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Latest Advances in Enzymology
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Latest Advances in Enzymology

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

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 6753

Special Issue Editor

Dr. Marko Novinec

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
Interests: proteins; protein expression; enzymes; protein biochemistry; protein structure; protein-protein interaction; enzyme activity

Special Issue Information

Dear Colleagues,

We are now entering the third decade of the 21st century, and, especially in recent years, the achievements made by scientists have been exceptional, leading to major advancements in the rapidly growing field of enzymology. Enzymes play pivotal roles in biological systems, and their dysregulation is associated with many diseases, qualifying them as drug targets. In addition, enzymes are indispensable tools in biotechnology and other industries. Many enzymes have been artificially improved or even created by protein engineering for this purpose. Functional and structural studies are essential for the characterization of natural and engineered enzymes, with a particular focus on their kinetic properties. Apart from the development of appropriate models and software for their interpretation, experimental methods and suitable reagents for precise experimental characterization must be developed.

IJMS has organized a series of Special Issues to highlight the latest advancements in science in order to be at the forefront of science in different fields of research. This editorial initiative of particular relevance, led by Prof. Dr. Marko Novinec of the Enzymology section, is focused on new insights, novel developments, current challenges, latest discoveries, recent advances, and future perspectives in the field of enzymology.

The present Special Issue, entitled “Latest advances in Enzymology”, aims to present recent research developments to the wider community involved in this field. We welcome contributions in the field of enzymology, which is at the intersection of physics, biology, chemistry, and/or chemical engineering.

Dr. Marko Novinec
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

  • microbial enzymes
  • biosynthesis and bioengineering
  • drug development and targets
  • enzymes in the environment
  • engineered enzymes
  • enzymes in agri-food
  • enzymatic formulations
  • enzyme engineering
  • enzyme kinetics
  • enzymes in biomedical sciences
  • green chemistry/technology
  • glycans
  • molecular evolution
  • nanocatalyst and nanotechnology
  • pharma enzymes
  • recombinant proteins production and purification
  • system and synthetic biology

Published Papers (4 papers)

