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Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 42706

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Dr. Giovanni Ribaudo

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Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
Interests: medicinal chemistry; organic synthesis; analytical chemistry; mass spectrometry; NMR; natural products; molecular modeling
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Dear Colleagues,

The world of chemistry of natural products is endowed with unpaired richness, and this can be noted from several perspectives. Plants, fungi, and marine organisms represent sources of small molecules characterized by a unique complexity due to their variety of scaffolds, functional groups, and stereochemistry. At the same time, extraction, de novo synthesis, derivatization, and semi-synthetic approaches represent challenging tasks for the organic chemist. In parallel, the field of analytical profiling of the content of organic compounds and microelements in natural matrices pushes experimental techniques to the edge of their potential, due to the complexity of sample preparation and data elaboration. Additionally, flavonoids, alkaloids, terpenes, and their semisynthetic derivatives constantly attract the interest of the medicinal chemist in light of their biological roles, which include, among the others, antioxidant, antiproliferative, antibacterial, and anti-inflammatory activities.

This Special Issue aims to collect original contributions describing the extraction, structural elucidation, and synthesis of natural, semisynthetic derivatives and nature-inspired molecules. Moreover, articles reporting the analysis of the content of natural compounds in complex matrices and their bioactivity, as well as review articles focusing on the chemistry of natural products, will be considered. Research articles describing significant results in terms of innovative synthetic and extractive techniques and advanced analysis (chromatography, 1D and 2D NMR, mass spectrometry, IR and UV spectroscopy) are particularly welcome.

Dr. Giovanni Ribaudo
Guest Editor

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Keywords

natural compounds
semisynthetic compounds
organic synthesis
analytical chemistry
flavonoids
alkaloids
drug design
stereochemistry

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Published Papers (12 papers)

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Editorial

Jump to: Research, Review

2 pages, 179 KiB

Open AccessEditorial

Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies

by Giovanni Ribaudo

Molecules 2023, 28(14), 5577; https://doi.org/10.3390/molecules28145577 - 22 Jul 2023

Viewed by 2741

Abstract

The chemistry of natural compounds inspired and still guides several branches of modern chemical sciences [...] Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

Research

Jump to: Editorial, Review

11 pages, 1673 KiB

Open AccessArticle

Two New 4-Hydroxy-2-pyridone Alkaloids with Antimicrobial and Cytotoxic Activities from Arthrinium sp. GZWMJZ-606 Endophytic with Houttuynia cordata Thunb

by Ying Yin, Dongyang Wang, Dan Wu, Wenwen He, Mingxing Zuo, Weiming Zhu, Yanchao Xu and Liping Wang

Molecules 2023, 28(5), 2192; https://doi.org/10.3390/molecules28052192 - 27 Feb 2023

Cited by 8 | Viewed by 2346

Abstract

Two new 4-hydroxy-2-pyridone alkaloids furanpydone A and B (1 and 2), along with two known compounds N-hydroxyapiosporamide (3) and apiosporamide (4) were isolated from the endophytic fungus Arthrinium sp. GZWMJZ-606 in Houttuynia cordata Thunb. Furanpydone A and B had unusual 5-(7-oxabicyclo[2.2.1]heptane)-4-hydroxy-2-pyridone skeleton. Their structures including absolute configurations were determined on the basis of spectroscopic analysis, as well as the X-ray diffraction experiment. Compound 1 showed inhibitory activity against ten cancer cell lines (MKN-45, HCT116, K562, A549, DU145, SF126, A-375, 786O, 5637, and PATU8988T) with IC₅₀ values from 4.35 to 9.72 µM. Compounds 1, 3 and 4 showed moderate inhibitory effects against four Gram-positive strains (Staphylococcus aureus, methicillin-resistant S. aureus, Bacillus Subtilis, Clostridium perfringens) and one Gram-negative strain (Ralstonia solanacarum) with MIC values from 1.56 to 25 µM. However, compounds 1–4 showed no obvious inhibitory activity against two Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and two pathogenic fungi (Candida albicans and Candida glabrata) at 50 µM. These results show that compounds 1–4 are expected to be developed as lead compounds for antibacterial or anti-tumor drugs. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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16 pages, 1545 KiB

