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Natural Products Mechanism of Action: Theoretical and Experimental Approaches

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 19723

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Prof. Dr. Guadalupe Virginia Nevárez-Moorillón

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Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua 31125, Mexico
Interests: natural antimicrobials; biofilms; essential oils; fermented foods
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Luz María Rodriguez-Valdez

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Guest Editor

Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua 31125, Mexico
Interests: computational chemistry; theoretical chemistry

Special Issue Information

Dear Colleagues,

Natural products derived from plants and animals have been used for all of human history as remedies, food additives, cosmetics, and in many other applications. Natural products have been valued as a rich source of bioactive compounds with anticarcinogenic, antioxidant, and antimicrobial activities, but also in the treatment of chronic diseases or mental health problems. Still, the mechanism of action of many of the bioactive compounds present in natural products is not fully understood.

In the last few years, the application of computational chemistry and chemical modeling techniques—including quantum chemical calculations, molecular docking analysis, and quantitative structure–activity relationships—has been used to study the interaction of bioactive compounds within the organism. These theoretical techniques can investigate, at the molecular level, the beneficial properties of bioactive compounds, and provide a possible mechanism of action or insights that support experimental methods.

In this Special Issue, we invite submissions from contributors that underline the most recent progress in experimental and theoretical studies on natural products or their bioactive components, with emphasis on the chemistry, semi-synthesis, isolation, identification, and chemical characterization of extracts and bioactive molecules, as well as on the structure–activity relationship, imaging properties, and in silico modeling. Contributions with theoretical experimental data are encouraged, where the bioactivity can be related to anticarcinogenic, anticancer, anti-inflammatory, and antimicrobial properties and the description of synergic effects of combined bioactive molecules.

Prof. Dr. Guadalupe Virginia Nevárez-Moorillón
Prof. Dr. Luz María Rodriguez-Valdez
Guest Editors

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Keywords

biological activities of natural products
antioxidants
antimicrobial
anticancer
molecular docking
quantitative structure-activity relationship QSAR
molecular dynamics

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Published Papers (6 papers)

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Research

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18 pages, 2499 KiB

Open AccessArticle

In Vitro Evaluation and In Silico Calculations of the Antioxidant and Anti-Inflammatory Properties of Secondary Metabolites from Leonurus sibiricus L. Root Extracts

by Anna Merecz-Sadowska, Przemysław Sitarek, Tomasz Kowalczyk, Marcin Palusiak, Marta Hoelm, Karolina Zajdel and Radosław Zajdel

Molecules 2023, 28(18), 6550; https://doi.org/10.3390/molecules28186550 - 10 Sep 2023

Cited by 3 | Viewed by 1501

Abstract

Leonurus sibiricus L. has great ethnobotanical and ethnomedicinal significance. This study aimed to assess the antioxidant and anti-inflammatory properties of Leonurus sibiricus L. transgenic roots extracts transformed by Rhizobium rhizogenes, with and without the AtPAP1 transcriptional factor. The study determined the total phenolic and flavonoid contents, as well as in vitro antioxidant assays, including hydrogen peroxide and nitric oxide scavenging activity. In addition, in silico computational studies and molecular docking were conducted to evaluate the antioxidant and anti-inflammatory potential of the identified compounds. The ligands were docked to NADPH oxidase, cyclooxygenase 2,5-lipoxygenase, inducible nitric synthase and xanthine oxidase: enzymes involved in the inflammatory process. The total phenolic and flavonoid contents ranged from 85.3 ± 0.35 to 57.4 ± 0.15 mg/g GAE/g and 25.6 ± 0.42 to 18.2 ± 0.44 mg/g QUE/g in hairy root extracts with and without AtPAP1, respectively. H₂O₂ scavenging activity (IC₅₀) was found to be 29.3 µg/mL (with AtPAP1) and 37.5 µg/mL (without AtPAP1 transcriptional factor), and NO scavenging activity (IC₅₀) was 48.0 µg/mL (with AtPAP1) and 68.8 µg/mL (without AtPAP1 transcriptional factor). Leonurus sibiricus L. transformed root extracts, both with and without AtPAP1, are a source of phytochemicals belonging to different classes of molecules, such as flavonoids (catechin and rutin), phenolic compounds (caffeic acid, coumaric acid, chlorogenic acid, ferulic acid) and phenylpropanoid (verbascoside). Among the radicals formed after H removal from the different -OH positions, the lowest bond dissociation enthalpy was observed for rutin (4′-OH). Rutin was found to bind with cyclooxygenase 2, inducible nitric synthases and xanthine oxidase, whereas chlorogenic acid demonstrated optimal binding with 5-lipoxygenase. Therefore, it appears that the Leonurus sibiricus L. transformed root extract, both with and without the AtPAP1 transcriptional factor, may serve as a potential source of active components with antioxidant and anti-inflammatory potential; however, the extract containing AtPAP1 demonstrates superior activities. These properties could be beneficial for human health. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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17 pages, 2306 KiB

