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Chemical Biology Research in Asia
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Chemical Biology Research in Asia

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

Deadline for manuscript submissions: closed (1 May 2022) | Viewed by 17110

Special Issue Editors

Prof. Dr. Minoru Ueda

E-Mail Website
Guest Editor
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
Interests: chemical biology; natural products; chemical probe; target ID of bioactive natural products; plant specialized metabolites; chemical communication in plants
Prof. Dr. Seung Bum Park

E-Mail Website
Guest Editor
Department of Chemistry, Seoul National University, Seoul, Republic of Korea
Interests: chemical biology; molecular diversity; drug discovery; bioimaging and high throughput/high content screening; target identification/validation; chemical probes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jianhua Qi

E-Mail Website
Guest Editor
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
Interests: bioactive natural products; chemical biology; mechanism of bioactive natural products; signalling molecule of microorganism; metabolites of microorganism

Special Issue Information

Dear Colleagues,

Chemical biology is an interdisciplinary field of study that is often defined as "chemistry-initiated biology." As biological processes all stem from chemical events, it is possible to use chemical approaches to understand and, in some cases, manipulate biological events. This rapidly growing field of study will continue to introduce new avenues for future drug discovery and novel medical applications. The current Special Issue focuses on basic aspects of chemical biology: the creation and application of “chemical probes” and “chemical tools” which allow us to analyze and understand important biological events and disease states, paving the way for medical and diagnostic innovations. This Special Issue will be composed of communications, full articles, and focused reviews containing recent advances in chemical biology in Asia.

Prof. Dr. Minoru Ueda
Prof. Dr. Seung Bum Park
Prof. Dr. Jianhua Qi
Guest Editors

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Keywords

  • chemical biology
  • chemical probes
  • natural products
  • phenotypic screening
  • target identification/validation
  • bioactive metabolites
  • signaling molecules

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Published Papers (6 papers)

