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Antimicrobial Agents and Resistance Mechanisms
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Antimicrobial Agents and Resistance Mechanisms

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: 20 January 2025 | Viewed by 11206

Special Issue Editor

Dr. Konstantin V. Kudryavtsev

E-Mail Website
Guest Editor
Vreden Russian Research Center of Traumatology and Orthopedics, Academician Baykov Street 8, 195427 St. Petersburg, Russia
Interests: medicinal chemistry; organic synthesis; structure-activity relationship; rational target-oriented drug design

Special Issue Information

Dear Colleagues,

Patients infected with drug-resistant bacteria (viruses, fungi, parasites) are usually at high risk of worse clinical outcomes. Major surgery, organ transplantation, cancer chemotherapy would not be possible without effective treatment and prevention of different infections by indispensable antibiotics. Extensive prescription of broad-spectrum antibiotics (antivirals, antifungals, antiparasitics) led to the changes in microbial populations resulting in the rapid evolution of antimicrobial resistance (AMR) mechanisms.

Development of efficient antimicrobial agents requires deep understanding of critical stages of microbial pathogenesis and innovative approaches to overcoming resistance mechanisms. In this Special issue we will consider novel principles and strategies to combat different opportunistic infections with the special emphasis on priority pathogens. Original research and review manuscripts corresponding to the declared themes are invited for submitting.

Dr. Konstantin V. Kudryavtsev
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • high-priority pathogens
  • superbugs
  • antimicrobial resistance
  • nosocomial infections
  • antibiotics
  • antivirals
  • antifungals
  • antiparasitics
  • virulence
  • bacterial biofilms

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Published Papers (7 papers)

