Chemical structures, biosynthesis, bioactivities, and utilisation values for the diterpenes produced in tobacco trichomes

Cembranoids and labdanes are two important types of diterpenes in tobacco (Nicotiana genus) that are predominantly found in the leaf and flower glandular trichome secretions. This is the first systematic review of the biosynthesis, chemical structures, bioactivities, and utilisation values of cembranoid and labdane diterpenes in tobacco. A total of 131 natural cembranoid diterpenes have been reported in tobacco since 1962; these were summarised and classified according to their chemical structure characteristics as isopropyl cembranoids (1-88), seco-cembranoids (89-103), chain cembranoids (104-123), and polycyclic cembranoids (124-131). Forty natural labdane diterpenes reported since 1961 were also summarised and divided into epoxy side chain labdanes (132-150) and epoxy-free side chain labdanes (151-171). Tobacco cembranoid and labdane diterpenes are both formed via the methylerythritol 4-phosphate pathway and are synthesised from geranylgeranyl diphosphate. Their biosynthetic pathways and the four key enzymes (cembratrienol synthase, cytochrome P450 hydroxylase, copalyl diphosphate synthase, and Z-abienol cyclase) that affect their biosynthesis have been described in detail. A systematic summary of the bioactivity and utilisation values of the cembranoid and labdane diterpenes is also provided. The agricultural bioactivities associated with cembranoid and labdane diterpenes include antimicrobial and insecticidal activities as well as induced resistance, while the medical bioactivities include cytotoxic and neuroprotective activities. Further research into the cembranoid and labdane diterpenes will help to promote their development and utilisation as plant-derived pesticides and medicines.

Response of fulvic acid linking to redox characteristics on methane and short-chain fatty acids in anaerobic digestion of chicken manure

Fulvic acids (FAs) is formed during the bioconversion of organic matter (OM) to biogas during anaerobic digestion (AD) and has a complex structure and redox function. However, the evolutionary mechanisms of FAs during AD and its interactions with acid and methane production have not been sufficiently investigated, especially at different stages of AD. Intermittent AD experiments by chicken manure and rice husk showed significant structural changes and reduced aromatization of FAs (e.g., O-H stretch6, 14.10-0%; SR, 0.22-0.60). The electron donating capacity (EDC) [9.76-45.39 μmole-/(g C)] and electron accepting capacity (EAC) [2.55-5.20 μmole-/(g C)] of FAs showed a tendency of decreasing and then increasing, and FAs had a stronger electron transfer capacity (ETC) in the methanogenic stage. Correlation analysis showed that the EDC of FAs was influenced by their own structure (C-O stretch2, C-H bend1, C-H bend4, and N-H bend) and also had an inhibitory effect on propionic production, which further inhibited acetic production. The EAC of FAs was affected by molecular weight and had a promoting effect on methane production. Structural equation modelling identified three possible pathways for AD. The C-O stretch2 structure of FAs alone inhibits the production of propionic. In addition, pH can directly affect the EDC of FAs. This study provides a theoretical basis for the structural and functional evolution of FAs in AD of chicken manure on the mechanism of methane production.

XGraphCDS: An explainable deep learning model for predicting drug sensitivity from gene pathways and chemical structures

Cancer is a highly complex disease characterized by genetic and phenotypic heterogeneity among individuals. In the era of precision medicine, understanding the genetic basis of these individual differences is crucial for developing new drugs and achieving personalized treatment. Despite the increasing abundance of cancer genomics data, predicting the relationship between cancer samples and drug sensitivity remains challenging. In this study, we developed an explainable graph neural network framework for predicting cancer drug sensitivity (XGraphCDS) based on comparative learning by integrating cancer gene expression information and drug chemical structure knowledge. Specifically, XGraphCDS consists of a unified heterogeneous network and multiple sub-networks, with molecular graphs representing drugs and gene enrichment scores representing cell lines. Experimental results showed that XGraphCDS consistently outperformed most state-of-the-art baselines (R2 = 0.863, AUC = 0.858). We also constructed a separate in vivo prediction model by using transfer learning strategies with in vitro experimental data and achieved good predictive power (AUC = 0.808). Simultaneously, our framework is interpretable, providing insights into resistance mechanisms alongside accurate predictions. The excellent performance of XGraphCDS highlights its immense potential in aiding the development of selective anti-tumor drugs and personalized dosing strategies in the field of precision medicine.