Open AccessArticle

Synthesis and In Vitro Anticancer Evaluation of Flavone—1,2,3-Triazole Hybrids

by Alexandra Németh-Rieder, Péter Keglevich, Attila Hunyadi, Ahmed Dhahir Latif, István Zupkó and László Hazai

Molecules 2023, 28(2), 626; https://doi.org/10.3390/molecules28020626 - 7 Jan 2023

Cited by 8 | Viewed by 2032

Abstract

Hybrid compounds of flavones, namely chrysin and kaempferol, and substituted 1,2,3-triazole derivatives, were synthesized by click reaction of the intermediate O-propargyl derivatives. 4-Fluoro- and 4-nitrobenzyl-1,2,3-triazole-containing hybrid molecules were prepared. The mono- and bis-coupled hybrids were investigated on 60 cell lines of 9 [...] Read more.

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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15 pages, 5274 KiB

Open AccessArticle

Molecular Cloning, Expression, and Functional Analysis of Glycosyltransferase (TbUGGT) Gene from Trapa bispinosa Roxb.

by Shijie Ye, Dongjie Yin, Xiaoyan Sun, Qinyi Chen, Ting Min, Hongxun Wang and Limei Wang

Molecules 2022, 27(23), 8374; https://doi.org/10.3390/molecules27238374 - 30 Nov 2022

Cited by 4 | Viewed by 2027

Abstract

Trapa bispinosa Roxb. is an economical crop for medicine and food. Its roots, stems, leaves, and pulp have medicinal applications, and its shell is rich in active ingredients and is considered to have a high medicinal value. One of the main functional components of the Trapa bispinosa Roxb. shell is 1-galloyl-beta-D-glucose (βG), which can be used in medical treatment and is also an essential substrate for synthesizing the anticancer drug beta-penta-o-Galloyl-glucosen (PGG). Furthermore, gallate 1-beta-glucosyltransferase (EC 2.4.1.136) has been found to catalyze gallic acid (GA) and uridine diphosphate glucose (UDPG) to synthesize βG. In our previous study, significant differences in βG content were observed in different tissues of Trapa bispinosa Roxb. In this study, Trapa bispinosa Roxb. was used to clone 1500 bp of the UGGT gene, which was named TbUGGT, to encode 499 amino acids. According to the specificity of the endogenous expression of foreign genes in Escherichia coli, the adaptation codon of the cloned original genes was optimized for improved expression. Bioinformatic and phylogenetic tree analyses revealed the high homology of TbUGGT with squalene synthases from other plants. The TbUGGT gene was constructed into a PET-28a expression vector and then transferred into Escherichia coli Transsetta (DE3) for expression. The recombinant protein had a molecular weight of 55 kDa and was detected using SDS-PAGE. The proteins were purified using multiple fermentation cultures to simulate the intracellular environment, and a substrate was added for in vitro reaction. After the enzymatic reaction, the levels of βG in the product were analyzed using HPLC and LC-MS, indicating the catalytic activity of TbUGGT. The cloning and functional analysis of TbUGGT may lay the foundation for further study on the complete synthesis of βG in E. coli. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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15 pages, 2940 KiB

Open AccessArticle

Transcriptomics and Proteomics Characterizing the Anticancer Mechanisms of Natural Rebeccamycin Analog Loonamycin in Breast Cancer Cells

by Xiao Sun, Zhanying Lu, Zhenzhen Liang, Bowen Deng, Yuping Zhu, Jing Shi and Xiaoling Lu

Molecules 2022, 27(20), 6958; https://doi.org/10.3390/molecules27206958 - 17 Oct 2022

Cited by 4 | Viewed by 1745

Abstract

The present study is to explore the anticancer effect of loonamycin (LM) in vitro and in vivo, and investigate the underlying mechanism with combined multi-omics. LM exhibited anticancer activity in human triple negative breast cancer cells by promoting cell apoptosis. LM administration inhibited the growth of MDA-MB-468 tumors in a murine xenograft model of breast cancer. Mechanistic studies suggested that LM could inhibit the topoisomerase I in a dose-dependent manner in vitro experiments. Combined with the transcriptomics and proteomic analysis, LM has a significant effect on O-glycan, p53-related signal pathway and EGFR/PI3K/AKT/mTOR signal pathway in enrichment of the KEGG pathway. The GSEA data also suggests that the TNBC cells treated with LM may be regulated by p53, O-glycan and EGFR/PI3K/AKT/mTOR signaling pathway. Taken together, our findings predicted that LM may target p53 and EGFR/PI3K/AKT/mTOR signaling pathway, inhibiting topoisomerase to exhibit its anticancer effect. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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25 pages, 7737 KiB