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Research

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19 pages, 4290 KiB  
Article
Co-Combination of Pregabalin and Withania coagulans-Extract-Loaded Topical Gel Alleviates Allodynia and Hyperalgesia in the Chronic Sciatic Nerve Constriction Injury for Neuropathic Pain in Animal Model
by Anam Asghar, Muhammad Naeem Aamir, Fatima Akbar Sheikh, Naveed Ahmad, Mervat A. Elsherif and Syed Nasir Abbas Bukhari
Molecules 2022, 27(14), 4433; https://doi.org/10.3390/molecules27144433 - 11 Jul 2022
Cited by 7 | Viewed by 2502
Abstract
The current study reports the fabrication of co-combination gel using Pregabalin and Withania coagulans fruit extract to validate its effectiveness for neuropathic pain in chronic constriction injury (CCI) rat models. Three topical gels were prepared using Carbopol 934 through a pseudo-ternary phase diagram [...] Read more.
The current study reports the fabrication of co-combination gel using Pregabalin and Withania coagulans fruit extract to validate its effectiveness for neuropathic pain in chronic constriction injury (CCI) rat models. Three topical gels were prepared using Carbopol 934 through a pseudo-ternary phase diagram incorporating the Pregabalin (2.5%), Withania coagulans extract (2%), and co-combination of both Pregabalin (2.5%) and Withania coagulans extract (2%). Gels were characterized. FTIR showed a successful polymeric network of the gel without any interaction. The drug distribution at the molecular level was confirmed by XRD. The AFM images topographically indicated the rough surface of gels with a size range from 0.25 to 330 nm. DSC showed the disappearance of sharp peaks of the drug and extract, showing successful incorporation into the polymeric network of gels. The in vitro drug release of co-combination gel was 73% over 48 h. The mechanism of drug release by combination gel was Higuchi+ fickian with values of n (0.282) and R2 (0.947). An in vivo study for pain assessment via four methods: (i) heat hyperalgesia, (ii) cold allodynia, (iii) mechano-hyperalgesia, and (iv) dynamic mechano-allodynia, confirmed that topical treatment with co-combination gel reduced the pain significantly as indicated by the p value: R1 (p < 0.001), R2 (p < 0.001), R3 (p < 0.015), and R4 (p < 0.0344). The significance order was R2 (****) > R1 (***) > R3 (**) > R4 (*) > R5 (ns). Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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22 pages, 3762 KiB  
Article
Dihydrotanshinone I Enhances Cell Adhesion and Inhibits Cell Migration in Osteosarcoma U−2 OS Cells through CD44 and Chemokine Signaling
by Lanyan Fan, Chen Peng, Xiaoping Zhu, Yawen Liang, Tianyi Xu, Peng Xu and Shihua Wu
Molecules 2022, 27(12), 3714; https://doi.org/10.3390/molecules27123714 - 9 Jun 2022
Cited by 5 | Viewed by 2471
Abstract
In the screening of novel natural products against cancer using an in vitro cancer cell model, we recently found that tanshinones from a traditional Chinese medicine, the rhizome of Salvia miltiorrhiza Bunge (Danshen), had potent effects on cell proliferation and migration. Especially for [...] Read more.
In the screening of novel natural products against cancer using an in vitro cancer cell model, we recently found that tanshinones from a traditional Chinese medicine, the rhizome of Salvia miltiorrhiza Bunge (Danshen), had potent effects on cell proliferation and migration. Especially for human osteosarcoma U−2 OS cells, tanshinones significantly enhanced the cell adherence, implying a possible role in cell adhesion and cell migration inhibition. In this work, therefore, we aimed to provide a new insight into the possible molecule mechanisms of dihydrotanshinone I, which had the strongest effects on cell adhesion among several candidate tanshinones. RNA−sequencing-based transcriptome analysis and several biochemical experiments indicated that there were comprehensive signals involved in dihydrotanshinone I-treated U−2 OS cells, such as cell cycle, DNA replication, thermogenesis, tight junction, oxidative phosphorylation, adherens junction, and focal adhesion. First, dihydrotanshinone I could potently inhibit cell proliferation and induce cell cycle arrest in the G0/G1 phase by downregulating the expression of CDK4, CDK2, cyclin D1, and cyclin E1 and upregulating the expression of p21. Second, it could significantly enhance cell adhesion on cell plates and inhibit cell migration, involving the hyaluronan CD44−mediated CXCL8–PI3K/AKT–FOXO1, IL6–STAT3–P53, and EMT signaling pathways. Thus, the increased expression of CD44 and lengthened protrusions around the cell yielded a significant increase in cell adhesion. In summary, these results suggest that dihydrotanshinone I might be an interesting molecular therapy for enhancing human osteosarcoma U−2 OS cell adhesion and inhibiting cell migration and proliferation. Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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9 pages, 1431 KiB  
Article
Preparation and Application of a Chemical Probe for Identifying the Targets of the Marine Cyclic Peptide Kapakahine A
by Rie Kamihira and Yoichi Nakao
Molecules 2022, 27(3), 1072; https://doi.org/10.3390/molecules27031072 - 5 Feb 2022
Viewed by 2531
Abstract
Marine organisms are a rich source of bioactive secondary metabolites. Although many marine natural products with bioactivities have been isolated, successful elucidation of their mechanisms of action remains limited. In this study, we prepared a probe molecule based on the marine cyclic peptide [...] Read more.
