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Advances in Antibacterial Molecules
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Advances in Antibacterial Molecules

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

Deadline for manuscript submissions: 30 April 2025 | Viewed by 7224

Special Issue Editor

Prof. Dr. Gildardo Rivera Sanchez

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Guest Editor
Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
Interests: medicinal chemistry; synthetic organic chemistry; immunology of infectious diseases; medicinal and pharmaceutical chemistry; antibodies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacteria are the cause of different infectious diseases that have an impact on public health worldwide, causing high morbidity and mortality rates. In the past, many drugs have been developed to prevent and control these infectious diseases. However, in the few last decades, multidrug resistance (MDR) has emerged as a significant public health problem that must be addressed. Despite its importance, current pharmacological treatment has unreliable efficacy against the group of bacteria denominated ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.). Therefore, there is an urgent need to develop new therapeutic options that are safer and more effective to combat MDR.

In the last two decades, new strategies in drug discovery have been implemented to combat infectious diseases. Despite these facts and the impressive advances in understanding the biology of these diseases, only a limited number of compounds are currently in clinical trials. Therefore, there is an urgent need to develop new therapeutic options that will help to combat MDR, increase effectiveness, decrease cost, and facilitate availability.

This research topic seeks manuscripts dealing with novel approaches in the discovery and development of drugs for infectious diseases. By considering both original research and review articles that could have an ever-increasing impact on the drug discovery pipeline, new trends could be discovered that would impact the field. Areas to be covered in this research topic may include but are not limited to the following:

  • Bioactive compounds;
  • Computer-aided drug design;
  • Synthesis and biological activity of small molecules;
  • Drug targets;
  • Drug repositioning.

Prof. Dr. Gildardo Rivera Sanchez
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. Molecules is an international peer-reviewed open access semimonthly 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 2700 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

  • bacteria
  • drug design
  • drug repositioning
  • molecular docking
  • molecular dynamics
  • bioinformatics
  • synthesis
  • biomolecules
  • targets
  • in vitro assays
  • in vivo assays
  • small molecules
  • peptides
  • natural products
  • mechanism of action

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Published Papers (6 papers)

