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Special Issue "Natural Products: Chemical Profiling, Computational Studies and Bioactivities"

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A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: 31 October 2023 | Viewed by 9820

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Special Issue Editors

Dr. Nada M. Mostafa

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Guest Editor

Department of Pharmacognosy, Ain Shams University, Cairo 11566, Egypt
Interests: natural products; phytochemistry; HPLC and GC analyses; essential oils; molecular docking; fungal endophytes; structural elucidation; nanoformulation; bioactivity
Special Issues, Collections and Topics in MDPI journals

Dr. Wagdy M. Eldehna

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Co-Guest Editor

1. School of Biotechnology, Badr University in Cairo, Badr City 11829, Cairo, Egypt
2. Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 13 33516, Egypt
Interests: drug design and development; pharmaceutical chemistry; anticancer agents; antimicrobial agents; molecular modeling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Issue presents different studies carried out on natural products isolated or identified from plants or fungal endophytes associated with those plants. Natural products can represent a wide variety of chemical classes, such as flavonoids, terpenoids, essential oils, alkaloids, and many others. Such compounds can be identified via LC-MS, GC-MS, TLC-MS, and different NMR spectroscopic techniques. Metabolomics studies can share in further classification and clustering of these secondary metabolites and the differentiation of closely-related varieties. Moreover, many natural products are well known for promising biological activities such as antioxidant, anti-inflammatory, cytotoxic, hepatoprotective, renoprotective, neuroprotective, etc. The study of such activities can be evaluated through both in vitro and in vivo studies and can be further supported by various histological and computational studies. In silico molecular docking and dynamics can present possible binding interactions with the receptor's active site proteins and binding stability. ADME studies are carried out nowadays for many natural products, such as drug-likeness and in silico toxicity profiles.

In the current Special Issue, we invite authors to share their research or review articles that can include (but are not limited to) one or more of the following topics:

Isolation of natural products and their identification using different spectroscopic techniques;
Isolation of essential oils and their GC-MS analysis profiles;
Metabolites dereplication via LC-MS analysis;
Chemometric studies of identified natural products, such as PCA, HCA, heatmap,…etc.;
Biological activity evaluation of different natural products extracts, fractions, pure compounds, or their formulations, including those applying nanotechnologies, are within the scope of this Issue;
Computational in-silico studies of natural products;
Study of the molecular mechanism of observed bioactivities of secondary metabolites are also welcomed;
Identification of biologically active semisynthetic small molecules.

Dr. Nada M. Mostafa
Dr. Wagdy M. Eldehna
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

natural products
essential oils
plants
fungal endophytes
secondary metabolites
spectroscopic techniques
chemical profiling
chemometrics
computational studies
formulations
nanotechnology
biological activities
molecular mechanism
molecular modeling

Published Papers (9 papers)

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Research

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Open AccessArticle

An Experimental and Computational Analysis of Plant Compounds from Whole Urtica dioica L. Plant’s Essential Oil for Antioxidant and Antibacterial Activities

Amin Malik Shah Abdul Majid

Ghadeer M. Albadrani

Nehal Ahmed Talaat Nouh

Jawaher A. Abdulhakim

and

Mohamed M. Abdel-Daim

Metabolites 2023, 13(4), 502; https://doi.org/10.3390/metabo13040502 - 30 Mar 2023

Cited by 1 | Viewed by 623

Abstract

As the Urtica dioica L. whole plant’s essential oil has presented significant multiple activities, it was therefore evaluated using the GC–MS technique. This essential oil was investigated for its antioxidant, phytotoxic, and antibacterial activities in vitro. The GC–MS analysis data assisted in the identification of various constituents. The study of the essential oil of U. dioica showed potential antioxidant effects and antibacterial activity against the selected pathogens Escherichia coli -ATCC 9837 (E. coli), Bacillus subtilis-ATCC 6633 (B. subtilis), Staphylococcus aureus-ATCC6538 (S. aureus), Pseudomonas aeruginosa-ATCC 9027 (P. aeruginosa), and Salmonella typhi-ATCC 6539 (S. typhi). The library of 23 phytochemicals was docked by using MOE software, and three top virtual hits with peroxiredoxin protein [PDB ID: 1HD2] and potential target protein [PDB ID: 4TZK] were used; hence, the protein–ligand docking results estimated the best binding conformations and a significant correlation with the experimental analysis, in terms of the docking score and binding interactions with the key residues of the native active binding site. The essential oil in the silico pharmacokinetic profile explained the structure and activity relationships of the selected best hits, and their additional parameters provided insight for further clinical investigations. Therefore, it is concluded that the U. dioica essential oil could be a potent antioxidant and antibacterial agent for aromatherapy through its topical application, if further tested in a laboratory and validated. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Diterpenoids from Euphorbia gedrosiaca as Potential Anti-Proliferative Agents against Breast Cancer Cells

