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Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”
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Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 4702

Special Issue Editors

Dr. Clemente Capasso

E-Mail Website
Guest Editor
Institute of Bioscience and Bioresources (IBBR), National Research Council, Via Pietro Castellino 111, 80131 Napoli, Italy
Interests: protein biochemistry; recombinant protein; heterologous expression; carbonic anhydrase; enzyme and protein purification; enzyme characterization; enzyme thermostability; cold-adapted enzymes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Alicja Wegrzyn

E-Mail Website
Guest Editor
Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland
Interests: biology of bacteriophages; biodiversity of bacteriophages; regulation of bacteriophage development; regulation of phage gene expression; control of phage DNA replication; phage therapy; phages bearing genes of toxins; bacteriophage genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Exploring the enzymes essential for key bacterial functions presents an opportunity to develop innovative strategies for combating bacterial infections. Enzymes involved in cell wall biosynthesis are critical for maintaining bacterial cell structure and integrity. By inhibiting these enzymes, it is possible to disrupt cell wall formation, rendering bacteria susceptible to immune responses or other treatments. Similarly, enzymes involved in DNA replication are essential for bacterial proliferation. Targeting these enzymes can impede DNA synthesis and disrupt bacterial replication, potentially curbing infection progression. Bacteria often harbor metabolic pathways distinct from those of human cells, presenting opportunities that allow bacterial enzymes to be selectively targeted without affecting host cells. Moreover, by focusing on enzymes pivotal for bacterial survival, such as carbonic anhydrase, novel therapeutic strategies can be designed to offer effective treatment options for bacterial infections. Thus, the process of understanding and targeting specific bacterial enzymes represents a promising avenue for the development of novel antibacterial agents, as well as for tackling infections and combating antibiotic resistance.

Prof. Dr. Clemente Capasso
Prof. Dr. Alicja Wegrzyn
Guest Editors

Manuscript Submission Information

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Keywords

  • enzymes
  • cell wall biosynthesis
  • DNA replication
  • metabolic pathway
  • vital bacterial function
  • enzyme inhibition
  • antibacterial agents
  • antibiotic resistance

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Published Papers (4 papers)

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Research

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14 pages, 2038 KiB  
Article
Sulfonamide-Based Inhibition of the β-Carbonic Anhydrase from A. baumannii, a Multidrug-Resistant Bacterium
by Viviana De Luca, Simone Giovannuzzi, Clemente Capasso and Claudiu T. Supuran
Int. J. Mol. Sci. 2024, 25(22), 12291; https://doi.org/10.3390/ijms252212291 - 15 Nov 2024
Cited by 2 | Viewed by 1246
Abstract
Acinetobacter baumannii is a Gram-negative opportunistic pathogen responsible for severe hospital-associated infections. Owing to its ability to develop resistance to a wide range of antibiotics, novel therapeutic strategies are urgently needed. One promising approach is to target bacterial carbonic anhydrases (CAs; EC 4.2.1.1), [...] Read more.
Acinetobacter baumannii is a Gram-negative opportunistic pathogen responsible for severe hospital-associated infections. Owing to its ability to develop resistance to a wide range of antibiotics, novel therapeutic strategies are urgently needed. One promising approach is to target bacterial carbonic anhydrases (CAs; EC 4.2.1.1), which are enzymes critical for various metabolic processes. The genome of A. baumannii encodes a β-CA (βAbauCA), which is essential for producing bicarbonate ions required in the early stages of uridine triphosphate (UTP) synthesis, a precursor for the synthesis of peptidoglycans, which are vital components of the bacterial cell wall. This study aimed to inhibit βAbauCA in vitro, with the potential to impair the vitality of the pathogen in vivo. We conducted sequence and structural analyses of βAbauCA to explore its differences from those of human CAs. Additionally, kinetic and inhibition studies were performed to investigate the catalytic efficiency of βAbauCAβ and its interactions with sulfonamides and their bioisosteres, classical CA inhibitors. Our results showed that βAbauCA has a turnover rate higher than that of hCA I but lower than that of hCA II and displays distinct inhibition profiles compared to human α-CAs. Based on the obtained data, there are notable differences between the inhibition profiles of the human isoforms CA I and CA II and bacterial βAbauCA. This could open the door to designing inhibitors that selectively target bacterial β-CAs without affecting human α-CAs, as well as offer a novel strategy to weaken A. baumannii and other multidrug-resistant pathogens. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”)
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13 pages, 2862 KiB  
Article
Benzothiadiazinone-1,1-Dioxide Carbonic Anhydrase Inhibitors Suppress the Growth of Drug-Resistant Mycobacterium tuberculosis Strains
by Silvia Bua, Alessandro Bonardi, Georgiana Ramona Mük, Alessio Nocentini, Paola Gratteri and Claudiu T. Supuran
Int. J. Mol. Sci. 2024, 25(5), 2584; https://doi.org/10.3390/ijms25052584 - 23 Feb 2024
Cited by 2 | Viewed by 1776
Abstract
2H-Benzo[e][1,2,4]thiadiazin-3(4H)-one 1,1-dioxide (BTD) based carbonic anhydrase (CA) inhibitors are here explored as new anti-mycobacterial agents. The chemical features of BTD derivatives meet the criteria for a potent inhibition of β-class CA isozymes. BTD derivatives show chemical features meeting the [...] Read more.
2H-Benzo[e][1,2,4]thiadiazin-3(4H)-one 1,1-dioxide (BTD) based carbonic anhydrase (CA) inhibitors are here explored as new anti-mycobacterial agents. The chemical features of BTD derivatives meet the criteria for a potent inhibition of β-class CA isozymes. BTD derivatives show chemical features meeting the criteria for a potent inhibition of β-class CA isozymes. Specifically, three β-CAs (MtCA1, MtCA2, and MtCA3) were identified in Mycobacterium tuberculosis and their inhibition was shown to exert an antitubercular action. BTDs derivatives 2a-q effectively inhibited the mycobacterial CAs, especially MtCA2 and MtCA3, with Ki values up to a low nanomolar range (MtCA3, Ki = 15.1–2250 nM; MtCA2, Ki = 38.1–4480 nM) and with a significant selectivity ratio over the off-target human CAs I and II. A computational study was conducted to elucidate the compound structure-activity relationship. Importantly, the most potent MtCA inhibitors demonstrated efficacy in inhibiting the growth of M. tuberculosis strains resistant to both rifampicin and isoniazid—standard reference drugs for Tuberculosis treatment. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”)
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Review