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Research

24 pages, 5642 KiB  
Article
Multi-Modal Design, Synthesis, and Biological Evaluation of Novel Fusidic Acid Derivatives
by Luqi Wang, Zhiyuan Geng, Yuhang Liu, Linhui Cao, Yao Liu, Hourui Zhang, Yi Bi and Jing Lu
Molecules 2025, 30(9), 1983; https://doi.org/10.3390/molecules30091983 - 29 Apr 2025
Abstract
Fusidic acid (FA), a tetracyclic triterpenoid, has been approved to treat methicillin-resistant Staphylococcus aureus (MRSA) infections. However, there are few reports about FA derivatives with high efficacy superior to FA, manifesting the difficulty of discovering the derivatives based on experience-based drug design. In [...] Read more.
Fusidic acid (FA), a tetracyclic triterpenoid, has been approved to treat methicillin-resistant Staphylococcus aureus (MRSA) infections. However, there are few reports about FA derivatives with high efficacy superior to FA, manifesting the difficulty of discovering the derivatives based on experience-based drug design. In this study, we employed a stepwise method to discover novel FA derivatives. First, molecular dynamics (MD) simulations were performed to identify the molecular mechanism of FA against elongation factor G (EF-G) and drug resistance. Then, we utilized a scaffold decorator to design novel FA derivatives at the 3- and 21-positions of FA. The ligand-based and structure-based screening models, including Chemprop and RTMScore, were employed to identify promising hits from the generated set. Ten generated FA derivatives with high efficacy in the Chemprop and RTMScore models were synthesized for in vitro testing. Compounds 4 and 10 demonstrated a 2-fold increase in potency against MRSA strains compared to FA. This study highlights the significant impact of AI-based methods on the design of novel FA derivatives with drug efficacy, which provides a new approach for drug discovery. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
16 pages, 1802 KiB  
Article
6-Bromoindole- and 6-Bromoindazole-Based Inhibitors of Bacterial Cystathionine γ-Lyase Containing 3-Aminothiophene-2-Carboxylate Moiety
by Roman A. Novikov, Dmitry N. Platonov, Alexander Yu. Belyy, Konstantin V. Potapov, Maxim A. Novikov, Yury V. Tomilov, Olga I. Kechko, Tatiana A. Seregina, Anastasia S. Zemskaya, Pavel N. Solyev and Vladimir A. Mitkevich
Molecules 2025, 30(2), 388; https://doi.org/10.3390/molecules30020388 - 17 Jan 2025
Viewed by 699
Abstract
In recent years, a number of synthetic potentiators of antibiotics have been discovered. Their action can significantly enhance the antibacterial effect and limit the spread of antibiotic resistance through inhibition of bacterial cystathionine-γ-lyase. To expand the known set of potentiators, we developed methods [...] Read more.
In recent years, a number of synthetic potentiators of antibiotics have been discovered. Their action can significantly enhance the antibacterial effect and limit the spread of antibiotic resistance through inhibition of bacterial cystathionine-γ-lyase. To expand the known set of potentiators, we developed methods for the synthesis of five new representatives of 6-bromoindole derivatives—potential inhibitors of bacterial cystathionine-γ-lyase—namely potassium 3-amino-5-((6-bromoindolyl)methyl)thiophene-2-carboxylate (MNS2) and its 6-bromoindazole analogs (MNS3 and MNS4), along with two 6-broindazole analogs of the parent compound NL2. Their syntheses are based on 6-bromoindole, 6-bromoindazole and methyl 5-(bromomethyl)-3-((ethoxycarbonyl)amino)thiophene-2-carboxylate as the main building blocks, assembling the rest of the heterocyclic system on their basis at the nitrogen atom. We assessed the ability of the new inhibitors to potentiate the antimicrobial activity of gentamicin. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
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10 pages, 787 KiB  
Article
Quinoxaline 1,4-di-N-oxide Derivatives as New Antinocardial Agents
by Isidro Palos, Alonzo González-González, Alma D. Paz-González, José C. Espinoza-Hicks, Debasish Bandyopadhyay, Norma Paniagua-Castro, Marlene S. Galeana-Salazar, Jorge Ismael Castañeda-Sánchez, Julieta Luna-Herrera and Gildardo Rivera
Molecules 2024, 29(19), 4652; https://doi.org/10.3390/molecules29194652 - 30 Sep 2024
Viewed by 1026
Abstract
Mycetoma is currently considered as a neglected tropical disease. The incidence of mycetoma is unknown but most of the worldwide cases are present in the “mycetoma belt” including countries like Mexico, India, Senegal, and others. The treatment of mycetoma depends on the etiological [...] Read more.
Mycetoma is currently considered as a neglected tropical disease. The incidence of mycetoma is unknown but most of the worldwide cases are present in the “mycetoma belt” including countries like Mexico, India, Senegal, and others. The treatment of mycetoma depends on the etiological agent responsible for the case. Treatment success reaches 60 to 90%; however, common treatment has been reported to be ineffective in some cases, due in part to resistance to the prescribed antibiotics. Therefore, it is necessary to develop new therapeutic options. In the past two decades, quinoxaline derivatives have shown relevance as antibacterial agents. Therefore, in this work, esters of quinoxaline 1,4-di-N-oxide derivatives were evaluated in vitro against the reference strain CECT-3052 from N. brasiliensis, six clinical isolates, and macrophages J774A.1 to determine their cytotoxicity and security index. Additionally, nine reference drugs were evaluated as controls. The results show that nine esters of quinoxaline 1,4-di-N-oxide derivatives had a minimum inhibitory concentration (MIC) < 1 µg/mL against the reference strain and four of them (N-05, N-09, N-11, and N-13) had an MIC < 1 µg/mL against the clinical isolates. Therefore, the scaffold quinoxaline 1,4-di-N-oxide could be used to develop new and more potent antinocardial agents. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
