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Natural Bioactive Compounds against Microorganisms: Sources and Mechanism of Action

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 12404

Special Issue Editor


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Guest Editor
Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
Interests: structural bioinformatics; molecular modeling; molecular dynamics; molecular docking; macromolecule electrostatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

For some time now, natural compounds have been becoming increasingly important in the fight against microorganisms and infectious diseases. As certain antibiotics and other anti-infective substances, though in use for a long time, have been deemed no longer adequate in their effectiveness against microorganisms, natural compounds, whose use is often only derived from traditional experimentation, have taken on an increasingly important role thanks to their capability, effectiveness and tolerability. The role of this Special Issue is to highlight their mechanism of action, often little known or not known at all, through experimental or mixed computational/experimental methods that often provide an atomistic mechanism for the clarification and elucidation of the macroscopically observed experimental behavior. Computational methods, in fact, if combined with experimental ones, can help to outline a mechanism of action. Especially in this pandemic period, the role of these substances, often coming from plants but also from other sources, has been widely re-evaluated. In fact, the phytoextracts can count on the synergistic action of a variety of compounds that actually amplify their properties and prevent microorganisms from being able to weaken or cancel their therapeutic properties with a bypass action.

This Special Issue welcomes original research and review articles in the field, with a focus on but not limited to the molecular and mechanistic basis of the natural compound activity against microorganisms.

I look forward to receiving your contributions.

Dr. Mattia Falconi
Guest Editor

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Keywords

  • natural compounds
  • phytoextracts
  • mechanism of action
  • anti-infective activity
  • experimental tests
  • computational studies
  • atomistic machinery

Published Papers (4 papers)

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Research

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19 pages, 3186 KiB  
Article
Deciphering the Broad Antimicrobial Activity of Melaleuca alternifolia Tea Tree Oil by Combining Experimental and Computational Investigations
by Federico Iacovelli, Alice Romeo, Patrizio Lattanzio, Serena Ammendola, Andrea Battistoni, Simone La Frazia, Giulia Vindigni, Valeria Unida, Silvia Biocca, Roberta Gaziano, Maurizio Divizia and Mattia Falconi
Int. J. Mol. Sci. 2023, 24(15), 12432; https://doi.org/10.3390/ijms241512432 - 04 Aug 2023
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Abstract
Tea Tree Oil (TTO) is an essential oil obtained from the distillation of Melaleuca alternifolia leaves and branches. Due to its beneficial properties, TTO is widely used as an active ingredient in antimicrobial preparations for topical use or in cosmetic products and contains [...] Read more.
Tea Tree Oil (TTO) is an essential oil obtained from the distillation of Melaleuca alternifolia leaves and branches. Due to its beneficial properties, TTO is widely used as an active ingredient in antimicrobial preparations for topical use or in cosmetic products and contains about 100 different compounds, with terpinen-4-ol, γ-terpinene and 1,8-cineole (or eucalyptol) being the molecules most responsible for its biological activities. In this work, the antimicrobial activity of whole TTO and these three major components was evaluated in vitro against fungi, bacteria and viruses. Molecular dynamics simulations were carried out on a bacterial membrane model and a Coxsackievirus B4 viral capsid, to propose an atomistic explanation of their mechanism of action. The obtained results indicate that the strong antimicrobial activity of TTO is attributable to the induction of an altered membrane functionality, mediated by the incorporation of its components within the lipid bilayer, and to a possible ability of the compounds to bind and alter the structural properties of the viral capsid. Full article
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17 pages, 4166 KiB  
Article
Natural Inhibitors Targeting the Localization of Lipoprotein System in Vibrio parahaemolyticus
by Jiawen Liu, Jinrong Tong, Qian Wu, Jing Liu, Mengqi Yuan, Cuifang Tian, Huan Xu, Pradeep K. Malakar, Yingjie Pan, Yong Zhao and Zhaohuan Zhang
Int. J. Mol. Sci. 2022, 23(22), 14352; https://doi.org/10.3390/ijms232214352 - 18 Nov 2022
Cited by 4 | Viewed by 1451
Abstract
The localization of lipoprotein (Lol) system is responsible for the transport of lipoproteins in the outer membrane (OM) of Vibrio parahaemolyticus. LolB catalyzes the last step in the Lol system, where lipoproteins are inserted into the OM. If the function of LolB [...] Read more.
The localization of lipoprotein (Lol) system is responsible for the transport of lipoproteins in the outer membrane (OM) of Vibrio parahaemolyticus. LolB catalyzes the last step in the Lol system, where lipoproteins are inserted into the OM. If the function of LolB is impeded, growth of V. parahaemolyticus is inhibited, due to lack of an intact OM barrier for protection against the external environment. Additionally, it becomes progressively harder to generate antimicrobial resistance (AMR). In this study, LolB was employed as the receptor for a high-throughput virtual screening from a natural compounds database. Compounds with higher glide score were selected for an inhibition assay against V. parahaemolyticus. It was found that procyanidin, stevioside, troxerutin and rutin had both exciting binding affinity with LolB in the micromolar range and preferable antibacterial activity in a concentration-dependent manner. The inhibition rates of 100 ppm were 87.89%, 86.2%, 91.39% and 83.71%, respectively. The bacteriostatic mechanisms of the four active compounds were explored further via fluorescence spectroscopy and molecular docking, illustrating that each molecule formed a stable complex with LolB via hydrogen bonds and pi–pi stacking interactions. Additionally, the critical sites for interaction with V. parahaemolyticus LolB, Tyr108 and Gln68, were also illustrated. This paper demonstrates the inhibition of LolB, thus, leading to antibacterial activity, and identifies LolB as a promising drug target for the first time. These compounds could be the basis for potential antibacterial agents against V. parahaemolyticus. Full article
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23 pages, 3956 KiB  
Article
The Discovery of Novel Ferulic Acid Derivatives Incorporating Substituted Isopropanolamine Moieties as Potential Tobacco Mosaic Virus Helicase Inhibitors
by Zhenxing Li, Binxin Yang, Hongwu Liu, Yue Ding, Zimian Fang, Wubin Shao, Puying Qi, Xiang Zhou, Liwei Liu and Song Yang
Int. J. Mol. Sci. 2022, 23(22), 13991; https://doi.org/10.3390/ijms232213991 - 13 Nov 2022
Cited by 3 | Viewed by 1443
Abstract
Target-based drug design, a high-efficiency strategy used to guide the development of novel pesticide candidates, has attracted widespread attention. Herein, various natural-derived ferulic acid derivatives incorporating substituted isopropanolamine moieties were designed to target the tobacco mosaic virus (TMV) helicase. Bioassays demonstrating the optimized [...] Read more.
Target-based drug design, a high-efficiency strategy used to guide the development of novel pesticide candidates, has attracted widespread attention. Herein, various natural-derived ferulic acid derivatives incorporating substituted isopropanolamine moieties were designed to target the tobacco mosaic virus (TMV) helicase. Bioassays demonstrating the optimized A19, A20, A29, and A31 displayed excellent in vivo antiviral curative abilities, affording corresponding EC50 values of 251.1, 336.2, 347.1, and 385.5 μg/mL, which visibly surpassed those of commercial ribavirin (655.0 μg/mL). Moreover, configurational analysis shows that the R-forms of target compounds were more beneficial to aggrandize antiviral profiles. Mechanism studies indicate that R-A19 had a strong affinity (Kd = 5.4 μM) to the TMV helicase and inhibited its ability to hydrolyze ATP (50.61% at 200 μM). Meanwhile, A19 could down-regulate the expression of the TMV helicase gene in the host to attenuate viral replication. These results illustrate the excellent inhibitory activity of A19 towards the TMV helicase. Additionally, docking simulations uncovered that R-A19 formed more hydrogen bonds with the TMV helicase in the binding pocket. Recent studies have unambiguously manifested that these designed derivatives could be considered as promising potential helicase-based inhibitors for plant disease control. Full article
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Review

