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Chemical Biology in Asia

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

Deadline for manuscript submissions: 31 October 2024 | Viewed by 2822

Special Issue Editors


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Guest Editor
Organization for Research and Development of Innovative Science and Technology (ORDIST), Kansai University, Suita, Osaka 564-8680, Japan
Interests: nucleic acid chemistry; DNA nanotechnology; supramolecular chemistry; molecular machines; molecular robotics; molecular technology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
Interests: G-quadruplex; i-motif; molecular crowding; phase separation; thermodynamics; kinetics; aptamer; ligand
Special Issues, Collections and Topics in MDPI journals
School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
Interests: DNA; oligodeoxynucleotide; degrader technologies

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Guest Editor
State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
Interests: protein–protein interaction; small-molecule inhibitors; kinase inhibitors; molecular glues; immunomodulators; anticancer therapeutics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Chemical Biology stands as a dynamic hub where the frontiers of chemistry and biology converge to unveil novel insights and innovations. Across the diverse landscapes of Asia, researchers passionately explore the intricate dance between molecules and living systems.

Asian scholars and researchers are actively engaged in unraveling the intricacies of biological systems from chemical perspectives, fostering a rich tapestry of knowledge. The region's contribution extends from elucidating molecular mechanisms to designing novel compounds with therapeutic potential.

The key areas of focus include drug discovery, bioorganic chemistry, enzymology, synthetic biology, and the development of cutting-edge analytical tools. Researchers in Asia are at the forefront of exploring chemical solutions to address pressing global challenges, making substantial strides in both fundamental understanding and practical applications.

The Special Issue facilitates international partnerships, enabling the exchange of ideas and methodologies. This initiative not only enhances the scientific landscape but also nurtures a diverse community of scientists dedicated to pushing the boundaries of knowledge.

Prof. Dr. Akinori Kuzuya
Prof. Dr. Daisuke Miyoshi
Dr. Li Wu
Prof. Dr. Yujun Zhao
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

  • chemical biology
  • drug discovery
  • bioorganic chemistry
  • enzymology
  • synthetic biology
  • analytical tools

Published Papers (5 papers)