Zeinab Yazdiniapour

Mohammad Hossein Sohrabi

and

Metabolites 2023, 13(2), 225; https://doi.org/10.3390/metabo13020225 - 03 Feb 2023

Viewed by 767

Abstract

Isolated diterpenes from various species of Euphorbia are important compounds for drug discovery with a broad spectrum of structures and biological effects. In this study, Euphorbia gedrosiaca, one of the endemic species of Iran, was analyzed in terms of the presence and structural determination of diterpenoid compounds. They were extracted with dichloromethane/acetone (2:1) from aerial parts of this plant and purified by chromatographic methods such as MPLC and HPLC. Four premyrsinane compounds and one myrsinane diterpene were isolated from Euphorbia gedrosiaca. They were characterized by extensive 1D and 2D NMR and HRMS analyses. Additionally, their activities were evaluated against two breast cancer cell lines, MDA-MB-231 and MCF-7, by MTT proliferation assay. They exhibited cytotoxic effects in a dose-dependent manner with promising results, which can help to find possible therapeutic application of diterpenoids in breast cancer treatment. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Comprehensive Metabolomic Fingerprinting Combined with Chemometrics Identifies Species- and Variety-Specific Variation of Medicinal Herbs: An Ocimum Study

Prabodh Kumar Trivedi

Christopher T. Elliott

and

Ratnasekhar Ch

Metabolites 2023, 13(1), 122; https://doi.org/10.3390/metabo13010122 - 13 Jan 2023

Cited by 1 | Viewed by 1396

Abstract

Identification of plant species is a crucial process in natural products. Ocimum, often referred to as the queen of herbs, is one of the most versatile and globally used medicinal herbs for various health benefits due to it having a wide variety of pharmacological activities. Despite there being significant global demand for this medicinal herb, rapid and comprehensive metabolomic fingerprinting approaches for species- and variety-specific classification are limited. In this study, metabolomic fingerprinting of five Ocimum species (Ocimum basilicum L., Ocimum sanctum L., Ocimum africanum Lour., Ocimum kilimandscharicum Gurke., and Hybrid Tulsi) and their varieties was performed using LC-MS, GC-MS, and the rapid fingerprinting approach FT-NIR combined with chemometrics. The aim was to distinguish the species- and variety-specific variation with a view toward developing a quality assessment of Ocimum species. Discrimination of species and varieties was achieved using principal component analysis (PCA), partial least squares discriminate analysis (PLS-DA), data-driven soft independent modelling of class analogy (DD-SIMCA), random forest, and K-nearest neighbours with specificity of 98% and sensitivity of 99%. Phenolics and flavonoids were found to be major contributing markers for species-specific variation. The present study established comprehensive metabolomic fingerprinting consisting of rapid screening and confirmatory approaches as a highly efficient means to identify the species and variety of Ocimum, being able to be applied for the quality assessment of other natural medicinal herbs. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Chromatomass-Spectrometric Method for the Quantitative Determination of Amino- and Carboxylic Acids in Biological Samples

Anna L. Kaysheva

Arthur T. Kopylov

Alexander A. Stepanov

Kristina A. Malsagova

Alexander A. Izotov

Yevgeniya I. Shurubor

and

Boris F. Krasnikov

Metabolites 2023, 13(1), 16; https://doi.org/10.3390/metabo13010016 - 22 Dec 2022

Viewed by 808

Abstract

A highly sensitive method for the qualitative and quantitative determination of amino- and carboxylic acids, as well as a number of urea and methionine cycle metabolites in the studied solutions, is presented. Derivatives (esterification) were obtained for amino acids by their reaction in a solution of 3 N of hydrochloric acid in n-butanol for 15 min at 65 °C and for carboxylic acids by their reaction with phenol in ethyl acetate with 3 N of hydrochloric acid for 20 min at 65 °C. Experimental work on the determination of individual metabolites was carried out using the HPLC-MS/MS method and included the creation of a library of spectra of the analyzed compounds and their quantitative determination. Multiplex methods have been developed for the quantitative analysis of the desired metabolites in a wide range of concentrations of 3–4 orders of magnitude. The approach to the analysis of metabolites was developed based on the method of the dynamic monitoring of multiple reactions of the formation of fragments for a mass analyzer with a triple quadrupole (QQQ). The effective chromatographic separation of endogenous metabolites was carried out within 13 min. The calibration curves of the analyzed compounds were stable throughout the concentration range and had the potential to fit below empirical levels. The developed methods and obtained experimental data are of interest for a wide range of biomedical studies, as well as for monitoring the content of endogenous metabolites in biological samples under various pathological conditions. The sensitivity limit of the methods for amino acids was about 4.8 nM and about 0.5 μM for carboxylic acids. Up to 19 amino- and up to 12 carboxy acids and about 10 related metabolites can be tested in a single sample. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Evaluation of Zamia floridana A. DC. Leaves and Its Isolated Secondary Metabolites as Natural Anti-Toxoplasma and Anti-Cancer Agents Using In Vitro and In Silico Studies