The alkynyl-containing compounds from mushrooms and their biological activities

Mushrooms have been utilized by humans for thousands of years due to their medicinal and nutritional properties. They are a crucial natural source of bioactive secondary metabolites, and recent advancements have led to the isolation of several alkynyl-containing compounds with potential medicinal uses. Despite their relatively low abundance, naturally occurring alkynyl compounds have attracted considerable attention due to their high reactivity. Bioactivity studies have shown that alkynyl compounds exhibit significant biological and pharmacological activities, including antitumor, antibacterial, antifungal, insecticidal, phototoxic, HIV-inhibitory, and immunosuppressive properties. This review systematically compiles 213 alkynyl-containing bioactive compounds isolated from mushrooms since 1947 and summarizes their diverse biological activities, focusing mainly on cytotoxicity and anticancer effects. This review serves as a detailed and comprehensive reference for the chemical structures and bioactivity of alkynyl-containing secondary metabolites from mushrooms. Moreover, it provides theoretical support for the development of chemical constituents containing alkynyl compounds in mushrooms based on academic research and theory.

DDI-GCN: Drug-drug interaction prediction via explainable graph convolutional networks

Drug-drug interactions (DDI) may lead to unexpected side effects, which is a growing concern in both academia and industry. Many DDIs have been reported, but the underlying mechanisms are not well understood. Predicting and understanding DDIs can help researchers to improve drug safety and protect patient health. Here, we introduce DDI-GCN, a method that utilizes graph convolutional networks (GCN) to predict DDIs based on chemical structures. We demonstrate that this method achieves state-of-the-art prediction performance on the independent hold-out set. It can also provide visualization of structural features associated with DDIs, which can help us to study the underlying mechanisms. To make it easy and accessible to use, we developed a web server for DDI-GCN, which is freely available at http://wengzq-lab.cn/ddi/.

Unusual 5/5 fused bicyclosesquiterpenoids from Eupatorium adenophorum

The chemical analysis on the aerial sections of Eupatorium adenophorum Spreng. resulted in the identification of four unprecedented 5/5 fused bicyclosesquiterpenoids, eupatorid A (1), and its analogues named eupatorester A-C (2-4) using various chromatographic techniques. Their structures were unambiguously confirmed by detailed spectroscopic investigations (including 1D, 2D-NMR and HRMS), and single crystal X-ray diffraction. The anti-inflammatory activities, in vitro tumor growth inhibitory activities and antibacterial activities of these compounds were evaluated.

Specialized metabolites of the fungal genus Phomopsis: Structures, bioactivities, biosynthesis

Fungi are important resources of novel bioactive compounds which have a high potential to be drug leads or candidates for further pharmacological applications. Phomopsis, a genus widely distributed in the environment, can produce various types of compounds including polyketides, alkaloids, terpenoids, cytochalasins, steroids and flavonoids. The metabolites of Phomopsis sp. showed diverse bioactivities such as antibacterial, anti-inflammatory, antimalarial, and so on, many of which may influence the physiological behaviour of the host plants. In this review, we focus on the chemical structures and biological activities of 183 specialized metabolites isolated from Phomopsis sp. in the decade (2013-2022). Moreover, the biosynthetic pathways of some typical components are summarized.