Open AccessArticle

Terpenic Constituents of Essential Oils with Larvicidal Activity against Aedes Aegypti: A QSAR and Docking Molecular Study

by Adrián Ulises Cruz-Castillo, Luz María Rodríguez-Valdez, José Correa-Basurto, Benjamín Nogueda-Torres, Sergio Andrade-Ochoa and Guadalupe Virginia Nevárez-Moorillón

Molecules 2023, 28(6), 2454; https://doi.org/10.3390/molecules28062454 - 7 Mar 2023

Cited by 4 | Viewed by 3312

Abstract

Aedes aegypti is a vector for the arbovirus responsible for yellow fever, Zika and Chikungunya virus. Essential oils and their constituents are known for their larvicidal properties and are strong candidates for mosquito control. This work aimed to develop a quantitative structure–activity study and molecular screening for the search and design of new larvicidal agents. Twenty-five monoterpenes with previously evaluated larvicidal activity were built and optimized using computational tools. QSAR models were constructed through genetic algorithms from the larvicidal activity and the calculation of theoretical descriptors for each molecule. Docking studies on acetylcholinesterase (AChE) and sterol carrier protein (SCP-2) were also carried out. Results demonstrate that the epoxide groups in the structure of terpenes hinder larvicidal activity, while lipophilicity plays an important role in enhancing biological activity. Larvicidal activity correlates with the interaction of the sterol-carrier protein. Of the 25 compounds evaluated, carvacrol showed the highest larvicidal activity with an LC₅₀ of 8.8 µg/mL. The information included in this work contributes to describing the molecular, topological, and quantum mechanical properties related to the larvicidal activity of monoterpenes and their derivatives. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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12 pages, 1754 KiB

Open AccessArticle

Study of Genotoxicity, Activities on Caspase 8 and on the Stabilization of the Topoisomerase Complex of Isoeleutherin and Analogues

by Kelly Cristina Oliveira de Albuquerque, Natasha Costa da Rocha Galucio, Gleison Gonçalves Ferreira, Ana Carolina Sousa Quaresma, Valdicley Vieira Vale, Marcelo de Oliveira Bahia, Rommel Mario Rodriguez Burbano, Fábio Alberto de Molfetta, Sandro Percario and Maria Fâni Dolabela

Molecules 2023, 28(4), 1630; https://doi.org/10.3390/molecules28041630 - 8 Feb 2023

Cited by 2 | Viewed by 1640

Abstract

This study evaluated the genotoxicity of Ethanol Extract (EEEp), Dichloromethane Fraction (FDCMEp) and isoeleutherin isolated from Eleutherine plicata, using the micronucleus test and the impact of structural alterations on toxicity and molecular docking (topoisomerase II and DNA complex). The extract was obtained by maceration and fractionation in a chromatography column. The genotoxicity was evaluated by the micronucleus test in human hepatoma cells (HepG2). Isoeleutherin was the starting molecule in the search for analogues by structural similarity, using the ZINC and e-Molecules databases. Isoeleutherin and analogues were subjected to in silico toxicity prediction, and compounds free of toxicological risks (CP13, CP14, CP17 and isoeleutherin) were selected for molecular docking in Topoisomerase II (PDB: 1ZXM). In the micronucleus test, isoeleutherin was less genotoxic. Among the 22 isoeleutherin analogues there were variations in the toxicity profile. Molecular docking studies showed that the compounds have good complementarity in the active site with important hydrogens bonds. Therefore, the structural changes of isoeleutherin led to the obtaining of a molecule with a lower mutagenic potential, and the CP13 can be considered a prototype compound for the development of new molecules with pharmacological potential. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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17 pages, 21995 KiB

Open AccessArticle

Identification of a Novel Angiogenesis Signalling circSCRG1/miR-1268b/NR4A1 Pathway in Atherosclerosis and the Regulatory Effects of TMP-PF In Vitro

by Rong Yuan, Qiqi Xin, Xiaochang Ma, Meng Yu, Yu Miao, Keji Chen and Weihong Cong

Molecules 2023, 28(3), 1271; https://doi.org/10.3390/molecules28031271 - 28 Jan 2023

