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Biologically Active Small Molecules Inspired by Plant Secondary Metabolites

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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 (30 September 2024) | Viewed by 46770

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Dr. Giovanni Lentini

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Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
Interests: medicinal chemistry; drug discovery; chirality
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Dr. Maria Maddalena Cavalluzzi

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Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Bari, Italy
Interests: organic synthesis; medicinal and pharmaceutical chemistry; small molecule synthesis; multistep synthesis; enantiomer; fluorine chemistry; sodium channels
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Prof. Dr. Solomon Habtemariam

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Herbal Analysis Services UK, Greenwich, University of Greenwich, London, UK
Interests: natural products chemistry; pharmacology; drug discovery; pharmacognosy
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Dear Colleagues,

It would seem that more than 500 centuries ago, our closest human relatives―the Neanderthals―used to place Ephedra plant flowers into graves. This might be the most ancient example of paleoethnobotany. As questionable as this statement might be, undoubtedly, the Plant Kingdom has been the most prodigal source of medicines for over 20 centuries.

The last four decades have witnessed a resurgence of interest in plant product research. Numerous and varied are the reasons for this:

Ever-increasing difficulty in developing new drugs;
The success of the natural product approach;
The uniqueness of plant secondary metabolites;
The impact of new screening methods and analytic techniques.

Unfortunately, plant secondary metabolites are not necessarily the best compounds for pharmaceutical uses, for the following reasons:

Limitations may exist that prevent the acquisition of sufficient biomass;
Isolation procedures may be long and expensive;
The structure of the secondary metabolites may be too complex to allow total synthesis;
The pharmacological profile may be promiscuous;
Toxicological aspects may cause concern;
Oral bioavailability can be too low.

For all of the above reasons, medicinal chemists use to prepare analogues of the starting secondary metabolites in order to unveil sound structure–activity relationships (SAR) and possibly overcome the above limitations.

This Special Issue is designed to scrutinize recent developments in the medicinal chemistry of biologically relevant compounds that were inspired by plant-derived compounds.

Between 1980 and 2013, 20% of the new drugs introduced into the market were either natural products or natural products derivatives, with the latter being highly predominant (18%). The contribution of natural product derivatives to the physician panoply is expected to rise in the next decade. The colleagues that would like to share their valuable work in the field by contributing to this Special Issue of Molecules will give shine to the issue, of course, and would possibly confer higher chances to this prophecy.

Dr. Giovanni Lentini
Dr. Maria Maddalena Cavalluzzi
Prof. Dr. Solomon Habtemariam
Guest Editors

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Keywords

Drug discovery
Secondary metabolites
Natural product scaffolds
Structure–activity relationships
Pharmacophore

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Published Papers (11 papers)

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Research

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16 pages, 11233 KiB

Open AccessArticle

Study on the Anti-Inflammatory Mechanism of Coumarins in Peucedanum decursivum Based on Spatial Metabolomics Combined with Network Pharmacology

by Zeyu Li and Qian Li

Molecules 2024, 29(14), 3346; https://doi.org/10.3390/molecules29143346 - 17 Jul 2024

Viewed by 1363

Abstract

Peucedanum decursivum (Miq.) Maxim (P. decursivum) is a traditional Chinese medicinal plant with pharmacological effects such as anti-inflammatory and anti-tumor effects, the root of which is widely used as medicine. Determining the spatial distribution and pharmacological mechanisms of metabolites is necessary when studying the effective substances of medicinal plants. As a means of obtaining spatial distribution information of metabolites, mass spectrometry imaging has high sensitivity and allows for molecule visualization. In this study, matrix-assisted laser desorption mass spectrometry (MALDI-TOF-MSI) and network pharmacology were used for the first time to visually study the spatial distribution and anti-inflammatory mechanism of coumarins, which are metabolites of P. decursivum, to determine their tissue localization and mechanism of action. A total of 27 coumarins were identified by MALDI-TOF-MSI, which mainly concentrated in the cortex, periderm, and phloem of the root of P. decursivum. Network pharmacology studies have identified key targets for the anti-inflammatory effect of P. decursivum, such as TNF, PTGS2, and PRAKA. GO enrichment and KEGG pathway analyses indicated that coumarins in P. decursivum mainly participated in biological processes such as inflammatory response, positive regulation of protein kinase B signaling, chemical carcinogenesis receptor activation, pathways in cancer, and other biological pathways. The molecular docking results indicated that there was good binding between components and targets. This study provides a basis for understanding the spatial distribution and anti-inflammatory mechanism of coumarins in P. decursivum. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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14 pages, 8049 KiB