Revisiting organic waste-source-dependent molecular-weight governing the characterization within humic acids liking to humic-reducing microorganisms in composting process

Humic acids (HAs) coupled with humic-reducing microorganisms (HRMs) can facilitate contaminants reduction. Molecular-weight (MW) of HA governs the chemical and HRMs behavior. However, MW of HAs with chemical characteristics linking to HRMs in different wastes composting have never been investigated. Results from the HPSEC-UV analysis showed that composting significantly increased weight-average molecular weight (M_w) of HA with a broad range from 675 Da to 27983 Da, and governing heterogeneous chemical characteristics. In proteinaceous composts, MW< 4000 Da of HAs were greatly related to alkyl and carbonyl, while MW> 20000 Da of HAs were presented by oxygen-nitrogenous functional groups, methyl, and alkyl groups. For cellulosic composts, MW< 1500 Da and 4000-10000 Da of HAs were characterized by aliphatic ethers and aromatic groups. MW> 20000 Da of HAs were constructed by phenols, methoxy and nitrogen functional groups. In lignocellulosic composts, MW> 20000 Da of HAs were only characterized by aromatic groups. Furthermore, seven groups of HRMs adapted to the heterogeneous chemical characteristics within HAs ranked by MW were recognized. Consequently, the possible routes that composting properties response to the connections of HRMs-chemical structures-MW of HAs in proteinaceous, cellulosic and lignocellulosic composts were constructed, respectively. Our results can help to develop the fine classification-oriented approach for recycling utilization of organic wastes.

Chemistry and bioactivities of alkaloids isolated from marine fungi (covering 2016-2022)

The ocean is a treasure house with rich resources of new chemical and biological molecules. A growing body of evidence suggests that marine fungi represent a huge and largely untapped resource of natural products that have been optimized by evolution for biological and ecological relevance. Alkaloids, the important components of natural products, have attracted much attention from medicinal and natural product chemists due to their unique structures and biological potential. The number and variety of alkaloids from marine fungi discovered in recent years maintain an upward trend. This review would give a systematic overview of the structures and bioactivities of marine fungal alkaloids obtained over the past six years and inspire the development of novel pharmaceutical agents.

Metabolic fates and response strategies of microorganisms to aromatic compounds with different structures

In this study, the metabolic fates and response strategies of microorganisms to aromatic compounds with different structures (phenol, naphthalene, phenanthrene, and pyrene) were comparatively studied. The results indicated that the phenol (90.9%), naphthalene (68.4%), phenanthrene (69.5%), and pyrene (67.1%) could be mineralized, and the biotoxicity also has been drastically reduced. The degradation characteristics and toxic effects were closely related to their chemical structure. The microorganisms showed different response strategies to aromatic compounds with different structures. Phenol had a simple structure and low toxicity, the microbial community structure was simple, and the rapid expression of key enzymes enabled it to be rapidly degraded. For the hydrophobic and complex naphthalene, phenanthrene, and pyrene, the more complex the structure, the higher the microbial diversity, the EPS showed different response for the purpose of improving their bioavailability, and the activity of key enzymes was positively correlated with their structural complexity.

The impact of phyto- and endo-cannabinoids on central nervous system diseases：A review

Background and aim

Cannabis sativa L. is a medicinal plant with a long history. Phyto-cannabinoids are a class of compounds from C. sativa L. with varieties of structures. Endocannabinoids exist in the human body. This article provides an overview of natural cannabinoids (phyto-cannabinoids and endocannabinoids) with an emphasis on their pharmacology activities.

Experimental procedure

The keywords "Cannabis sativa L″, "cannabinoids", and "central nervous system (CNS) diseases" were used for searching and collecting pieces of literature from PubMed, ScienceDirect, Web of Science, and Google Scholar. The data were extracted and analyzed to explore the effects of cannabinoids on CNS diseases.

Result and conclusion

In this paper, schematic diagrams are used to intuitively show the phyto-cannabinoids skeletons' mutual conversion and pharmacological activities, with special emphasis on their relevant pharmacological activities on central nervous system (CNS) diseases. It was found that the endocannabinoid system and microglia play a crucial role in the treatment of CNS diseases. In the past few years, pharmacological studies focused on Δ⁹-THC, CBD, and the endocannabinoids system. It is expected to encourage new studies on a more deep exploration of other types of cannabinoids and the mechanism of their pharmacological activities in the future.

