Exploring gabosine and chlorogentisyl alcohol derivatives from a marine-derived fungus as EcGUS inhibitors with informatic assisted approaches

Discovery of therapeutic promising natural products to target Kv1.3 channel, a transmembrane protein regulating immune disorders, through multidimensional virtual screening, molecular dynamics simulations and biological validation

Kv1.3 voltage-gated potassium channel, is a transmembrane protein that facilitates K+ movement through cell membranes via its intrinsic pores, regulating the cell signaling cascades, especially in immune disorders. In this paper, we employed multidimensional virtual screening to identify 24 potential Kv1.3 inhibitors from a library of 27,637 compounds, with electrophysiological assays confirming 8 active inhibitors (33.33 % hit rate). Structure-activity relationship (SAR) analysis demonstrated that 4-methylpentyl group in side chain and furan ring in Furanocoumarins skeleton are crucial to the bioactivity of target compounds. Orthogonal projection to latent structures model reveals that increasing the QPlogPo/w of the compound can increase activity. Molecular dynamics simulations revealed key roles of residues (VAL469 and ILE472) as active binding sites of Kv1.3 for binding of specific compound. Notopterol (Z4), the most potent Kv1.3 inhibitor (IC50 = 311.90 ± 1.24 nM), significantly suppressed IFN-γ release from CD4+ T cells, whereas, Kv1.3 inactive compound Z20 at 5 μM showed no significant difference in IFN-γ release from CD4+ T cells. In atopic dermatitis rat model, Notopterol reduced epidermal thickening, IgE, Kv1.3, IL-1β production, and infiltration of CD4+ T cells and mast cells. These findings establish Notopterol as a promising Kv1.3 inhibitor for therapeutic applications in immune disorders.

Overview on Building Blocks and Applications of Efficient and Robust Extended Tight Binding

The extended tight binding (xTB) family of methods opened many new possibilities in the field of computational chemistry. Within just 5 years, the GFN2-xTB parametrization for all elements up to Z = 86 enabled more than a thousand applications, which were previously not feasible with other electronic structure methods. The xTB methods provide a robust and efficient way to apply quantum mechanics-based approaches for obtaining molecular geometries, computing free energy corrections or describing noncovalent interactions and found applicability for many more targets. A crucial contribution to the success of the xTB methods is the availability within many simulation packages and frameworks, supported by the open source development of its program library and packages. We present a comprehensive summary of the applications and capabilities of xTB methods in different fields of chemistry. Moreover, we consider the main software packages for xTB calculations, covering their current ecosystem, novel features, and usage by the scientific community.

The Natural Products Atlas 3.0: extending the database of microbially derived natural products

The Natural Products Atlas is a database of microbially derived natural products that contains structures, producing organism taxonomy, biosynthetic and chemical ontology classifications, grouping by compound classes and cross-links to a suite of other natural product-related data resources. The database is supported by a web server that includes functionality to browse the collection, search the database using both chemical structures and text/numerical terms and visualize the chemical diversity it contains using interactive dashboards. In the current database release, we have curated 1347 papers, increasing the number of compounds to 36 545. In addition, we have initiated a large-scale effort to incorporate data from papers reporting structural reassignments and revisions to previously published structures. This effort led to the incorporation of 590 corrections to existing entries, significantly improving the accuracy of the dataset. The Natural Products Atlas may be accessed at www.npatlas.org.

Antimicrobial spiroketal macrolides and dichloro-diketopiperazine from Micromonospora sp. FIMYZ51

Four compounds (1-4) featuring with an L-rhodinose and spiroketal, possess uncommon continuous hydroxy groups in the macrolide skeleton, and a dichloro-diketopiperazine (5) were isolated from a marine derived Micromonospora sp. FIMYZ51. The determination of the relative and absolute configurations of all isolates was achieved by extensive spectroscopic analyses, single-crystal X-ray diffraction analysis, and ECD calculations. According to structural characteristic and genomic sequences, a plausible biosynthetic pathway for compound 1-4 was proposed and a spirocyclase was inferred to be responsible for the formation of the rare spirocyclic moiety. Compounds 1-4 exhibited potent antifungal activities which is equal to itraconazole against Aspergillus niger. Compounds 1-5 exhibited different degree of inhibitory activities against opportunistic pathogenic bacteria of endocarditis (Micrococcus luteus) with MIC values ranging from 0.0625 μg/mL to 32 μg/mL. Compounds 2 and 3 showed moderate cytotoxicity against drug-resistant tumor cell lines (Namalwa and U266). The result not only provides active lead-compounds, but also reveal the potential of the spirocyclase gene resources from Micromonospora sp., which highlights the promising potential of the strain for biomedical applications.