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Research

13 pages, 3227 KiB  
Article
Development of a Fluorescent Assay and Imidazole-Containing Inhibitors by Targeting SARS-CoV-2 Nsp13 Helicase
by Chuang Zhang, Junhui Yu, Mingzhenlong Deng, Qingqing Zhang, Fei Jin, Lei Chen, Yan Li and Bin He
Molecules 2024, 29(10), 2301; https://doi.org/10.3390/molecules29102301 - 14 May 2024
Viewed by 247
Abstract
Nsp13, a non-structural protein belonging to the coronavirus family 1B (SF1B) helicase, exhibits 5′–3′ polarity-dependent DNA or RNA unwinding using NTPs. Crucially, it serves as a key component of the viral replication–transcription complex (RTC), playing an indispensable role in the coronavirus life cycle [...] Read more.
Nsp13, a non-structural protein belonging to the coronavirus family 1B (SF1B) helicase, exhibits 5′–3′ polarity-dependent DNA or RNA unwinding using NTPs. Crucially, it serves as a key component of the viral replication–transcription complex (RTC), playing an indispensable role in the coronavirus life cycle and thereby making it a promising target for broad-spectrum antiviral therapies. The imidazole scaffold, known for its antiviral potential, has been proposed as a potential scaffold. In this study, a fluorescence-based assay was designed by labeling dsDNA substrates with a commercial fluorophore and monitoring signal changes upon Nsp13 helicase activity. Optimization and high-throughput screening validated the feasibility of this approach. In accordance with the structural characteristics of ADP, we employed a structural-based design strategy to synthesize three classes of imidazole-based compounds through substitution reaction. Through in vitro activity research, pharmacokinetic parameter analysis, and molecular docking simulation, we identified compounds A16 (IC50 = 1.25 μM) and B3 (IC50 = 0.98 μM) as potential lead antiviral compounds for further targeted drug research. Full article
(This article belongs to the Special Issue Chemical Biology in Asia)
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11 pages, 3131 KiB  
Article
Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations
by Xuan Ding, Chao Xu, Bin Zheng, Hanyang Yu and Peng Zheng
Molecules 2024, 29(10), 2215; https://doi.org/10.3390/molecules29102215 - 9 May 2024
Viewed by 488
Abstract
The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our [...] Read more.
The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer–RBD interaction, demonstrating the aptamer’s potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer–RBD for possible antiviral therapy but also introduces a computational method to study aptamer–protein interactions. Full article
(This article belongs to the Special Issue Chemical Biology in Asia)
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13 pages, 1875 KiB  
Article
Probing the Immunoreceptor Tyrosine-Based Inhibition Motif Interaction Protein Partners with Proteomics
by Yujun Gao, Shu Xing and Lianghai Hu
Molecules 2024, 29(9), 1977; https://doi.org/10.3390/molecules29091977 - 25 Apr 2024
Viewed by 337
Abstract
Phosphorylation of tyrosine is the basic mode of protein function and signal transduction in organisms. This process is regulated by protein tyrosine kinases (PTKs) and protein tyrosinases (PTPs). Immunoreceptor tyrosine-based inhibition motif (ITIM) has been considered as regulating the PTP activity through the [...] Read more.
Phosphorylation of tyrosine is the basic mode of protein function and signal transduction in organisms. This process is regulated by protein tyrosine kinases (PTKs) and protein tyrosinases (PTPs). Immunoreceptor tyrosine-based inhibition motif (ITIM) has been considered as regulating the PTP activity through the interaction with the partner proteins in the cell signal pathway. The ITIM sequences need to be phosphorylated first to active the downstream signaling proteins. To explore potential regulatory mechanisms, the ITIM sequences of two transmembrane immunoglobulin proteins, myelin P0 protein-related protein (PZR) and programmed death 1 (PD-1), were analyzed to investigate their interaction with proteins involved in regulatory pathways. We discovered that phosphorylated ITIM sequences can selectively interact with the tyrosine phosphatase SHP2. Specifically, PZR-N-ITIM (pY) may be critical in the interaction between the ITIM and SH2 domains of SHP2, while PD1-C-ITSM (pY) may play a key role in the interaction between the ITIM and SH2 domains of SHP2. Quite a few proteins were identified containing the SH2 domain, exhibiting phosphorylation-mediated interaction with PZR-ITIM. In this study, 14 proteins with SH2 structural domains were identified by GO analysis on 339 proteins associated to the affinity pull-down of PZR-N-ITIM (pY). Through the SH2 domains, these proteins may interact with PZR-ITIM in a phosphorylation-dependent manner. Full article
(This article belongs to the Special Issue Chemical Biology in Asia)
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22 pages, 2124 KiB  
Article
Modeling Studies of the Mechanism of Context-Dependent Bidirectional Movements of Kinesin-14 Motors
by Ping Xie
Molecules 2024, 29(8), 1792; https://doi.org/10.3390/molecules29081792 - 15 Apr 2024
Viewed by 507
Abstract
Kinesin-14s, a subfamily of the large superfamily of kinesin motor proteins, function mainly in spindle assembly and maintenance during mitosis and meiosis. KlpA from Aspergillus nidulans and GiKIN14a from Giardia intestinalis are two types of kinesin-14s. Available experimental results puzzlingly showed that while [...] Read more.
Kinesin-14s, a subfamily of the large superfamily of kinesin motor proteins, function mainly in spindle assembly and maintenance during mitosis and meiosis. KlpA from Aspergillus nidulans and GiKIN14a from Giardia intestinalis are two types of kinesin-14s. Available experimental results puzzlingly showed that while KlpA moves preferentially toward the minus end in microtubule-gliding setups and inside parallel microtubule overlaps, it moves preferentially toward the plus end on single microtubules. More puzzlingly, the insertion of an extra polypeptide linker in the central region of the neck stalk switches the motility direction of KlpA on single microtubules to the minus end. Prior experimental results showed that GiKIN14a moves preferentially toward the minus end on single microtubules in either tailless or full-length forms. The tail not only greatly enhances the processivity but also accelerates the ATPase rate and velocity of GiKIN14a. The insertion of an extra polypeptide linker in the central region of the neck stalk reduces the ATPase rate of GiKIN14a. However, the underlying mechanism of these puzzling dynamical features for KlpA and GiKIN14a is unclear. Here, to understand this mechanism, the dynamics of KlpA and GiKIN14a were studied theoretically on the basis of the proposed model, incorporating potential changes between the kinesin head and microtubule, as well as the potential between the tail and microtubule. The theoretical results quantitatively explain the available experimental results and provide predicted results. It was found that the elasticity of the neck stalk determines the directionality of KlpA on single microtubules and affects the ATPase rate and velocity of GiKIN14a on single microtubules. Full article
(This article belongs to the Special Issue Chemical Biology in Asia)
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20 pages, 4503 KiB  
Article
The Evolution and Application of a Novel DNA Aptamer Targeting Bone Morphogenetic Protein 2 for Bone Regeneration
by Mengping Liu, Andrew B. Kinghorn, Lin Wang, Soubhagya K. Bhuyan, Simon Chi-Chin Shiu and Julian A. Tanner
Molecules 2024, 29(6), 1243; https://doi.org/10.3390/molecules29061243 - 11 Mar 2024
Viewed by 685
Abstract
Recombinant human bone morphogenetic protein 2 (rhBMP-2) is an FDA-approved growth factor for bone regeneration and repair in medical practice. The therapeutic effects of rhBMP-2 may be enhanced through specific binding to extracellular matrix (ECM)-like scaffolds. Here, we report the selection of a [...] Read more.
Recombinant human bone morphogenetic protein 2 (rhBMP-2) is an FDA-approved growth factor for bone regeneration and repair in medical practice. The therapeutic effects of rhBMP-2 may be enhanced through specific binding to extracellular matrix (ECM)-like scaffolds. Here, we report the selection of a novel rhBMP-2-specific DNA aptamer, functionalization of the aptamer in an ECM-like scaffold, and its application in a cellular context. A DNA aptamer BA1 was evolved and shown to have high affinity and specificity to rhBMP-2. A molecular docking model demonstrated that BA1 was probably bound to rhBMP-2 at its heparin-binding domain, as verified with experimental competitive binding assays. The BA1 aptamer was used to functionalize a type I collagen scaffold, and fraction ratios were optimized to mimic the natural ECM. Studies in the myoblast cell model C2C12 showed that the aptamer-enhanced scaffold could specifically augment the osteo-inductive function of rhBMP-2 in vitro. This aptamer-functionalized scaffold may have value in enhancing rhBMP-2-mediated bone regeneration. Full article
(This article belongs to the Special Issue Chemical Biology in Asia)
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