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39 pages, 990 KiB  
Review
Kaempferol: Antimicrobial Properties, Sources, Clinical, and Traditional Applications
by Argyrios Periferakis, Konstantinos Periferakis, Ioana Anca Badarau, Elena Madalina Petran, Delia Codruta Popa, Ana Caruntu, Raluca Simona Costache, Cristian Scheau, Constantin Caruntu and Daniel Octavian Costache
Int. J. Mol. Sci. 2022, 23(23), 15054; https://doi.org/10.3390/ijms232315054 - 30 Nov 2022
Cited by 44 | Viewed by 6928
Abstract
Flavonoids are a category of plant-derived compounds which exhibit a large number of health-related effects. One of the most well-known and studied flavonoids is kaempferol, which can be found in a wide variety of herbs and plant families. Apart from their anticarcinogenic and [...] Read more.
Flavonoids are a category of plant-derived compounds which exhibit a large number of health-related effects. One of the most well-known and studied flavonoids is kaempferol, which can be found in a wide variety of herbs and plant families. Apart from their anticarcinogenic and anti-inflammatory effects, kaempferol and its associated compounds also exhibit antibacterial, antifungal, and antiprotozoal activities. The development of drugs and treatment schemes based on these compounds is becoming increasingly important in the face of emerging resistance of numerous pathogens as well as complex molecular interactions between various drug therapies. In addition, many of the kaempferol-containing plants are used in traditional systems all over the world for centuries to treat numerous conditions. Due to its variety of sources and associated compounds, some molecular mechanisms of kaempferol antimicrobial activity are well known while others are still under analysis. This paper thoroughly documents the vegetal and food sources of kaempferol as well as the most recent and significant studies regarding its antimicrobial applications. Full article
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