Plant antibacterials: The challenges and opportunities

Nature possesses an inexhaustible reservoir of agents that could serve as alternatives to combat the growing threat of antimicrobial resistance (AMR). While some of the most effective drugs for treating bacterial infections originate from natural sources, they have predominantly been derived from fungal and bacterial species. However, a substantial body of literature is available on the promising antibacterial properties of plant-derived compounds. In this comprehensive review, we address the major challenges associated with the discovery and development of plant-derived antimicrobial compounds, which have acted as obstacles preventing their clinical use. These challenges encompass limited sourcing, the risk of agent rediscovery, suboptimal drug metabolism, and pharmacokinetics (DMPK) properties, as well as a lack of knowledge regarding molecular targets and mechanisms of action, among other pertinent issues. Our review underscores the significance of these challenges and their implications in the quest for the discovery and development of effective plant-derived antimicrobial agents. Through a critical examination of the current state of research, we give valuable insights that will advance our understanding of these classes of compounds, offering potential solutions to the global crisis of AMR. © 2017 Elsevier Inc. All rights reserved.

Advancing Natural Product Discovery: A Structure-Oriented Fractions Screening Platform for Compound Annotation and Isolation

Natural product discovery is hindered by the lack of tools that integrate untargeted nuclear magnetic resonance and mass spectrometry data on a library scale. This article describes the first application of the innovative NMR/MS-based machine learning tool, the "Structure-Oriented Fractions Screening Platform (SFSP)", enabling functional-group-guided fractionation and accelerating the discovery and characterization of undescribed natural products. The concept was applied to the extract of a marine fungus known to be a prolific producer of diverse natural products. With the assistance of SFSP, we isolated 24 flavipidin derivatives and five phenalenone analogues from Aspergillus sp. GE2-6, revealing 27 undescribed compounds. Compounds 7-22 were proposed as isomeric derivatives featuring a 5/6-ring fusion, formed by the dimerization of flavipidin E (5). Compounds 23 and 24 were envisaged as isomeric derivatives with a 6/5/6-ring fusion, generated through the degradation of two flavipidin E molecules. Furthermore, flavipidin A (1) and asperphenalenone E (28) exhibited potent anti-influenza (PR8) activities, with IC50 values of 21.9 ± 0.2 and 12.9 ± 0.1 μM, respectively. Meanwhile, asperphenalenone (26) and asperphenalenone P (27) treatments exhibited significant inhibition of HIV pseudovirus infection in 293FT cells, boasting IC50 values of 6.1 ± 0.9 and 4.6 ± 1.1 μM, respectively. Overall, SFSP streamlines natural product isolation through NMR and MS data integration, as showcased by the discovery of numerous undescribed flavipidins and phenalenones based on NMR olefinic signals and low-field hydroxy signals.

Marine natural products

Covering: January to the end of December 2022This review covers the literature published in 2022 for marine natural products (MNPs), with 645 citations (633 for the period January to December 2022) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, the submerged parts of mangroves and other intertidal plants. The emphasis is on new compounds (1417 in 384 papers for 2022), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of NP structure class diversity in relation to biota source and biome is discussed.

Antifungal polyketides from the marine-derived fungus Nigrospora sp. MG36-1

Three new polyketides, a griseofulvin derivative 1, a hydroanthraquinone derivative 8 and a pyranolactone derivative 10, together with eight known compounds (2-7, 9 and 11), were isolated from the marine-derived fungus Nigrospora sp. MG36-1. The structures of the three new compounds were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, ¹³C NMR calculation in combination with DP4+ and ECD calculations. The antitumor, antibacterial and antifungal activities of the compounds 1-9 were evaluated in vitro. Compound 1 showed antibacterial activity against Acinetobacter baumannii with MIC 42.5 μg/mL. Compounds 1 and 8 exhibited antifungal activity against Candida albicans with MICs 21.5 μg/mL and 17.5 μg/mL, respectively.

Spirocyclic polyketides from the marine fungus Talaromyces sp. CX11

Three new spirocyclic polyketides, talaromyacins A - C, were identified from the endophytic fungus Talaromyces sp. CX11. Their structures including absolute configurations were determined by extensive spectroscopic analysis, Snatzke's method and quantum chemical calculations. Talaromyacin A is identical to the known sequoiamonascin A, for which a structural revision is required.