators of miRNAs. With an interest in the identification of new chemical space for targeting miRNAs, we developed a high-throughput screening (HTS) technology, catalytic enzyme-linked click chemistry assay (cat-ELCCA), aimed at the discovery of small molecule ligands for pre-miR-21, a miRNA that is frequently overexpressed in human cancers. From our HTS campaign, we found that natural products, a source of many impactful human medicines, may be a promising source of potential pre-miR-21-selective maturation inhibitors. Herein we describe our first efforts in natural product inhibitor discovery leading to the identification of a depsipeptide class of natural products as RNA-binding inhibitors of Dicer-mediated miRNA processing.

The pregnancy-associated spontaneous coronary artery dissection in a young woman with a novel missense mutation in NOTCH1: a case report.

BACKGROUND: Spontaneous coronary artery dissection (SCAD) is frequently reported as a disorder that primarily affects women without risk factors for cardiovascular disease. Although it has been recognized as one of the genetically mediated vascular disorders, the genetic pathogenesis of SCAD remains obscure to date. CASE PRESENTATION: In this report, we presented a rare case of pregnancy-associated SCAD in a young woman that occurred in multiple coronary arteries within a short period. The initial conservative management and then intravascular ultrasound-guided primary percutaneous coronary intervention (PCI) were adopted to achieve optimal results of revascularization in affected coronary arteries and avoid potential risks for PCI-associated complications. We further performed the whole-exome sequencing and Sanger sequencing and, for the first time, reported a novel heterozygous missense variant, c.4574 C > T (p.Arg1438Cys), in the NOTCH1 gene. This variant has never been documented in the medical literature and was predicted as being potentially damaging or disease-causing variant. CONCLUSIONS: We described a rare case of recurrent SCAD in a young woman after baby delivery. The initial conservative management and PCI with multiple stent implantations were successfully implemented to achieve optimal results of revascularization in coronary arteries. We, for the first time, identified a novel missense variant in the NOTCH1 gene, which appears to be a potential predisposing factor for artery fragility.

A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild.

A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild microbiomes is described. Wild organisms that can use camphor, terpineol, pinene and limonene were isolated from soils rich in coniferous waste. Cell free extracts and growth beers were analyzed by gas chromatography/mass spectrometry to identify primary oxidative metabolites. For one organism, Pseudomonas nitroreducens TPJM, a cytochrome P450 (CYP108B1) isolated from cell free extracts was demonstrated to catalyze the oxidation of α-terpineol in assays combining the native ferredoxin and putidaredoxin reductase, and the resulting oxidation products identified by gas chromatography/mass spectrometry. Shotgun sequencing of PnTPJM identified four candidate P450 genes, including an apparently fragmentary gene with a high degree of homology with the known enzyme CYP108 (P450terp).

NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450.

The existence of a substrate-sensitive equilibrium between high spin (S=5/2) and low spin (S=1/2) ferric iron is a well-established phenomenon in the cytochrome P450 (CYP) superfamily, although its origins are still a subject of discussion. A series of mutations that strongly perturb the spin state equilibrium in the camphor hydroxylase CYP101A1 were recently described (Colthart et al., Sci. Rep. 6, 22035 (2016)). Wild type CYP101A1 as well as some CYP101A1 mutants are herein shown to be capable of catalyzing the reduction of nitroacetophenones by NADH to the corresponding anilino compounds (nitroreductase or NRase activity). The distinguishing characteristic between those mutants that catalyze the reduction and those that cannot appears to be the extent to which residual high spin form exists in the absence of the native substrate d-camphor, with those showing the largest spin state shifts upon camphor binding also exhibiting NRase activity. Optical and EPR spectroscopy was used to further examine these phenomena. These results suggest that reduction of nitroaromatics may provide a useful probe of residual high spin states in the CYP superfamily. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.