Open AccessArticle

LMWP (S3-3) from the Larvae of Musca domestica Alleviate D-IBS by Adjusting the Gut Microbiota

by Siyuan Peng, Xiwen Ling, Wenjing Rui, Xiaobao Jin and Fujiang Chu

Molecules 2022, 27(14), 4517; https://doi.org/10.3390/molecules27144517 - 15 Jul 2022

Cited by 2 | Viewed by 2273

Abstract

Diarrhea-based Irritable Bowel Syndrome (D-IBS) and diarrhea are both associated with ecological imbalance of the gut microbiota. Low Molecular Weight Peptides (LMWP) from the larvae of Musca domestica have been shown to be effective in the treatment of diarrhea and regulation of gut microbiota. Meanwhile, the single polypeptide S3-3 was successfully isolated and identified from LMWP in our previous studies. It remains unclear exactly whether and how LMWP (S3-3) alleviate D-IBS through regulating gut microbiota. We evaluated the gut microbiota and pharmacology to determine the regulation of gut microbiota structure and the alleviating effect on D-IBS through LMWP (S3-3). The rates of loose stools, abdominal withdrawal reflex (AWR) and intestinal tract motility results revealed that LMWP (S3-3) from the larvae of Musca domestica had a regulating effect against diarrhea, visceral hypersensitivity and gastrointestinal (GI) dysfunction in D-IBS model mice. Additionally, 16S rRNA gene sequencing was utilized to examine the gut microbiota, which suggests that LMWP induce structural changes in the gut microbiota and alter the levels of the following gut microbiota: Bacteroidetes, Proteobacteria and Verrucomicrobia. LMWP putatively functioned through regulating 5-HT, SERT, 5-HT2AR, 5-HT3AR and 5-HT4R according to the results of ELISA, qRT-PCR and IHC. The findings of this study will contribute to further understanding how LMWP (S3-3) attenuate the effects of D-IBS on diarrhea, visceral hypersensitivity and GI dysfunction. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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14 pages, 3696 KiB

Open AccessArticle

A Docosahexaenoic Acid Derivative (N-Benzyl Docosahexaenamide) as a Potential Therapeutic Candidate for Treatment of Ovarian Injury in the Mouse Model

by Lirong Guo, Qing Gao, Jieqiong Zhu, Xiaobao Jin, Hui Yin and Tao Liu

Molecules 2022, 27(9), 2754; https://doi.org/10.3390/molecules27092754 - 25 Apr 2022

Cited by 3 | Viewed by 2128

Abstract

Commonly used clinical chemotherapy drugs, such as cyclophosphamide (CTX), may cause injury to the ovaries. Hormone therapies can reduce the ovarian injury risk; however, they do not achieve the desired effect and have obvious side effects. Therefore, it is necessary to find a potential therapeutic candidate for ovarian injury after chemotherapy. N-Benzyl docosahexaenamide (NB-DHA) is a docosahexaenoic acid derivative. It was recently identified as the specific macamide with a high degree of unsaturation in maca (Lepidium meyenii). In this study, the purified NB-DHA was administered intragastrically to the mice with CTX-induced ovarian injury at three dose levels. Blood and tissue samples were collected to assess the regulation of NB-DHA on ovarian function. The results indicated that NB-DHA was effective in improving the disorder of estrous cycle, and the CTX+NB-H group can be recovered to normal levels. NB-DHA also significantly increased the number of primordial follicles, especially in the CTX+NB-M and CTX+NB-H groups. Follicle-stimulating hormone and luteinizing hormone levels in all treatment groups and estradiol levels in the CTX+NB-H group returned to normal. mRNA expression of ovarian development-related genes was positive regulated. The proportion of granulosa cell apoptosis decreased significantly, especially in the CTX+NB-H group. The expression of anti-Müllerian hormone and follicle-stimulating hormone receptor significantly increased in ovarian tissues after NB-DHA treatment. NB-DHA may be a promising agent for treating ovarian injury. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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8 pages, 4240 KiB