Recent advances on next generation of polyzwitterion-based nano-vectors for targeted drug delivery

Poly (ethylene glycol) (PEG)-based nanomedicines are perplexed by the challenges of oxidation damage, immune responses after repeated injections, and limited excretion from the body. As an alternative to PEG, bioinspired zwitterions bearing an identical number of positive and negative ions, exhibit exceptional hydrophilicity, excellent biomimetic nature and chemical malleability, endowing zwitterionic nano-vectors with biocompatibility, non-fouling feature, extended blood circulation and multifunctionality. In this review, we innovatively classify zwitterionic nano-vectors into linear, hyperbranched, crosslinked, and hybrid nanoparticles according to different chemical architectures in rational design of zwitterionic nano-vectors for enhanced drug delivery with an emphasis on zwitterionic engineering innovations as alternatives of PEG-based nanomedicines. Through combination with other nanostratagies, the intelligent zwitterionic nano-vectors can orchestrate stealth and other biological functionalities together to improve the efficacy in the whole journey of drug delivery.

Cytotoxic compounds from marine actinomycetes: Sources, Structures and Bioactivity

Marine actinomycetes produce a substantial number of natural products with cytotoxic activity. The strains of actinomycetes were isolated from different sources like fishes, coral, sponges, seaweeds, mangroves, sediments etc. These cytotoxic compounds can be categorized briefly into four classes: polyketides, non-ribosomal peptides and hybrids, isoprenoids and hybrids, and others, among which majority are polyketides (146). Twenty two out of the 254 compounds showed potent cytotoxicity with IC₅₀ values at ng/mL or nM level. This review highlights the sources, structures and antitumor activity of 254 natural products isolated from marine actinomycetes, which were new when they were reported from 1989 to 2020.

Anaerobic digestion of chicken manure: Sequences of chemical structures in dissolved organic matter and its effect on acetic acid production

The use of chicken manure (CM) leads to serious environmental pollution due to the existence of bacteria and insect pests. Anaerobic digestion (AD) is one of the important technologies of CM treatment. However, methane production is limited by the accumulation of short-chain fatty acids (SCFAs) from AD. Therefore, the study explored the possible formation mechanism of acetic acid by understanding the effect of sequences of chemical structure variation in DOM on acetic acid production. The chemical structures of DOM were observed. The tyrosine-like substances (C1, 53.53-29.99%) and humic-like substances (C3, 18.38-5.96%) showed a tendency to decrease. Tryptophan-like substances (C2, 28.09-64.04%) showed the increasing trend. The results indicated that C2 was unwilling to biodegrade. In DOM, the order of biodegradability was C2< C1< C3. AD resulted in the enrichment of N-H in-plane (0-22.75%) and COO- stretch (7.53-18.57%) and the loss of O-H stretch (19.39-13.72%), C-H stretch (4.56%-0), CC stretch (12.04-9.61%) and C-O stretch (10.02-5.03%). Two-dimensional correlation spectroscopy is applied to investigate the sequences of chemical structures in DOM, the order is as follows: CC stretch > COO- stretch > N-H in-plane > C-O stretch. The result confirmed that protein was rapidly decomposed and utilized, which would result in the increase of microorganism metabolism and hydrolysis rate, polysaccharide was hydrolyzed to form phenol and carboxylic acid. Four possible pathways were identified in AD by the structural equation model. C1and hydroxyl can promote propionic and butyric acid formation by the pathway of valeric or iso-butyric acid production and further effected acetic acid production. This study proposed the possible formative mechanisms of acetic acid according to sequences of chemical structures variation in DOM during AD, which can provide the theoretical basis for directional regulating the conversion of different chemical structures of DOM into acetic acid in AD.

Z-matrix template-based substitution approach for enumeration of 3D molecular structures

The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of compounds of identical formula by quantum chemical methods. This paper provides a comprehensive description of the overall concept followed by a practical tutorial to the approach.•The four steps required for Z-matrix template-based substitution are template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template.•The generated tuples can be used to create chemical identifiers to query compound properties from chemical databases.•All of these steps are demonstrated in this paper by common model compounds and are very straightforward for an undergraduate audience to reproduce. A comparison of the approach in this paper and other options is also discussed.