Cited by 9 | Viewed by 2321

Abstract

Angiogenesis contributes to plaque instability in atherosclerosis and further increases cardio-cerebrovascular risk. Circular RNAs (circRNAs) are promising biomarkers and potential therapeutic targets for atherosclerosis. Previous studies have demonstrated that tetramethylpyrazine (TMP) and paeoniflorin (PF) combination treatment (TMP-PF) inhibited oxidized low-density lipoprotein (ox-LDL)-induced angiogenesis in vitro. However, whether circRNAs regulate angiogenesis in atherosclerosis and whether TMP-PF can regulate angiogenesis-related target circRNAs in atherosclerosis are unknown. In this study, human RNA sequencing (RNA-seq) data were analysed to identify differentially expressed (DE) circRNAs in atherosclerosis and to obtain angiogenesis-associated circRNA-microRNA (miRNA)-messenger RNA (mRNA) networks. Target circRNA-related mechanisms in angiogenesis in atherosclerosis and the regulatory effects of TMP-PF on target circRNA signalling were studied in ox-LDL-induced human umbilical vein endothelial cells (HUVECs) by cell proliferation, migration, tube formation, and luciferase reporter assays, real-time quantitative polymerase chain reaction (RT-qPCR) and Western blotting. A novel circRNA (circular stimulator of chondrogenesis 1, circSCRG1) was initially identified associated with angiogenesis in atherosclerosis, and circSCRG1 silencing up-regulated miR-1268b expression, increased nuclear receptor subfamily 4 group A member 1 (NR4A1) expression and then promoted ox-LDL-induced angiogenesis. TMP-PF (1 μmol/L TMP combined with 10 μmol/L PF) up-regulated circSCRG1 expression, mediated miR-1268b to suppress NR4A1 expression and then inhibited ox-LDL-induced angiogenesis. However, circSCRG1 silencing abolished the inhibitory effects of TMP-PF on ox-LDL-induced angiogenesis, which were rescued by the miR-1268b inhibitor. In conclusion, circSCRG1 might serve as a new target regulating angiogenesis in atherosclerosis via the circSCRG1/miR-1268b/NR4A1 axis and TMP-PF could regulate the circSCRG1/miR-1268b/NR4A1 axis to inhibit angiogenesis in atherosclerosis in vitro, indicating a novel angiogenesis signalling circSCRG1/miR-1268b/NR4A1 pathway in atherosclerosis and the regulatory effects of TMP-PF, which might provide a new pharmaceutical strategy to combat atherosclerotic plaque instability. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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16 pages, 3854 KiB

Open AccessArticle

Evaluation of Genotoxicity and Toxicity of Annona muricata L. Seeds and In Silico Studies

by Gleison Gonçalves Ferreira, Ana Carolina Sousa Quaresma, Dayse Lúcia do Nascimento Brandão, Andrey Moacir do Rosario Marinho, José Edson de Sousa Siqueira, Kamila Leal Correa, José Otávio Carréra Silva-Júnior, Sandro Percario and Maria Fâni Dolabela

Molecules 2023, 28(1), 231; https://doi.org/10.3390/molecules28010231 - 27 Dec 2022

Cited by 7 | Viewed by 3073

Abstract

Cancer is a multifactorial organic dysfunction for which great efforts are being devoted in searching for new treatments and therapeutic adjuvants. Annona muricata is a fruit that has promising activity against several types of cancer, as it contains acetogenins, the metabolite group associated with this action. Thus, the objective of this study was to evaluate, in experimental models, the toxic behavior of an extract and fraction rich in acetogenins from A. muricata seeds and study the acetogenin, Annonacin, in silico. Phytochemical characterization was made by thin layer chromatography, spectroscopy in the infrared region and nuclear magnetic resonance. Toxicity was evaluated by tests of Allium cepa and Artemia salina, and in silico studies using the SwissDock servers DockThor, PharmMapper, ADMETLab, PreADME, Osiris and ProTox. The extract and fraction showed genotoxic activity against meristematic cells of A. cepa, reducing the mitotic index; however, the extract produced great deleterious effects on the system, even causing cell necrosis. In A. Saline, the extract was more toxic than the fraction, but both samples were considered toxic. Annonacin was effectively linked to complex I, and presented different activities regarding toxicity. Thus, the results of this study are promising, highlighting the anticancer potential of acetogenins. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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Review

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12 pages, 1257 KiB

Open AccessReview

Essential Oils and COVID-19

by Mahmoud Fahmi Elsebai and Marzough Aziz Albalawi

Molecules 2022, 27(22), 7893; https://doi.org/10.3390/molecules27227893 - 15 Nov 2022

Cited by 20 | Viewed by 5867

Abstract

Herbal products are a major source of herbal medicines and other medicines. Essential oils have shown various pharmacological activities, such as antiviral activity, and therefore are proposed to have potential activity against SARS-CoV-2. Due to their lipophilicity, essential oils can easily penetrate the viral membrane and cause the viral membrane to rupture. In addition, crude essential oils usually have many active constituents that can act on different parts of the virus including its cell entry, translation, transcription, and assembly. They have further beneficial pharmacological effects on the host’s respiratory system, including anti-inflammatory, immune regulation, bronchiectasis, and mucolytics. This review reported potential essential oils which could be promising drugs for COVID-19 eradication. Essential oils have many advantages because they are promising volatile antiviral molecules, making them potential drug targets for the prevention and treatment of COVID-19, whether used alone or in combination with other chemotherapeutic drugs. The aim of the current review is to shed light on the potential essential oils against enveloped viruses and their proposed activity against SARS-CoV-2 which is also an enveloped virus. The objectives were to present all data reflecting the promising activities of diverse essential oils against enveloped viruses and how they could contribute to the eradication of COVID disease, especially in indoor places. The data collected for the current review were obtained through the SciFinder database, Google scholar, PubMed, and Mendeley database. The data of the current review focused on the most common essential oils which are available in the pharmaceutical market and showed noticeable activities against enveloped viruses such as HSV and influenza. Full article

(This article belongs to the Special Issue Natural Products Mechanism of Action: Theoretical and Experimental Approaches)

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