Open AccessCommunication

Synthesis of Deuterium-Labeled Vitamin D Metabolites as Internal Standards for LC-MS Analysis

by Akiko Nagata, Kazuto Iijima, Ryota Sakamoto, Yuka Mizumoto, Miho Iwaki, Masaki Takiwaki, Yoshikuni Kikutani, Seketsu Fukuzawa, Minami Odagi, Masayuki Tera and Kazuo Nagasawa

Molecules 2022, 27(8), 2427; https://doi.org/10.3390/molecules27082427 - 9 Apr 2022

Cited by 5 | Viewed by 2481

Abstract

Blood levels of the vitamin D₃ (D₃) metabolites 25-hydroxyvitamin D₃ (25(OH)D₃), 24R,25-dihydroxyvitamin D₃, and 1α,25-dihydroxyvitamin D₃ (1,25(OH)₂D₃) are recognized indicators for the diagnosis of bone metabolism-related diseases, D₃ deficiency-related diseases, and hypercalcemia, and are generally measured by liquid-chromatography tandem mass spectrometry (LC-MS/MS) using an isotope dilution method. However, other D₃ metabolites, such as 20-hydroxyvitamin D₃ and lactone D₃, also show interesting biological activities and stable isotope-labeled derivatives are required for LC-MS/MS analysis of their concentrations in serum. Here, we describe a versatile synthesis of deuterium-labeled D₃ metabolites using A-ring synthons containing three deuterium atoms. Deuterium-labeled 25(OH)D₃ (2), 25(OH)D₃-23,26-lactone (6), and 1,25(OH)₂D₃-23,26-lactone (7) were synthesized, and successfully applied as internal standards for the measurement of these compounds in pooled human serum. This is the first quantification of 1,25(OH)₂D₃-23,26-lactone (7) in human serum. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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Review

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27 pages, 4212 KiB

Open AccessReview

The Role of Natural and Semi-Synthetic Compounds in Ovarian Cancer: Updates on Mechanisms of Action, Current Trends and Perspectives

by Md. Rezaul Islam, Md. Mominur Rahman, Puja Sutro Dhar, Feana Tasmim Nowrin, Nasrin Sultana, Muniya Akter, Abdur Rauf, Anees Ahmed Khalil, Alessandra Gianoncelli and Giovanni Ribaudo

Molecules 2023, 28(5), 2070; https://doi.org/10.3390/molecules28052070 - 22 Feb 2023

Cited by 10 | Viewed by 2710

Abstract

Ovarian cancer represents a major health concern for the female population: there is no obvious cause, it is frequently misdiagnosed, and it is characterized by a poor prognosis. Additionally, patients are inclined to recurrences because of metastasis and poor treatment tolerance. Combining innovative therapeutic techniques with established approaches can aid in improving treatment outcomes. Because of their multi-target actions, long application history, and widespread availability, natural compounds have particular advantages in this connection. Thus, effective therapeutic alternatives with improved patient tolerance hopefully can be identified within the world of natural and nature-derived products. Moreover, natural compounds are generally perceived to have more limited adverse effects on healthy cells or tissues, suggesting their potential role as valid treatment alternatives. In general, the anticancer mechanisms of such molecules are connected to the reduction of cell proliferation and metastasis, autophagy stimulation and improved response to chemotherapeutics. This review aims at discussing the mechanistic insights and possible targets of natural compounds against ovarian cancer, from the perspective of medicinal chemists. In addition, an overview of the pharmacology of natural products studied to date for their potential application towards ovarian cancer models is presented. The chemical aspects as well as available bioactivity data are discussed and commented on, with particular attention to the underlying molecular mechanism(s). Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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43 pages, 735 KiB

Open AccessReview

Therapeutic Potential of Phenolic Compounds in Medicinal Plants—Natural Health Products for Human Health

by Wenli Sun and Mohamad Hesam Shahrajabian

Molecules 2023, 28(4), 1845; https://doi.org/10.3390/molecules28041845 - 15 Feb 2023