Natural product derived phytochemicals in managing acute lung injury by multiple mechanisms

Acute lung injury (ALI) and its more severe form, acute respiratory distress syndrome (ARDS) as common life-threatening lung diseases with high mortality rates are mostly associated with acute and severe inflammation in lungs. With increasing in-depth studies of ALI/ARDS, significant breakthroughs have been made, however, there are still no effective pharmacological therapies for treatment of ALI/ARDS. Especially, the novel coronavirus pneumonia (COVID-19) is ravaging the globe, and causes severe respiratory distress syndrome. Therefore, developing new drugs for therapy of ALI/ARDS is in great demand, which might also be helpful for treatment of COVID-19. Natural compounds have always inspired drug development, and numerous natural products have shown potential therapeutic effects on ALI/ARDS. Therefore, this review focuses on the potential therapeutic effects of natural compounds on ALI and the underlying mechanisms. Overall, the review discusses 159 compounds and summarizes more than 400 references to present the protective effects of natural compounds against ALI and the underlying mechanism.

Laboratory culture and bioactive natural products of myxomycetes

Myxomycetes, one of the lowest classes of eukaryote (true slime molds), are an unusual group of primitive organisms. Their life cycle consists of two stages, namely the free-living plasmodium and the fruiting body with unique structures and colors. The chemical studies on the secondary metabolites of the myxomycetes are limited due to a lack of understanding of their laboratory cultivation. In this review, 93 natural products from myxomycetes, including their chemical structures and bioactivities were described. We also provided a conceptual overview over five culture methods of myxomycetes, including moist chamber culture, feeding culture, pure culture, liquid culture and hanging drop culture.

Antimicrobial compounds from marine actinomycetes

Marine actinomycetes were the main origin of marine natural products in the past 40 years. This review was to present the sources, structures and antimicrobial activities of 313 new natural products from marine actinomycetes reported from 1976 to 2019.

Structural features, selenization modification, antioxidant and anti-tumor effects of polysaccharides from alfalfa roots

Hot water extraction and chromatographic purification methods were used to extract and purify two polysaccharides (RAPS-1 and RAPS-2) from the roots of alfalfa. Subsequently, RAPS-2 was modified using the HNO₃/Na₂SeO₃ method to obtain Se-RAPS-2. The structural features, antioxidant and in vitro anti-tumor activities of the three polysaccharides were evaluated. The structural analysis revealed that RAPS-1 (Mw = 10.0 kDa) was composed of rhamnose, xylose, arabinose, galacturonic acid, mannose and glucose, whereas RAPS-2 (Mw = 15.8 kDa) consisted of rhamnose, xylose, galacturonic acid, mannose, glucose and galactose. RAPS-1 contained 1 → 2, 1 → 4, 1 → 3, and 1 → 6 or 1 → glycosidic bonds; however, while RAPS-2 lacked 1 → 4 glycosidic linkages. The molecular weight of Se-RAPS-2 was 11.0 kDa less than that of RAPS-2. The results of activities demonstrated that Se-RAPS-2 displayed superior antioxidant activity and inhibitory effect in HepG2 cells than RAPS-1 and RAPS-2.

Natural barrigenol-like triterpenoids: A comprehensive review of their contributions to medicinal chemistry

Barrigenol-like triterpenoids (BATs), which contain an unusual oleanane substituted by many hydroxyl groups as the skeleton, are subdivided into five subtypes: barrigenol A₁, barrigenol A₂, barrigenol R₁, barringtogenol C, and 16-deoxybarringtogenol C. The variations in acyl derivatives, hydroxyl groups, and carbohydrate chains in their structures have enhanced the diversity of BATs. Moreover, the stable polyhydroxy-replaced pentacyclic skeleton provides an ideal platform for structural modifications. To date, more than 500 BAT derivatives have been isolated from plants. Synchronously, BATs possess anti-tumour, anti-Alzheimer's disease, anti-inflammatory, anti-microbial, anti-obesity and anti-allergic activities by regulating numerous cellular molecules. Some BAT derivatives, such as escin obtained from Aesculus hippocastanum L. and xanthoceraside isolated from Xanthoceras sorbifolia Bunge, have been used to treat encephaloedema or inflammatory diseases. This review aims to provide comprehensive information about the chemistry, sources, bioavailability, and anti-tumour effects of BATs, with a particular emphasis on the molecular mechanisms of action. The pharmacokinetics and clinical progress are also concerned. More than 300 structures identified over past 25 years are summarized here (249 compounds) and in the supplementary information (114 compounds). Accordingly, the pharmaceutical activity of barrigenol triterpenoids suggests that some compounds should be developed as promising anti-tumour or anti- Alzheimer's disease agents in future.