Open AccessArticle

Discovery of Nine Dipeptidyl Peptidase-4 Inhibitors from Coptis chinensis Using Virtual Screening, Bioactivity Evaluation, and Binding Studies

by Zixi Zhao, Ruonan Ma, Yuqing Ma, Liqiang Zhao, Lele Wang, Yuzhen Fang, Yuxin Zhang, Xia Wu and Xing Wang

Molecules 2024, 29(10), 2304; https://doi.org/10.3390/molecules29102304 - 14 May 2024

Cited by 1 | Viewed by 1169

Abstract

The objective of this study was to identify multiple alkaloids in Coptis chinensis that demonstrate inhibitory activity against DPP-4 and systematically evaluate their activity and binding characteristics. A combined strategy that included molecular docking, a DPP-4 inhibition assay, surface plasmon resonance (SPR), and a molecular dynamics simulation technique was employed. The results showed that nine alkaloids in Coptis chinensis directly inhibited DPP-4, with IC₅₀ values of 3.44–53.73 μM. SPR-based binding studies revealed that these alkaloids display rapid binding and dissociation characteristics when interacting with DPP-4, with K_D values ranging from 8.11 to 29.97 μM. A molecular dynamics analysis revealed that equilibrium was rapidly reached by nine DPP-4–ligand systems with minimal fluctuations, while binding free energy calculations showed that the ∆G_bind values for the nine test compounds ranged from −31.84 to −16.06 kcal/mol. The most important forces for the binding of these alkaloids with DPP-4 are electrostatic interactions and van der Waals forces. Various important amino acid residues, such as Arg125, His126, Phe357, Arg358, and Tyr547, were involved in the inhibition of DPP-4 by the compounds, revealing a mechanistic basis for the further optimization of these alkaloids as DPP-4 inhibitors. This study confirmed nine alkaloids as direct inhibitors of DPP-4 and characterized their binding features, thereby providing a basis for further research and development on novel DPP-4 inhibitors. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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30 pages, 11157 KiB

Open AccessArticle

4-Hydroxybenzoic Acid-Based Hydrazide–Hydrazones as Potent Growth Inhibition Agents of Laccase-Producing Phytopathogenic Fungi That Are Useful in the Protection of Oilseed Crops

by Halina Maniak, Konrad Matyja, Elżbieta Pląskowska, Joanna Jarosz, Paulina Majewska, Joanna Wietrzyk, Hanna Gołębiowska, Anna Trusek and Mirosław Giurg

Molecules 2024, 29(10), 2212; https://doi.org/10.3390/molecules29102212 - 8 May 2024

Cited by 2 | Viewed by 2101

Abstract

The research on new compounds against plant pathogens is still socially and economically important. It results from the increasing resistance of pests to plant protection products and the need to maintain high yields of crops, particularly oilseed crops used to manufacture edible and industrial oils and biofuels. We tested thirty-five semi-synthetic hydrazide–hydrazones with aromatic fragments of natural origin against phytopathogenic laccase-producing fungi such as Botrytis cinerea, Sclerotinia sclerotiorum, and Cerrena unicolor. Among the investigated molecules previously identified as potent laccase inhibitors were also strong antifungal agents against the fungal species tested. The highest antifungal activity showed derivatives of 4-hydroxybenzoic acid and salicylic aldehydes with 3-tert-butyl, phenyl, or isopropyl substituents. S. sclerotiorum appeared to be the most susceptible to the tested compounds, with the lowest IC₅₀ values between 0.5 and 1.8 µg/mL. We applied two variants of phytotoxicity tests for representative crop seeds and selected hydrazide–hydrazones. Most tested molecules show no or low phytotoxic effect for flax and sunflower seeds. Moreover, a positive impact on seed germination infected with fungi was observed. With the potential for application, the cytotoxicity of the hydrazide–hydrazones of choice toward MCF-10A and BALB/3T3 cell lines was lower than that of the azoxystrobin fungicide tested. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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20 pages, 4046 KiB

Open AccessArticle

Role of Stereochemistry on the Biological Activity of Nature-Inspired 3-Br-Acivicin Isomers and Derivatives

by Andrea Galbiati, Aureliano Zana, Chiara Borsari, Marco Persico, Stefania Bova, Oleh Tkachuk, Alexandra Ioana Corfu, Lucia Tamborini, Nicoletta Basilico, Caterina Fattorusso, Stefano Bruno, Silvia Parapini and Paola Conti