Hosam M. El-Seadawy

Kamilia A. Abo El-Seoud

and

Metabolites 2023, 13(1), 10; https://doi.org/10.3390/metabo13010010 - 21 Dec 2022

Cited by 1 | Viewed by 922

Abstract

Toxoplasmosis and cancer are life-threatening diseases with worldwide distribution. However, currently used chemosynthetic treatments are not devoid of their own intrinsic problems. Natural metabolites are gaining attention due to their lower side effects. In this study, we investigated for the first time Zamia floridana leaves extract and its different fractions for their toxoplasmocidal activity, using Virulent RH Toxoplasma gondii, and cytotoxic activity against MCF-7 and HCT-116 cancer cell lines using MTT assay. The n-butanol fraction was the most potent fraction against T. gondii with an EC₅₀ of 7.16 ± 0.4 µg/mL compared to cotrimoxazole (4.18 ± 0.3 µg/mL). In addition, the n-BuOH fraction showed a significant cytotoxicity against MCF-7 and HCT-116 with IC₅₀ of 12.33 ± 1.1 and 17.88 ± 1.4 µg/mL, respectively, compared to doxorubicin (4.17 ± 0.2 and 5.23 ± 0.3 µg/mL, respectively), with higher safety index against normal cell line (WISH). Therefore, the n-BuOH fraction was investigated for its phytochemicals using extensive chromatographic techniques, which led to the isolation of six compounds that were fully characterized using different spectroscopic techniques. Three biflavonoids (1, 2 and 4) in addition to two phenolic acid derivatives (3 and 5) and a flavonoid glycoside (6) were isolated. Compounds (1, 3, 5 and 6) were reported for the first time from Z. floridana. In silico docking studies for toxoplasmocidal and cytotoxic effects of these compounds revealed that compounds (1, 2, 4 and 6) have promising inhibition potential of either thymidylate synthase-dihydrofolate reductase (TS-DHFR) or cyclin dependent kinase 2 (CDK2) target proteins. This study is considered the first report of chemical and biological investigation of Z. floridana leaves. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Bioactive Compounds from Endophytic Bacteria Bacillus subtilis Strain EP1 with Their Antibacterial Activities

and

Metabolites 2022, 12(12), 1228; https://doi.org/10.3390/metabo12121228 - 07 Dec 2022

Cited by 1 | Viewed by 1201

Abstract

Endophytic bacteria boost host plant defense and growth by producing vital compounds. In the current study, a bacterial strain was isolated from the Boswellia sacra plant and identified as Bacillus subtilis strain EP1 (accession number: MT256301) through 16S RNA gene sequencing. From the identified bacteria, four compounds—1 (4-(4-cinnamoyloxy)phenyl)butanoic acid), 2 (cyclo-(L-Pro-D-Tyr)), 3 (cyclo-(L-Val-L-Phe)), and 4 (cyclo-(L-Pro-L-Val))—were isolated and characterized by 1D and 2D NMR and mass spectroscopy. Moreover, antibacterial activity and beta-lactam-producing gene inhibition (δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) and aminoadipate aminotransferase (AADAT)) assays were performed. Significant antibacterial activity was observed against the human pathogenic bacterial strains (E. coli) by compound 4 with a 13 ± 0.7 mm zone of inhibition (ZOI), followed by compound 1 having an 11 ± 0.7 mm ZOI. In contrast, the least antibacterial activity among the tested samples was offered by compound 2 with a 10 ± 0.9 mm ZOI compared to the standard (26 ± 1.2 mm). Similarly, the molecular analysis of beta-lactam inhibition determined that compounds 3 and 4 inhibited the two genes (2- to 4-fold) in the beta-lactam biosynthesis (ACVS and AADAT) pathway. From these results, it can be concluded that future research on these compounds could lead to the inhibition of antibiotic-resistant pathogenic bacterial strains. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Phytochemical Study of Euphorbia turcomanica Boiss.

and

Metabolites 2022, 12(12), 1200; https://doi.org/10.3390/metabo12121200 - 30 Nov 2022