Triterpenoid Saponins from the Seeds of Aesculus chinensis and Their Cytotoxicities

Six new triterpenoid saponins, aesculusosides A-F (1-6), together with 19 known ones, were isolated from the seeds of Aesculus chinensis. The new structures were elucidated through extensive spectroscopic analyses and by comparison with previously reported data. Some of the isolates were evaluated for their cytotoxic activities against MCF-7 cell line by an MTT assay, and compounds 15, 16, 19, and 23-25 exhibited inhibitory activities against MCF-7 with IC₅₀ values ranging from 7.1 to 31.3 μM.

Pharmaceutical prospects of naturally occurring quinazolinone and its derivatives

Quinazolinones belong to a family of heterocyclic nitrogen compounds that have attracted increasing interest because of their broad spectrum of biological functions. This review describes three types of natural quinazolinones and their synthesized derivatives and summarizes their various pharmacological activities, including antifungal, anti-tumor, anti-malaria, anticonvulsant, anti-microbial, anti-inflammatory and antihyperlipidemic activities. In addition, structure-activity relationships of quinazolinone derivatives are also reviewed.

Curating and Preparing High-Throughput Screening Data for Quantitative Structure-Activity Relationship Modeling

Publicly available bioassay data often contains errors. Curating massive bioassay data, especially high-throughput screening (HTS) data, for Quantitative Structure-Activity Relationship (QSAR) modeling requires the assistance of automated data curation tools. Using automated data curation tools are beneficial to users, especially ones without prior computer skills, because many platforms have been developed and optimized based on standardized requirements. As a result, the users do not need to extensively configure the curation tool prior to the application procedure. In this chapter, a freely available automatic tool to curate and prepare HTS data for QSAR modeling purposes will be described.

Antioxidants: Characterization, natural sources, extraction and analysis

Recently many review papers regarding antioxidants from different sources and different extraction and quantification procedures have been published. However none of them has all the information regarding antioxidants (chemistry, sources, extraction and quantification). This article tries to take a different perspective on antioxidants for the new researcher involved in this field. Antioxidants from fruit, vegetables and beverages play an important role in human health, for example preventing cancer and cardiovascular diseases, and lowering the incidence of different diseases. In this paper the main classes of antioxidants are presented: vitamins, carotenoids and polyphenols. Recently, many analytical methodologies involving diverse instrumental techniques have been developed for the extraction, separation, identification and quantification of these compounds. Antioxidants have been quantified by different researchers using one or more of these methods: in vivo, in vitro, electrochemical, chemiluminescent, electron spin resonance, chromatography, capillary electrophoresis, nuclear magnetic resonance, near infrared spectroscopy and mass spectrometry methods.

Marine actinobacteria: an important source of bioactive natural products

Marine environment is largely an untapped source for deriving actinobacteria, having potential to produce novel, bioactive natural products. Actinobacteria are the prolific producers of pharmaceutically active secondary metabolites, accounting for about 70% of the naturally derived compounds that are currently in clinical use. Among the various actinobacterial genera, Actinomadura, Actinoplanes, Amycolatopsis, Marinispora, Micromonospora, Nocardiopsis, Saccharopolyspora, Salinispora, Streptomyces and Verrucosispora are the major potential producers of commercially important bioactive natural products. In this respect, Streptomyces ranks first with a large number of bioactive natural products. Marine actinobacteria are unique enhancing quite different biological properties including antimicrobial, anticancer, antiviral, insecticidal and enzyme inhibitory activities. They have attracted global in the last ten years for their ability to produce pharmaceutically active compounds. In this review, we have focused attention on the bioactive natural products isolated from marine actinobacteria, possessing unique chemical structures that may form the basis for synthesis of novel drugs that could be used to combat resistant pathogenic microorganisms.