Molecules 2023, 28(7), 3172; https://doi.org/10.3390/molecules28073172 - 3 Apr 2023

Cited by 6 | Viewed by 2838

Abstract

Chiral natural compounds are often biosynthesized in an enantiomerically pure fashion, and stereochemistry plays a pivotal role in biological activity. Herein, we investigated the significance of chirality for nature-inspired 3-Br-acivicin (3-BA) and its derivatives. The three unnatural isomers of 3-BA and its ester and amide derivatives were prepared and characterized for their antimalarial activity. Only the (5S, αS) isomers displayed significant antiplasmodial activity, revealing that their uptake might be mediated by the L-amino acid transport system, which is known to mediate the acivicin membrane’s permeability. In addition, we investigated the inhibitory activity towards Plasmodium falciparum glyceraldehyde 3-phosphate dehydrogenase (PfGAPDH) since it is involved in the multitarget mechanism of action of 3-BA. Molecular modeling has shed light on the structural and stereochemical requirements for an efficient interaction with PfGAPDH, leading to covalent irreversible binding and enzyme inactivation. While stereochemistry affects the target binding only for two subclasses (1a–d and 4a–d), it leads to significant differences in the antimalarial activity for all subclasses, suggesting that a stereoselective uptake might be responsible for the enhanced biological activity of the (5S, αS) isomers. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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11 pages, 8299 KiB

Open AccessArticle

Furanocoumarins from Ruta chalepensis with Amebicide Activity

by Aldo Fabio Bazaldúa-Rodríguez, Ramiro Quintanilla-Licea, María Julia Verde-Star, Magda Elizabeth Hernández-García, Javier Vargas-Villarreal and Jesús Norberto Garza-González

Molecules 2021, 26(12), 3684; https://doi.org/10.3390/molecules26123684 - 16 Jun 2021

Cited by 11 | Viewed by 2713

Abstract

Entamoeba histolytica (protozoan; family Endomoebidae) is the cause of amoebiasis, a disease related to high morbidity and mortality. Nowadays, this illness is considered a significant public health issue in developing countries. In addition, parasite resistance to conventional medicinal treatment has increased in recent years. Traditional medicine around the world represents a valuable source of alternative treatment for many parasite diseases. In a previous paper, we communicated about the antiprotozoal activity in vitro of the methanolic (MeOH) extract of Ruta chalepensis (Rutaceae) against E. histolytica. The plant is extensively employed in Mexican traditional medicine. The following workup of the MeOH extract of R. chalepensis afforded the furocoumarins rutamarin (1) and chalepin (2), which showed high antiprotozoal activity on Entamoeba histolytica trophozoites employing in vitro tests (IC₅₀ values of 6.52 and 28.95 µg/mL, respectively). Therefore, we offer a full scientific report about the bioguided isolation and the amebicide activity of chalepin and rutamarin. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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11 pages, 1143 KiB

Open AccessFeature PaperArticle

Synthesis and In Vitro Growth Inhibition of 2-Allylphenol Derivatives Against Phythopthora cinnamomi Rands

by Andrés F. Olea, Luis Espinoza, Claudia Sedan, Mario Thomas, Rolando Martínez, Marco Mellado, Héctor Carrasco and Katy Díaz

Molecules 2019, 24(22), 4196; https://doi.org/10.3390/molecules24224196 - 19 Nov 2019

Cited by 9 | Viewed by 3711

Abstract

Phytophthora cinnamomi is a phytopathogen that causes extensive damage in different crops, and therefore, produces important economic losses all around the world. Chemical fungicides are a key factor for the control of this disease. However, ecological and environmental considerations, as well as the appearance of strains that are resistant to commercial fungicides, have prompted the quest for new antifungal agents which are of low ecological impact. In this work, a series of new 2-allylphenol derivatives was synthesized, and their structures were confirmed by FT-IR, NMR, and MS. Some of the synthesized compounds, more specifically nitro derivatives, exhibit strong growth inhibition of P. cinnamomi with EC₅₀ as low as 10.0 µg/mL. This level of activity is similar to that exhibited by METALAXYL MZ 58 WP, a commonly-used commercial fungicide; therefore, these compounds might be of agricultural interest due to their potential use as fungicides against P. cinnamomi. The results indicate that this activity depends on the chemical structures of the 2-allylphenol derivatives, and that it is strongly enhanced in molecules where nitro and hydroxyl groups adopt a -para configuration. These effects are discussed in terms of the electronic distribution of the aromatic ring induced by substituent groups. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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Review