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Research

14 pages, 6790 KiB  
Article
The Effect of 8,5′-Cyclo 2′-deoxyadenosine on the Activity of 10-23 DNAzyme: Experimental and Theoretical Study
by Marcin Cieślak and Bolesław T. Karwowski
Int. J. Mol. Sci. 2024, 25(5), 2519; https://doi.org/10.3390/ijms25052519 - 21 Feb 2024
Viewed by 452
Abstract
The in vivo effectiveness of DNAzymes 10-23 (Dz10-23) is limited due to the low concentration of divalent cations. Modifications of the catalytic loop are being sought to increase the activity of Dz10-23 in physiological conditions. We investigated the effect of 5′S or 5′R [...] Read more.
The in vivo effectiveness of DNAzymes 10-23 (Dz10-23) is limited due to the low concentration of divalent cations. Modifications of the catalytic loop are being sought to increase the activity of Dz10-23 in physiological conditions. We investigated the effect of 5′S or 5′R 5′,8-cyclo-2′deoxyadenosine (cdA) on the activity of Dz10-23. The activity of Dz10-23 was measured in a cleavage assay using radiolabeled RNA. The Density Functional Tight Binding methodology with the self-consistent redistribution of Mulliken charge modification was used to explain different activities of DNAzymes. The substitution of 2′-deoxyadenosine with cdA in the catalytic loop decreased the activity of DNAzymes. Inhibition was dependent on the position of cdA and its absolute configuration. The order of activity of DNAzymes was as follows: wt-Dz > ScdA5-Dz ≈ RcdA15-Dz ≈ ScdA15-Dz > RcdA5-Dz. Theoretical studies revealed that the distance between phosphate groups at position 5 in RcdA5-Dz was significantly increased compared to wt-Dz, while the distance between O4 of dT4 and nonbonding oxygen of PO2 attached to 3′O of dG2 was much shorter. The strong inhibitory effect of RcdA5 may result from hampering the flexibility of the catalytic loop (increased rigidity), which is required for the proper positioning of Me2+ and optimal activity. Full article
(This article belongs to the Special Issue Latest Advances in Enzymology)
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15 pages, 2221 KiB  
Article
Enzymatic Synthesis of 2-Chloropurine Arabinonucleosides with Chiral Amino Acid Amides at the C6 Position and an Evaluation of Antiproliferative Activity In Vitro
by Barbara Z. Eletskaya, Maria Ya. Berzina, Ilya V. Fateev, Alexei L. Kayushin, Elena V. Dorofeeva, Olga I. Lutonina, Ekaterina A. Zorina, Konstantin V. Antonov, Alexander S. Paramonov, Inessa S. Muzyka, Olga S. Zhukova, Mikhail V. Kiselevskiy, Anatoly I. Miroshnikov, Roman S. Esipov and Irina D. Konstantinova
Int. J. Mol. Sci. 2023, 24(7), 6223; https://doi.org/10.3390/ijms24076223 - 25 Mar 2023
Cited by 2 | Viewed by 1572
Abstract
A number of purine arabinosides containing chiral amino acid amides at the C6 position of the purine were synthesized using a transglycosylation reaction with recombinant E. coli nucleoside phosphorylases. Arsenolysis of 2-chloropurine ribosides with chiral amino acid amides at C6 was used for [...] Read more.
A number of purine arabinosides containing chiral amino acid amides at the C6 position of the purine were synthesized using a transglycosylation reaction with recombinant E. coli nucleoside phosphorylases. Arsenolysis of 2-chloropurine ribosides with chiral amino acid amides at C6 was used for the enzymatic synthesis, and the reaction equilibrium shifted towards the synthesis of arabinonucleosides. The synthesized nucleosides were shown to be resistant to the action of E. coli adenosine deaminase. The antiproliferative activity of the synthesized nucleosides was studied on human acute myeloid leukemia cell line U937. Among all the compounds, the serine derivative exhibited an activity level (IC50 = 16 μM) close to that of Nelarabine (IC50 = 3 μM) and was evaluated as active. Full article
(This article belongs to the Special Issue Latest Advances in Enzymology)
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20 pages, 9023 KiB  
Article
A Key Role in Catalysis and Enzyme Thermostability of a Conserved Helix H5 Motif of Human Glutathione Transferase A1-1
by Evangelia G. Chronopoulou, Lana Mutabdzija, Nirmal Poudel, Anastassios C. Papageorgiou and Nikolaos E. Labrou
Int. J. Mol. Sci. 2023, 24(4), 3700; https://doi.org/10.3390/ijms24043700 - 12 Feb 2023
Cited by 1 | Viewed by 1368
Abstract
Glutathione transferases (GSTs) are promiscuous enzymes whose main function is the detoxification of electrophilic compounds. These enzymes are characterized by structural modularity that underpins their exploitation as dynamic scaffolds for engineering enzyme variants, with customized catalytic and structural properties. In the present work, [...] Read more.
Glutathione transferases (GSTs) are promiscuous enzymes whose main function is the detoxification of electrophilic compounds. These enzymes are characterized by structural modularity that underpins their exploitation as dynamic scaffolds for engineering enzyme variants, with customized catalytic and structural properties. In the present work, multiple sequence alignment of the alpha class GSTs allowed the identification of three conserved residues (E137, K141, and S142) at α-helix 5 (H5). A motif-directed redesign of the human glutathione transferase A1-1 (hGSTA1-1) was performed through site-directed mutagenesis at these sites, creating two single- and two double-point mutants (E137H, K141H, K141H/S142H, and E137H/K141H). The results showed that all the enzyme variants displayed enhanced catalytic activity compared to the wild-type enzyme hGSTA1-1, while the double mutant hGSTA1-K141H/S142H also showed improved thermal stability. X-ray crystallographic analysis revealed the molecular basis of the effects of double mutations on enzyme stability and catalysis. The biochemical and structural analysis presented here will contribute to a deeper understanding of the structure and function of alpha class GSTs. Full article
(This article belongs to the Special Issue Latest Advances in Enzymology)
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13 pages, 2301 KiB  
Article
Kinetic Characterization of Cerium and Gallium Ions as Inhibitors of Cysteine Cathepsins L, K, and S
by Marko Novinec, Primož Bembič, Milica Janković, Marija Kisilak, Jakob Kljun and Iztok Turel
Int. J. Mol. Sci. 2022, 23(16), 8993; https://doi.org/10.3390/ijms23168993 - 12 Aug 2022
Cited by 2 | Viewed by 1393
Abstract
Heavy metal ions can disrupt biological functions via multiple molecular mechanisms, including inhibition of enzymes. We investigate the interactions of human papain-like cysteine endopeptidases cathepsins L, K, and S with gallium and cerium ions, which are associated with medical applications. We compare these [...] Read more.
Heavy metal ions can disrupt biological functions via multiple molecular mechanisms, including inhibition of enzymes. We investigate the interactions of human papain-like cysteine endopeptidases cathepsins L, K, and S with gallium and cerium ions, which are associated with medical applications. We compare these results with zinc and lead, which are known to inhibit thiol enzymes. We show that Ga3+, Ce3+, and Ce4+ ions inhibit all tested peptidases with inhibition constants in the low micromolar range (between 0.5 µM and 10 µM) which is comparable to Zn2+ ions, whereas inhibition constants of Pb2+ ions are one order of magnitude higher (30 µM to 150 µM). All tested ions are linear specific inhibitors of cathepsin L, but cathepsins K and S are inhibited by Ga3+, Ce3+, and Ce4+ ions via hyperbolic inhibition mechanisms. This indicates a mode of interaction different from that of Zn2+ and Pb2+ ions, which act as linear specific inhibitors of all peptidases. All ions also inhibit the degradation of insoluble elastin, which is a common target of these peptidases in various inflammatory diseases. Our results suggest that these ions and their compounds have the potential to be used as cysteine cathepsin inhibitors in vitro and possibly in vivo. Full article
(This article belongs to the Special Issue Latest Advances in Enzymology)
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