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Research

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22 pages, 4850 KiB  
Article
Ensemble Docking as a Tool for the Rational Design of Peptidomimetic Staphylococcus aureus Sortase A Inhibitors
by Dmitry A. Shulga and Konstantin V. Kudryavtsev
Int. J. Mol. Sci. 2024, 25(20), 11279; https://doi.org/10.3390/ijms252011279 - 20 Oct 2024
Viewed by 722
Abstract
Sortase A (SrtA) of Staphylococcus aureus has long been shown to be a relevant molecular target for antibacterial development. Moreover, the designed SrtA inhibitors act via the antivirulence mechanism, potentially causing less evolutional pressure and reduced antimicrobial resistance. However, no marketed drugs or [...] Read more.
Sortase A (SrtA) of Staphylococcus aureus has long been shown to be a relevant molecular target for antibacterial development. Moreover, the designed SrtA inhibitors act via the antivirulence mechanism, potentially causing less evolutional pressure and reduced antimicrobial resistance. However, no marketed drugs or even drug candidates have been reported until recently, despite numerous efforts in the field. SrtA has been shown to be a tough target for rational structure-based drug design (SBDD), which hampers the regular development of small-molecule inhibitors using the available arsenal of drug discovery tools. Recently, several oligopeptides resembling the sorting sequence LPxTG (Leu-Pro-Any-Thr-Gly) of the native substrates of SrtA were reported to be active in the micromolar range. Despite the good experimental design of those works, their molecular modeling parts are still not convincing enough to be used as a basis for a rational modification of peptidic inhibitors. In this work, we propose to use the ensemble docking approach, in which the relevant SrtA conformations are extracted from the molecular dynamics simulation of the LPRDA (Leu-Pro-Arg-Asp-Ala)-SrtA complex, to effectively represent the most significant and diverse target conformations. The developed protocol is shown to describe the known experimental data well and then is applied to a series of new peptidomimetic molecules resembling the active oligopeptide structures reported previously in order to prioritize structures from this work for further synthesis and activity testing. The proposed approach is compared to existing alternatives, and further directions for its development are outlined. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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14 pages, 3235 KiB  
Article
An Antimicrobial Copper–Plastic Composite Coating: Characterization and In Situ Study in a Hospital Environment
by Alexandre M. Emelyanenko, Fadi S. Omran, Maria A. Teplonogova, Marina Y. Chernukha, Lusine R. Avetisyan, Eugenia G. Tselikina, Gleb A. Putsman, Sergey K. Zyryanov, Olga I. Butranova, Kirill A. Emelyanenko and Ludmila B. Boinovich
Int. J. Mol. Sci. 2024, 25(8), 4471; https://doi.org/10.3390/ijms25084471 - 18 Apr 2024
Cited by 1 | Viewed by 1411
Abstract
A method has been proposed for creating an operationally durable copper coating with antimicrobial properties for the buttons of electrical switches based on the gas dynamic spray deposition of copper on acrylonitrile butadiene styrene (ABS) plastic. It is shown that during the coating [...] Read more.
A method has been proposed for creating an operationally durable copper coating with antimicrobial properties for the buttons of electrical switches based on the gas dynamic spray deposition of copper on acrylonitrile butadiene styrene (ABS) plastic. It is shown that during the coating process, a polymer film is formed on top of the copper layer. Comparative in situ studies of microbial contamination have shown that the copper-coated buttons have a significant antimicrobial effect compared to standard buttons. Analysis of swabs over a 22-week study in a hospital environment showed that the frequency of contamination for a copper-coated button with various microorganisms was 2.7 times lower than that of a control button. The presented results allow us to consider the developed copper coating for plastic switches an effective alternative method in the fight against healthcare-associated infections. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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27 pages, 5163 KiB  
Article
Anti Gram-Positive Bacteria Activity of Synthetic Quaternary Ammonium Lipid and Its Precursor Phosphonium Salt
by Francesca Bacchetti, Anna Maria Schito, Marco Milanese, Sara Castellaro and Silvana Alfei
Int. J. Mol. Sci. 2024, 25(5), 2761; https://doi.org/10.3390/ijms25052761 - 27 Feb 2024
Cited by 3 | Viewed by 1455
Abstract
Organic ammonium and phosphonium salts exert excellent antimicrobial effects by interacting lethally with bacterial membranes. Particularly, quaternary ammonium lipids have demonstrated efficiency both as gene vectors and antibacterial agents. Here, aiming at finding new antibacterial devices belonging to both classes, we prepared a [...] Read more.
Organic ammonium and phosphonium salts exert excellent antimicrobial effects by interacting lethally with bacterial membranes. Particularly, quaternary ammonium lipids have demonstrated efficiency both as gene vectors and antibacterial agents. Here, aiming at finding new antibacterial devices belonging to both classes, we prepared a water-soluble quaternary ammonium lipid (6) and a phosphonium salt (1) by designing a synthetic path where 1 would be an intermediate to achieve 6. All synthesized compounds were characterized by Fourier-transform infrared spectroscopy and Nuclear Magnetic Resonance. Additionally, potentiometric titrations of NH3+ groups 1 and 6 were performed to further confirm their structure by determining their experimental molecular weight. The antibacterial activities of 1 and 6 were assessed first against a selection of multi-drug-resistant clinical isolates of both Gram-positive and Gram-negative species, observing remarkable antibacterial activity of both compounds against Gram-positive isolates of Enterococcus and Staphylococcus genus. Further investigations on a wider variety of strains of these species confirmed the remarkable antibacterial effects of 1 and 6 (MICs = 4–16 and 4–64 µg/mL, respectively), while 24 h-time-killing experiments carried out with 1 on different S. aureus isolates evidenced a bacteriostatic behavior. Moreover, both compounds 1 and 6, at the lower MIC concentration, did not show significant cytotoxic effects when exposed to HepG2 human hepatic cell lines, paving the way for their potential clinical application. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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15 pages, 3352 KiB  
Article