Viewed by 786

Abstract

The attraction to the Euphorbia genus, with its remarkable diversity in species, is due to its variety of chemical compositions. Euphorbia turcomanica is one of the species of the spurge family growing wildly in Iran. This research aims to investigate the presence of secondary metabolites, specially terpenoid compounds, in terms of structural determination. Samples of E. tucomanica were finely powdered and macerated with acetone/dichloromethane 2:1. Repeated column chromatography using silica gel, MPLC, and HPLC methods followed by the analysis of data obtained from spectroscopic means was carried out to purify and identify the terpenoid constituents. The chemical structures of nine known terpenoids were determined for the first time from E. turcomanica during this study. Loliolide (1), a monoterpene, and eight steroids and triterpenes, including simiarenol (2), isomultiflorenol (3), cycloart-25-ene-3β,24-diol (4), β-sitosterol (5), cycloart-23-ene-3β,25-diol (6), 3α, 11α-dihydroxyurs-12-ene (7), 3β, 24β, 25-trihydroxycycloartane (8), and 7α-hydroxystigmasterol (9) were isolated and identified. E. tucomanica, with a rich terpenoid profile, can be one of the valuable and economic sources providing compounds for drug development. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Open AccessArticle

Investigating the Potential Anti-SARS-CoV-2 and Anti-MERS-CoV Activities of Yellow Necklacepod among Three Selected Medicinal Plants: Extraction, Isolation, Identification, In Vitro, Modes of Action, and Molecular Docking Studies

Howaida I. Abd-Alla

Omnia Kutkat

Heba-tollah M. Sweelam

and

Ahmed A. Al-Karmalawy

Metabolites 2022, 12(11), 1109; https://doi.org/10.3390/metabo12111109 - 13 Nov 2022

Cited by 4 | Viewed by 1159

Abstract

The anti-MERS-CoV activities of three medicinal plants (Azadirachta indica, Artemisia judaica, and Sophora tomentosa) were evaluated. The highest viral inhibition percentage (96%) was recorded for S. tomentosa. Moreover, the mode of action for both S. tomentosa and A. judaica showed 99.5% and 92% inhibition, respectively, with virucidal as the main mode of action. Furthermore, the anti-MERS-CoV and anti-SARS-CoV-2 activities of S. tomentosa were measured. Notably, the anti-SARS-CoV-2 activity of S. tomentosa was very high (100%) and anti-MERS-CoV inhibition was slightly lower (96%). Therefore, the phytochemical investigation of the very promising S. tomentosa L. led to the isolation and structural identification of nine compounds (1–9). Then, both the CC₅₀ and IC₅₀ values for the isolated compounds against SARS-CoV-2 were measured. Compound 4 (genistein 4’-methyl ether) achieved superior anti-SARS-CoV-2 activity with an IC₅₀ value of 2.13 µm. Interestingly, the mode of action of S. tomentosa against SARS-CoV-2 showed that both virucidal and adsorption mechanisms were very effective. Additionally, the IC₅₀ values of S. tomentosa against SARS-CoV-2 and MERS-CoV were found to be 1.01 and 3.11 µg/mL, respectively. In addition, all the isolated compounds were subjected to two separate molecular docking studies against the spike (S) and main protease (M^pr°) receptors of SARS-CoV-2. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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Review

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Open AccessReview

Phytochemistry, Pharmacology and Molecular Mechanisms of Herbal Bioactive Compounds for Sickness Behaviour

Ghallab Hamoud Sinhat Alotaibi

Thippeswamy Boreddy Shivanandappa

Maheswari Chinnadhurai

Sudharshan Reddy Dachani

Mahmad Dabeer Ahmad

and

Khalid Abdullah Aldaajanii

Metabolites 2022, 12(12), 1215; https://doi.org/10.3390/metabo12121215 - 02 Dec 2022

Viewed by 849

Abstract

The host’s response to acute infections or tissue injury is a sophisticated and coordinated adaptive modification called sickness behaviour. Many herbs have been studied for their ability to protect animals against experimentally induced sickness behaviour. However, there is a lack of knowledge and experimental evidence on the use of herbal bioactive compounds (HBACs) in the management of sick behaviour. The goal of this review is to provide a concise summary of the protective benefits and putative mechanisms of action of phytochemicals on the reduction of lipopolysaccharide (LPS)-induced sickness behaviour. Relevant studies were gathered from the search engines Scopus, ScienceDirect, PubMed, Google Scholar, and other scientific databases (between 2000 and to date). The keywords used for the search included “Lipopolysaccharide” OR “LPS” OR “Sickness behaviour” OR “Sickness” AND “Bioactive compounds” OR “Herbal medicine” OR “Herbal drug” OR “Natural products” OR “Isolated compounds”. A total of 41 published articles that represented data on the effect of HBACs in LPS-induced sickness behaviour were reviewed and summarised systemically. There were 33 studies that were conducted in mice and 8 studies in rats. A total of 34 HBACs have had their effects against LPS-induced changes in behaviour and biochemistry investigated. In this review, we examined 34 herbal bioactive components that have been tested in animal models to see if they can fight LPS-induced sickness behaviour. Future research should concentrate on the efficacy, safety, and dosage needed to protect against illness behaviour in humans, because there is a critical shortage of data in this area. Full article

(This article belongs to the Special Issue Natural Products: Chemical Profiling, Computational Studies and Bioactivities)

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