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19 pages, 596 KiB

Open AccessReview

Pharmacological Properties of Four Plant Species of the Genus Anabasis, Amaranthaceae

by Zhanybek Shegebayev, Aknur Turgumbayeva, Ubaidilla Datkhayev, Kairat Zhakipbekov, Assem Kalykova, Elmira Kartbayeva, Ahmet Beyatli, Kuanysh Tastambek, Gulmira Altynbayeva, Bassymbek Dilbarkhanov, Aiman Akhelova, Rabiga Anarbayeva and Kulpan Orynbassarova

Molecules 2023, 28(11), 4454; https://doi.org/10.3390/molecules28114454 - 31 May 2023

Cited by 16 | Viewed by 2660

Abstract

The genus Anabasis is a member of the family Amaranthaceae (former name: Chenopodiaceae) and includes approximately 102 genera and 1400 species. The genus Anabasis is one of the most significant families in salt marshes, semi-deserts, and other harsh environments. They are also renowned for their abundance in bioactive compounds, including sesquiterpenes, diterpenes, triterpenes, saponins, phenolic acids, flavonoids, and betalain pigments. Since ancient times, these plants have been used to treat various diseases of the gastrointestinal tract, diabetes, hypertension, and cardiovascular diseases and are used as an antirheumatic and diuretic. At the same time, the genus Anabasis is very rich in biologically active secondary metabolites that exhibit great pharmacological properties such as antioxidant, antibacterial, antiangiogenic, antiulcer, hypoglycemic, hepatoprotective, antidiabetic, etc. All of the listed pharmacological activities have been studied in practice by scientists from different countries and are presented in this review article to familiarize the entire scientific community with the results of these studies, as well as to explore the possibilities of using four plant species of the genus Anabasis as medicinal raw materials and developing medicines based on them. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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29 pages, 1539 KiB

Open AccessReview

Antibacterial and Antifungal Terpenes from the Medicinal Angiosperms of Asia and the Pacific: Haystacks and Gold Needles

by Christophe Wiart, Geethanjali Kathirvalu, Chandramathi Samudi Raju, Veeranoot Nissapatorn, Mohammed Rahmatullah, Alok K. Paul, Mogana Rajagopal, Jaya Seelan Sathiya Seelan, Nor Azizun Rusdi, Scholastica Lanting and Mazdida Sulaiman

Molecules 2023, 28(9), 3873; https://doi.org/10.3390/molecules28093873 - 4 May 2023

Cited by 9 | Viewed by 3644

Abstract

This review identifies terpenes isolated from the medicinal Angiosperms of Asia and the Pacific with antibacterial and/or antifungal activities and analyses their distribution, molecular mass, solubility, and modes of action. All data in this review were compiled from Google Scholar, PubMed, Science Direct, Web of Science, ChemSpider, PubChem, and library searches from 1968 to 2022. About 300 antibacterial and/or antifungal terpenes were identified during this period. Terpenes with a MIC ≤ 2 µg/mL are mostly amphiphilic and active against Gram-positive bacteria, with a molecular mass ranging from about 150 to 550 g/mol, and a polar surface area around 20 Å². Carvacrol, celastrol, cuminol, dysoxyhainic acid I, ent-1β,14β-diacetoxy-7α-hydroxykaur-16-en-15-one, ergosterol-5,8-endoperoxide, geranylgeraniol, gossypol, 16α-hydroxy-cleroda-3,13 (14)Z-diene-15,16-olide, 7-hydroxycadalene, 17-hydroxyjolkinolide B, (20R)-3β-hydroxy-24,25,26,27-tetranor-5α cycloartan-23,21-olide, mansonone F, (+)-6,6′-methoxygossypol, polygodial, pristimerin, terpinen-4-ol, and α-terpineol are chemical frameworks that could be candidates for the further development of lead antibacterial or antifungal drugs. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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21 pages, 2458 KiB

Open AccessReview

Papaverine: A Miraculous Alkaloid from Opium and Its Multimedicinal Application

by Sania Ashrafi, Safaet Alam, Arifa Sultana, Asef Raj, Nazim Uddin Emon, Fahmida Tasnim Richi, Tasnuva Sharmin, Myunghan Moon, Moon Nyeo Park and Bonglee Kim