Cited by 188 | Viewed by 14568

Abstract

Phenolic compounds and flavonoids are potential substitutes for bioactive agents in pharmaceutical and medicinal sections to promote human health and prevent and cure different diseases. The most common flavonoids found in nature are anthocyanins, flavones, flavanones, flavonols, flavanonols, isoflavones, and other sub-classes. The impacts of plant flavonoids and other phenolics on human health promoting and diseases curing and preventing are antioxidant effects, antibacterial impacts, cardioprotective effects, anticancer impacts, immune system promoting, anti-inflammatory effects, and skin protective effects from UV radiation. This work aims to provide an overview of phenolic compounds and flavonoids as potential and important sources of pharmaceutical and medical application according to recently published studies, as well as some interesting directions for future research. The keyword searches for flavonoids, phenolics, isoflavones, tannins, coumarins, lignans, quinones, xanthones, curcuminoids, stilbenes, cucurmin, phenylethanoids, and secoiridoids medicinal plant were performed by using Web of Science, Scopus, Google scholar, and PubMed. Phenolic acids contain a carboxylic acid group in addition to the basic phenolic structure and are mainly divided into hydroxybenzoic and hydroxycinnamic acids. Hydroxybenzoic acids are based on a C6-C1 skeleton and are often found bound to small organic acids, glycosyl moieties, or cell structural components. Common hydroxybenzoic acids include gallic, syringic, protocatechuic, p-hydroxybenzoic, vanillic, gentistic, and salicylic acids. Hydroxycinnamic acids are based on a C6-C3 skeleton and are also often bound to other molecules such as quinic acid and glucose. The main hydroxycinnamic acids are caffeic, p-coumaric, ferulic, and sinapic acids. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

20 pages, 1863 KiB

Open AccessReview

Research Advances of Bioactive Sesquiterpenoids Isolated from Marine-Derived Aspergillus sp.

by Lixiang Sun, Huannan Wang, Maocai Yan, Chunmei Sai and Zhen Zhang

Molecules 2022, 27(21), 7376; https://doi.org/10.3390/molecules27217376 - 30 Oct 2022

Cited by 11 | Viewed by 2372

Abstract

Marine fungi Aspergillus sp. is an important source of natural active lead compounds with biological and chemical diversity, of which sesquiterpenoids are an extremely important class of bioactive secondary metabolites. In this paper, we review the sources, chemical structures, bioactivity, biosynthesis, and druggability evaluation of sesquiterpenoids discovered from marine fungi Aspergillus sp. since 2008. The Aspergillus species involved include mainly Aspergillus fumigatus, Aspergillus versicolor, Aspergillus flavus, Aspergillus ustus, Aspergillus sydowii, and so on, which originate from sponges, marine sediments, algae, mangroves, and corals. In recent years, 268 sesquiterpenoids were isolated from secondary metabolites of marine Aspergillus sp., 131 of which displayed bioactivities such as antitumor, antimicrobial, anti-inflammatory, and enzyme inhibitory activity. Furthermore, the main types of active sesquiterpenoids are bisabolanes, followed by drimanes, nitrobenzoyl, etc. Therefore, these novel sesquiterpenoids will provide a large number of potential lead compounds for the development of marine drugs. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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16 pages, 2790 KiB

Open AccessReview

Current Progress in the Chemoenzymatic Synthesis of Natural Products

by Evan P. Vanable, Laurel G. Habgood and James D. Patrone

Molecules 2022, 27(19), 6373; https://doi.org/10.3390/molecules27196373 - 27 Sep 2022

Cited by 6 | Viewed by 3504

Abstract

Natural products, with their array of structural complexity, diversity, and biological activity, have inspired generations of chemists and driven the advancement of techniques in their total syntheses. The field of natural product synthesis continuously evolves through the development of methodologies to improve stereoselectivity, yield, scalability, substrate scope, late-stage functionalization, and/or enable novel reactions. One of the more interesting and unique techniques to emerge in the last thirty years is the use of chemoenzymatic reactions in the synthesis of natural products. This review highlights some of the recent examples and progress in the chemoenzymatic synthesis of natural products from 2019–2022. Full article

(This article belongs to the Special Issue Natural Products Chemistry: Advances in Synthetic, Analytical and Bioactivity Studies)

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