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Bioorganic Chemistry in Asia
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Bioorganic Chemistry in Asia

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 2941

Special Issue Editors

Prof. Dr. Xingyue Ji

E-Mail Website
Guest Editor
Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou 215021, China
Interests: gasotransmitter prodrugs; drug delivery; biorthogonal prodrug; antiviral drug development; host targeting antivirals
Special Issues, Collections and Topics in MDPI journals
Dr. Situ Xue

E-Mail Website
Guest Editor
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100850, China
Interests: new tumor targets; anti-aging drug; pharmacochemical biology; hepatocellular carcinoma drug; host targeting antivirals

Special Issue Information

Dear Colleagues,

Bioorganic chemistry is emerging as a new field at the interface between chemistry and biology. As an interdisciplinary science, its scope covers multiple aspects, including enzyme catalysis, biotransformation and enzyme inhibition, nucleic acid chemistry, medicinal chemistry, natural product chemistry, biological probes, and bioorthogonal chemistry, among others. In recent years, some strategies in bioorganic chemistry have substantially facilitated the development of precision medicine, providing a more precise approach to the prevention, diagnosis, as well as treatment of human disease. In addition, some new concepts have also been conceived to tackle the undruggable targets (i.e., proteolysis-targeting chimeric molecules), with encouraging clinical results. In this Special Issue, we intend to gather significant studies in bioorganic chemistry and we welcome any topic as long as it falls under the field of bioorganic chemistry. We invite authors in Asia as well as other regions to contribute, and full articles, short communications, and reviews are all welcomed.

Prof. Dr. Xingyue Ji
Dr. Situ Xue
Guest Editors

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

  • bioorganic chemistry
  • precision medicine
  • drug development
  • diagnostic probe
  • drug synthesis
  • mechanism of action

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Published Papers (2 papers)

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Research

16 pages, 5121 KiB  
Article
Mutational Analysis of Substrate Recognition in Trypsin-like Protease Cocoonase: Protein Memory Induced by Alterations in Substrate-Binding Site
by Nana Sakata, Shigeru Shimamoto, Yuri Murakami, Orika Ashida, Toshiki Takei, Mitsuhiro Miyazawa and Yuji Hidaka
Molecules 2024, 29(22), 5476; https://doi.org/10.3390/molecules29225476 - 20 Nov 2024
Viewed by 683
Abstract
To investigate the substrate recognition mechanism of trypsin-like protease cocoonase (CCN), mutational analyses were conducted at key substrate recognition sites, Asp187 and Ser188, and their effects on substrate specificity and enzymatic activity were evaluated. Mutants with the Asp187 substitution exhibited a significant reduction [...] Read more.
To investigate the substrate recognition mechanism of trypsin-like protease cocoonase (CCN), mutational analyses were conducted at key substrate recognition sites, Asp187 and Ser188, and their effects on substrate specificity and enzymatic activity were evaluated. Mutants with the Asp187 substitution exhibited a significant reduction in catalytic activity compared with the wild-type enzyme, whereas the Ser188 mutants displayed a comparatively minor effect on activity. This indicates that Asp187 plays a crucial role in catalytic function, whereas Ser188 serves a complementary role in substrate recognition. Interestingly, the substitution of the Asp187 to Glu or Ser caused novel substrate specificities, resulting in the recognition of Orn and His residues. In addition, when Asp187 and Ser188 were substituted with acidic residues (Glu or Asp), both the precursor proCCN and mature CCN proteins retained highly similar secondary and tertiary structures. This reveals that the structural characteristics of precursor proteins are maintained in the mature proteins, potentially influencing substrate recognition and catalytic function. These findings suggest that the pro-regions of these mutants interact much more tightly with the mature enzyme than in the wild-type CCN. These results provide fruitful insights into the structural determinants governing substrate recognition in enzyme variants. Full article
(This article belongs to the Special Issue Bioorganic Chemistry in Asia)
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13 pages, 3959 KiB  
Article
The Programmable Catalytic Core of 8-17 DNAzymes
by Fumei Zhang, Weiguo Shi, Lei Guo, Shihui Liu and Junlin He
Molecules 2024, 29(11), 2420; https://doi.org/10.3390/molecules29112420 - 21 May 2024
Viewed by 1599
Abstract
8-17 DNAzymes (8-17, 17E, Mg5, and 17EV1) are in vitro-selected catalytic DNA molecules that are capable of cleaving complementary RNAs. The conserved residues in their similar catalytic cores, together with the metal ions, were suggested to contribute to the catalytic reaction. Based on [...] Read more.
8-17 DNAzymes (8-17, 17E, Mg5, and 17EV1) are in vitro-selected catalytic DNA molecules that are capable of cleaving complementary RNAs. The conserved residues in their similar catalytic cores, together with the metal ions, were suggested to contribute to the catalytic reaction. Based on the contribution of the less conserved residues in the bulge loop residues (W12, A15, A15.0) and the internal stem, new catalytic cores of 8-17 DNAzymes were programmed. The internal stem CTC-GAG seems to be more favorable for the DNAzymes than CCG-GGC, while an extra W12.0 led to a significant loss of activity of DNAzymes, which is contrary to the positive effect of A15.0, by which a new active DNAzyme 17EM was derived. It conducts a faster reaction than 17E. It is most active in the presence of Pb2+, with the metal ion preference of Pb2+ >> Zn2+ > Mn2+ > Ca2+ ≈ Mg2+. In the Pb2+ and Zn2+-mediated reactions of 17EM and 17E, the same Na+- and pH dependence were also observed as what was observed for 17E and other 8-17 DNAzymes. Therefore, 17EM is another member of the 8-17 DNAzymes, and it could be applied as a potential biosensor for RNA and metal ions. Full article
(This article belongs to the Special Issue Bioorganic Chemistry in Asia)
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