Molecules 2023, 28(7), 3149; https://doi.org/10.3390/molecules28073149 - 31 Mar 2023

Cited by 17 | Viewed by 8051

Abstract

The pharmacological actions of benzylisoquinoline alkaloids are quite substantial, and have recently attracted much attention. One of the principle benzylisoquinoline alkaloids has been found in the unripe seed capsules of Papaver somniferum L. Although it lacks analgesic effects and is unrelated to the compounds in the morphine class, it is a peripheral vasodilator and has a direct effect on vessels. It is reported to inhibit the cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) phosphodiesterase in smooth muscles, and it has been observed to increase intracellular levels of cAMP and cGMP. It induces coronary, cerebral, and pulmonary artery dilatation and helps to lower cerebral vascular resistance and enhance cerebral blood flow. Current pharmacological research has revealed that papaverine demonstrates a variety of biological activities, including activity against erectile dysfunction, postoperative vasospasms, and pulmonary vasoconstriction, as well as antiviral, cardioprotective, anti-inflammatory, anticancer, neuroprotective, and gestational actions. It was recently demonstrated that papaverine has the potential to control SARS-CoV-2 by preventing its cytopathic effect. These experiments were carried out both in vitro and in vivo and require an extensive understanding of the mechanisms of action. With its multiple mechanisms, papaverine can be considered as a natural compound that is used to develop therapeutic drugs. To validate its applications, additional research is required into its precise therapeutic mechanisms as well as its acute and chronic toxicities. Therefore, the goal of this review is to discuss the major studies and reported clinical studies looking into the pharmacological effects of papaverine and the mechanisms of action underneath these effects. Additionally, it is recommended to conduct further research via significant pharmacodynamic and pharmacokinetic studies. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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24 pages, 15461 KiB

Open AccessReview

Role of Phenylpropanoids and Flavonoids in Plant Resistance to Pests and Diseases

by Marie-Louisa Ramaroson, Claude Koutouan, Jean-Jacques Helesbeux, Valérie Le Clerc, Latifa Hamama, Emmanuel Geoffriau and Mathilde Briard

Molecules 2022, 27(23), 8371; https://doi.org/10.3390/molecules27238371 - 30 Nov 2022

Cited by 94 | Viewed by 7548

Abstract

Phenylpropanoids and flavonoids are specialized metabolites frequently reported as involved in plant defense to biotic or abiotic stresses. Their biosynthetic accumulation may be constitutive and/or induced in response to external stimuli. They may participate in plant signaling driving plant defense responses, act as a physical or chemical barrier to prevent invasion, or as a direct toxic weapon against microbial or insect targets. Their protective action is described as the combinatory effect of their localization during the host’s interaction with aggressors, their sustained availability, and the predominance of specific compounds or synergy with others. Their biosynthesis and regulation are partly deciphered; however, a lot of gaps in knowledge remain to be filled. Their mode of action on microorganisms and insects probably arises from an interference with important cellular machineries and structures, yet this is not fully understood for all type of pests and pathogens. We present here an overview of advances in the state of the art for both phenylpropanoids and flavonoids with the objective of paving the way for plant breeders looking for natural sources of resistance to improve plant varieties. Examples are provided for all types of microorganisms and insects that are targeted in crop protection. For this purpose, fields of phytopathology, phytochemistry, and human health were explored. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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4 pages, 361 KiB

Open AccessCommentary

COVID-19, Chloroquine Repurposing, and Cardiac Safety Concern: Chirality Might Help

by Giovanni Lentini, Maria Maddalena Cavalluzzi and Solomon Habtemariam

Molecules 2020, 25(8), 1834; https://doi.org/10.3390/molecules25081834 - 16 Apr 2020

Cited by 42 | Viewed by 8898

Abstract

The desperate need to find drugs for COVID-19 has indicated repurposing strategies as our quickest way to obtain efficacious medicines. One of the options under investigation is the old antimalarial drug, chloroquine, and its analog, hydroxychloroquine. Developed as synthetic succedanea of cinchona alkaloids, these chiral antimalarials are currently in use as the racemate. Besides the ethical concern related to accelerated large-scale clinical trials of drugs with unproven efficacy, the known potential detrimental cardiac effects of these drugs should also be considered. In principle, the safety profile might be ameliorated by using chloroquine/hydroxychloroquine single enantiomers in place of the racemate. Full article

(This article belongs to the Special Issue Biologically Active Small Molecules Inspired by Plant Secondary Metabolites)

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