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19 pages, 3255 KiB  
Review
Insights into Active Site Cysteine Residues in Mycobacterium tuberculosis Enzymes: Potential Targets for Anti-Tuberculosis Intervention
by Abayomi S. Faponle, James W. Gauld and Sam P. de Visser
Int. J. Mol. Sci. 2025, 26(8), 3845; https://doi.org/10.3390/ijms26083845 - 18 Apr 2025
Viewed by 395
Abstract
Cysteine, a semi-essential amino acid, is found in the active site of a number of vital enzymes of the bacterium Mycobacterium tuberculosis (Mtb) and in particular those that relate to its survival, adaptability and pathogenicity. Mtb is the causative agent of [...] Read more.
Cysteine, a semi-essential amino acid, is found in the active site of a number of vital enzymes of the bacterium Mycobacterium tuberculosis (Mtb) and in particular those that relate to its survival, adaptability and pathogenicity. Mtb is the causative agent of tuberculosis, an infectious disease that affects millions of people globally. Common anti-tuberculosis targets are focused on immobilizing a vital cysteine amino acid residue in enzymes that plays critical roles in redox and non-redox catalysis, the modulation of the protein, enzyme activity, protein structure and folding, metal coordination, and posttranslational modifications of newly synthesized proteins. This review examines five Mtb enzymes that contain an active site cysteine residue and are considered as key targets for anti-tuberculosis drugs, namely alkyl hydroperoxide reductase (AhpC), dihydrolipoamide dehydrogenase (Lpd), aldehyde dehydrogenase (ALDH), methionine aminopeptidase (MetAP) and cytochromes P450. AhpC and Lpd protect Mtb against oxidative and nitrosative stress, whereas AhpC neutralizes peroxide/peroxynitrite substrates with two active site cysteine residues. Mtb ALDH detoxifies aldehydes, using a nucleophilic active site cysteine to form an oxyanion thiohemiacetal intermediate, whereas MtMetAP’s active site cysteine is essential for substrate recognition. The P450s metabolize various endogenous and exogenous compounds. Targeting these critical active site cysteine residues could disrupt enzyme functions, presenting a promising avenue for developing anti-mycobacterial agents. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”)
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34 pages, 5499 KiB  
Review
Targeting Siderophore Biosynthesis to Thwart Microbial Growth
by Beatriz M. Rocha, Eugénia Pinto, Emília Sousa and Diana I. S. P. Resende
Int. J. Mol. Sci. 2025, 26(8), 3611; https://doi.org/10.3390/ijms26083611 - 11 Apr 2025
Viewed by 494
Abstract
The growing threat of antibiotic resistance has made treating bacterial and fungal infections increasingly difficult. With the discovery of new antibiotics slowing down, alternative strategies are urgently needed. Siderophores, small iron-chelating molecules produced by microorganisms, play a crucial role in iron acquisition and [...] Read more.
The growing threat of antibiotic resistance has made treating bacterial and fungal infections increasingly difficult. With the discovery of new antibiotics slowing down, alternative strategies are urgently needed. Siderophores, small iron-chelating molecules produced by microorganisms, play a crucial role in iron acquisition and serve as virulence factors in many pathogens. Because iron is essential for microbial survival, targeting siderophore biosynthesis and transport presents a promising approach to combating drug-resistant infections. This review explores the key genetic and biochemical mechanisms involved in siderophore production, emphasizing potential drug targets within these pathways. Three major biosynthetic routes are examined: nonribosomal peptide synthetase (NRPS)-dependent, polyketide synthase (PKS)-based, and NRPS-independent (NIS) pathways. Additionally, microbial iron uptake mechanisms and membrane-associated transport systems are discussed, providing insights into their role in sustaining pathogenic growth. Recent advances in inhibitor development have shown that blocking critical enzymes in siderophore biosynthesis can effectively impair microbial growth. By disrupting these pathways, new antimicrobial strategies can be developed, offering alternatives to traditional antibiotics and potentially reducing the risk of resistance. A deeper understanding of siderophore biosynthesis and its regulation not only reveals fundamental microbial processes but also provides a foundation for designing targeted therapeutics. Leveraging these insights could lead to novel drugs that overcome antibiotic resistance, offering new hope in the fight against persistent infections. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: “Bacterial Enzymes as Targets”)
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