The Effect of the Stringent Response and Oxidative Stress Response on Fitness Costs of De Novo Acquisition of Antibiotic Resistance
by Wenxi Qi, Martijs J. Jonker, Drosos Katsavelis, Wim de Leeuw, Meike Wortel and Benno H. ter Kuile
Int. J. Mol. Sci. 2024, 25(5), 2582; https://doi.org/10.3390/ijms25052582 - 23 Feb 2024
Viewed by 1820
Abstract
Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress [...] Read more.
Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of wild-type strains and single-gene knockout strains in stress response pathways using four different antibiotics. Throughout resistance development, the increase in minimum inhibitory concentration (MIC) is accompanied by a gradual decrease in growth rate, most pronounced in amoxicillin or kanamycin. By measuring biomass yield on glucose and whole-genome sequences at intermediate and final time points, we identified two patterns of how the stress responses affect the correlation between MIC and growth rate. First, single-gene knockout E. coli strains associated with reactive oxygen species (ROS) acquire resistance faster, and mutations related to antibiotic permeability and pumping out occur earlier. This increases the metabolic burden of resistant bacteria. Second, the ΔrelA knockout strain, which has reduced (p)ppGpp synthesis, is restricted in its stringent response, leading to diminished growth rates. The ROS-related mutagenesis and the stringent response increase metabolic burdens during resistance development, causing lower growth rates and higher fitness costs. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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14 pages, 3009 KiB  
Article
Bavachin Rejuvenates Sensitivity of Colistin against Colistin-Resistant Gram-Negative Bacteria
by Jie Li, Ning Han, Zhengyuan He, Xiaolan Dai, Feifei Zhao, Yangyang Li, Wenguang Xiong and Zhenling Zeng
Int. J. Mol. Sci. 2024, 25(4), 2349; https://doi.org/10.3390/ijms25042349 - 16 Feb 2024
Cited by 2 | Viewed by 1408
Abstract
The emergence of plasmid-mediated colistin resistance threatens the efficacy of colistin as a last-resort antibiotic used to treat infection caused by Gram-negative bacteria (GNB). Given the shortage of new antibiotics, the discovery of adjuvants to existing antibiotics is a promising strategy to combat [...] Read more.
The emergence of plasmid-mediated colistin resistance threatens the efficacy of colistin as a last-resort antibiotic used to treat infection caused by Gram-negative bacteria (GNB). Given the shortage of new antibiotics, the discovery of adjuvants to existing antibiotics is a promising strategy to combat infections caused by multidrug-resistant (MDR) GNB. This study was designed to investigate the potential synergistic antibacterial activity of bavachin, a bioactive compound extracted from the Psoralea Fructus, combined with colistin against MDR GNB. Herein, the synergistic efficacy in vitro and the therapeutic efficacy of colistin combined with bavachin in vivo were evaluated. The synergistic mechanism was detected by fluorescent probe and the transcript levels of mcr-1. Bavachin combined with colistin showed an excellent synergistic activity against GNB, as the FICI ≤ 0.5. In contrast to colistin alone, combination therapy dramatically increased the survival rate of Galleria mellonella and mice in vivo. Moreover, the combination of bavachin and colistin significantly reduced the amount of bacterial biofilm formation, improved the membrane disruption of colistin and inhibited mcr-1 transcription. These findings show that bavachin is a potential adjuvant of colistin, which may provide a new strategy to combat colistin-resistant bacteria infection with lower doses of colistin. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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19 pages, 386 KiB  
Article
Five Different Artemisia L. Species Ethanol Extracts’ Phytochemical Composition and Their Antimicrobial and Nematocide Activity
by Evgeny Nikitin, Igor Fitsev, Anastasia Egorova, Lidia Logvinenko, Dmitriy Terenzhev, Feruzakhon Bekmuratova, Adelya Rakhmaeva, Georgiy Shumatbaev, Alsu Gatiyatullina, Oksana Shevchuk and Tatiana Kalinnikova
Int. J. Mol. Sci. 2023, 24(18), 14372; https://doi.org/10.3390/ijms241814372 - 21 Sep 2023
Cited by 3 | Viewed by 1877
Abstract
Among the plants that exhibit significant or established pharmacological activity, the genus Artemisia L. deserves special attention. This genus comprises over 500 species belonging to the largest Asteraceae family. Our study aimed at providing a comprehensive evaluation of the phytochemical composition of the [...] Read more.
Among the plants that exhibit significant or established pharmacological activity, the genus Artemisia L. deserves special attention. This genus comprises over 500 species belonging to the largest Asteraceae family. Our study aimed at providing a comprehensive evaluation of the phytochemical composition of the ethanol extracts of five different Artemisia L. species (collected from the southwest of the Russian Federation) and their antimicrobial and nematocide activity as follows: A. annua cv. Novichok., A. dracunculus cv. Smaragd, A. santonica cv. Citral, A. abrotanum cv. Euxin, and A. scoparia cv. Tavrida. The study of the ethanol extracts of the five different Artemisia L. species using the methods of gas chromatography–mass spectrometry (GC–MS) and high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (HPLC–MS/MS) allowed establishing their phytochemical profile. The obtained data on the of five different Artemisia L. species ethanol extracts’ phytochemical composition were used to predict the antibacterial and antifungal activity against phytopathogenic microorganisms and nematocidal activity against the free-living soil nematode Caenorhabditis elegans. The major compounds found in the composition of the Artemisia L. ethanol extracts were monoterpenes, sesquiterpenes, flavonoids, flavonoid glycosides, coumarins, and phenolic acids. The antibacterial and antifungal activity of the extracts began to manifest at a concentration of 150 µg/mL. The A. dracunculus cv. Smaragd extract had a selective effect against Gram-positive R. iranicus and B. subtilis bacteria, whereas the A. scoparia cv. Tavrida extract had a selective effect against Gram-negative A. tumefaciens and X. arboricola bacteria and A. solani, R. solani and F. graminearum fungi. The A. annua cv. Novichok, A. dracunculus cv. Smaragd, and A. santonica cv. Citral extracts in the concentration range of 31.3–1000 µg/mL caused the death of nematodes. It was established that A. annua cv. Novichok affects the UNC-63 protein, the molecular target of which is the nicotine receptor of the N-subtype. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)