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19 pages, 6587 KiB  
Article
Molecular Periphery Design Allows Control of the New Nitrofurans Antimicrobial Selectivity
by Lyubov Vinogradova, Alexey Lukin, Kristina Komarova, Maxim Zhuravlev, Artem Fadeev, Mikhail Chudinov, Elizaveta Rogacheva, Lyudmila Kraeva, Maxim Gureev, Yuri Porozov, Marine Dogonadze and Tatiana Vinogradova
Molecules 2024, 29(14), 3364; https://doi.org/10.3390/molecules29143364 - 17 Jul 2024
Viewed by 1316
Abstract
A series of 13 new 3-substituted 5-(5-nitro-2-furyl)-1,2,4-oxadiazoles was synthesized from different aminonitriles. All compounds were screened in the disc diffusion test at a 100 μg/mL concentration to determine the bacterial growth inhibition zone presence and diameter, and then the minimum inhibitory concentrations (MICs) [...] Read more.
A series of 13 new 3-substituted 5-(5-nitro-2-furyl)-1,2,4-oxadiazoles was synthesized from different aminonitriles. All compounds were screened in the disc diffusion test at a 100 μg/mL concentration to determine the bacterial growth inhibition zone presence and diameter, and then the minimum inhibitory concentrations (MICs) were determined for the most active compounds by serial dilution. The compounds showed antibacterial activity against ESKAPE bacteria, predominantly suppressing the growth of 5 species out of the panel. Some compounds had similar or lower MICs against ESKAPE pathogens compared to ciprofloxacin, nitrofurantoin, and furazidin. In particular, 3-azetidin-3-yl-5-(5-nitro-2-furyl)-1,2,4-oxadiazole (2h) inhibited S. aureus at a concentration lower than all comparators. Compound 2e (5-(5-nitro-2-furyl)-3-[4-(pyrrolidin-3-yloxy)phenyl]-1,2,4-oxadiazole) was active against Gram-positive ESKAPE pathogens as well as M. tuberculosis. Differences in the molecular periphery led to high selectivity for the compounds. The induced-fit docking (IFD) modeling technique was applied to in silico research. Molecular docking results indicated the targeting of compounds against various nitrofuran-associated biological targets. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
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14 pages, 2187 KiB  
Article
The Nitrofuran-Warhead-Equipped Spirocyclic Azetidines Show Excellent Activity against Mycobacterium tuberculosis
by Kristina Komarova, Lyubov Vinogradova, Alexey Lukin, Maxim Zhuravlev, Dmitry Deniskin, Mikhail Chudinov, Maxim Gureev, Marine Dogonadze, Natalia Zabolotnykh, Tatiana Vinogradova, Anastasia Lavrova and Petr Yablonskiy
Molecules 2024, 29(13), 3071; https://doi.org/10.3390/molecules29133071 - 27 Jun 2024
Viewed by 1163
Abstract
A series of 21 new 7′H-spiro[azetidine-3,5′-furo [3,4-d]pyrimidine]s substituted at the pyrimidine ring second position were synthesized. The compounds showed high antibacterial in vitro activity against M. tuberculosis. Two compounds had lower minimum inhibitory concentrations against Mtb (H37Rv strain) compared with isoniazid. The [...] Read more.
A series of 21 new 7′H-spiro[azetidine-3,5′-furo [3,4-d]pyrimidine]s substituted at the pyrimidine ring second position were synthesized. The compounds showed high antibacterial in vitro activity against M. tuberculosis. Two compounds had lower minimum inhibitory concentrations against Mtb (H37Rv strain) compared with isoniazid. The novel spirocyclic scaffold shows excellent properties for anti-tuberculosis drug development. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
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18 pages, 2328 KiB  
Article
Structural Analysis and Activity Correlation of Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W4R4] Scaffold
by Shaima A. El-Mowafi, Anastasia G. Konshina, Eman H. M. Mohammed, Nikolay A. Krylov, Roman G. Efremov and Keykavous Parang
Molecules 2023, 28(24), 8049; https://doi.org/10.3390/molecules28248049 - 12 Dec 2023
Cited by 1 | Viewed by 2333
Abstract
In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure [...] Read more.
In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, [W4R4], incorporating an extra aromatic hydrophobic residue (W), a positively charged residue (R), or the unique 2,5-diketopiperazine (DKP). This study systematically explored the structure–activity relationships (SARs) of a series of cyclic peptides derived from the [W4R4] scaffold, including the first synthesis and evaluation of [W4R4(DKP)]. Structural, dynamic, hydrophobic, and membrane-binding properties of four cyclic peptides ([W4R4], [W5R4], [W4R5], [W4R4(DKP)]) were explored using molecular dynamics simulations within a DOPC/DOPG lipid bilayer that mimics the bacterial membrane. The results revealed distinct SARs linking antimicrobial activity to parameters such as conformational plasticity, immersion depth in the bilayer, and population of the membrane binding mode. Notably, [W4R5] exhibited an optimal “activity/binding to the bacterial membrane” pattern. This multidisciplinary approach efficiently decoded finely regulated SAR profiles, laying a foundation for the rational design of novel antimicrobial peptides. Full article
(This article belongs to the Special Issue Advances in Antibacterial Molecules)
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