Review

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22 pages, 7560 KiB  
Review
Monoterpene Thiols: Synthesis and Modifications for Obtaining Biologically Active Substances
by Denis V. Sudarikov, Liliya E. Nikitina, Patrick Rollin, Evgeniy S. Izmest’ev and Svetlana A. Rubtsova
Int. J. Mol. Sci. 2023, 24(21), 15884; https://doi.org/10.3390/ijms242115884 - 1 Nov 2023
Cited by 1 | Viewed by 1739
Abstract
Monoterpene thiols are one of the classes of natural flavors that impart the smell of citrus fruits, grape must and wine, black currants, and guava and are used as flavoring agents in the food and perfume industries. Synthetic monoterpene thiols have found an [...] Read more.
Monoterpene thiols are one of the classes of natural flavors that impart the smell of citrus fruits, grape must and wine, black currants, and guava and are used as flavoring agents in the food and perfume industries. Synthetic monoterpene thiols have found an application in asymmetric synthesis as chiral auxiliaries, derivatizing agents, and ligands for metal complex catalysis and organocatalysts. Since monoterpenes and monoterpenoids are a renewable source, there are emerging trends to use monoterpene thiols as monomers for producing new types of green polymers. Monoterpene thioderivatives are also known to possess antioxidant, anticoagulant, antifungal, and antibacterial activity. The current review covers methods for the synthesis of acyclic, mono-, and bicyclic monoterpene thiols, as well as some investigations related to their usage for the preparation of the compounds with antimicrobial properties. Full article
(This article belongs to the Special Issue Antimicrobial Agents and Resistance Mechanisms)
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