Marine organisms are a rich source of bioactive secondary metabolites. Although many marine natural products with bioactivities have been isolated, successful elucidation of their mechanisms of action remains limited. In this study, we prepared a probe molecule based on the marine cyclic peptide kapakahine A (1) by introducing a linker with an azide terminal group, which enables the introduction of fluorescent groups for the effective monitoring of subcellular localization, or coupling to affinity beads for the pull-down of target proteins. The results of LC/MS/MS measurements, ProteinPilot analysis, and Western blotting suggest that kapakahine A interacts with the mitochondrial inner membrane proteins PHB1, PHB2, and ANT2, which is consistent with the results of the subcellular localization analysis using a fluorescent probe. Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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10 pages, 3733 KiB  
Communication
Preparation of Oxysterols by C–H Oxidation of Dibromocholestane with Ru(Bpga) Catalyst
by Yui Fujii, Makoto Yoritate, Kana Makino, Kazunobu Igawa, Daiki Takeda, Daiki Doiuchi, Katsuhiko Tomooka, Tatsuya Uchida and Go Hirai
Molecules 2022, 27(1), 225; https://doi.org/10.3390/molecules27010225 - 30 Dec 2021
Cited by 2 | Viewed by 2669
Abstract
Seven mono- and dihydroxycholesterols were prepared by direct C–H oxidation of the cholestane skeleton with a recently developed Ru(Bpga) catalyst (Ru(Bpga) = [RuCl (bpga) (PPh3)] Cl; bpga = 2-(bis(pyridin-2-ylmethyl)amino)-N-(2,6-dimethylphenyl)acetamide)). Due to the high selectivity of the Ru(Bpga) complex for [...] Read more.
Seven mono- and dihydroxycholesterols were prepared by direct C–H oxidation of the cholestane skeleton with a recently developed Ru(Bpga) catalyst (Ru(Bpga) = [RuCl (bpga) (PPh3)] Cl; bpga = 2-(bis(pyridin-2-ylmethyl)amino)-N-(2,6-dimethylphenyl)acetamide)). Due to the high selectivity of the Ru(Bpga) complex for tertiary C–H, the reaction afforded a mixture of 25-, 20-, 17-, and 14-oxygenated cholesterols that could be easily separated by high-performance liquid chromatography. These results suggest that late-stage C–H oxidation could be a viable strategy for preparing candidate metabolites of biologically important molecules. Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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24 pages, 5118 KiB  
Article
Synthesis, Antimicrobial, Anticancer, PASS, Molecular Docking, Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs
by Md. Ruhul Amin, Farhana Yasmin, Mohammed Anowar Hosen, Sujan Dey, Shafi Mahmud, Md. Abu Saleh, Talha Bin Emran, Imtiaj Hasan, Yuki Fujii, Masao Yamada, Yasuhiro Ozeki and Sarkar Mohammad Abe Kawsar
Molecules 2021, 26(22), 7016; https://doi.org/10.3390/molecules26227016 - 20 Nov 2021
Cited by 49 | Viewed by 3784
Abstract
A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the [...] Read more.
A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antibacterial activities. Minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) tests were conducted for four compounds (4, 5, 6, and 9) based on their activity. MTT assay showed low antiproliferative activity of compound 9 against Ehrlich’s ascites carcinoma (EAC) cells with an IC50 value of 2961.06 µg/mL. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties whereas molecular docking identified potential inhibitors of the SARS-CoV-2 main protease (6Y84). A 150-ns molecular dynamics simulation study revealed the stable conformation and binding patterns in a stimulating environment. In-silico ADMET study suggested all the designed molecules to be non-carcinogenic, with low aquatic and non-aquatic toxicity. In summary, all these antimicrobial, anticancer and in silico studies revealed that newly synthesized MGP analogs possess promising antiviral activity, to serve as a therapeutic target for COVID-19. Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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15 pages, 3435 KiB  
Brief Report
miR-370-3p Regulates Adipogenesis through Targeting Mknk1
by Peiwen Zhang, Xinrong Li, Shunhua Zhang, Shuang Wu, Qian Xiao, Yang Gu, Xinyu Guo, Xutao Lin, Lei Chen, Ye Zhao, Lili Niu, Guoqing Tang, Yanzhi Jiang, Linyuan Shen and Li Zhu
Molecules 2021, 26(22), 6926; https://doi.org/10.3390/molecules26226926 - 17 Nov 2021
Cited by 7 | Viewed by 2141
Abstract
Excessive fat accumulation can lead to obesity, diabetes, hyperlipidemia, atherosclerosis, and other diseases. MicroRNAs are a class of microRNAs that regulate gene expression and are highly conserved in function among species. microRNAs have been shown to act as regulatory factors to inhibit fat [...] Read more.
Excessive fat accumulation can lead to obesity, diabetes, hyperlipidemia, atherosclerosis, and other diseases. MicroRNAs are a class of microRNAs that regulate gene expression and are highly conserved in function among species. microRNAs have been shown to act as regulatory factors to inhibit fat accumulation in the body. We found that miR-370-3p was expressed at lower levels in the fat mass of mice on a high-fat diet than in mice on a normal control diet. Furthermore, our data showed that the overexpression of miR-370-3p significantly suppressed the mRNA expression levels of adipogenic markers. Thus, miR-370-3p overexpression reduced lipid accumulation. Conversely, the inhibition of miR-370-3p suppressed 3T3-L1 preadipocyte proliferation and promoted preadipocyte differentiation. In addition, Mknk1, a target gene of miR-370-3p, plays an opposing role in preadipocyte proliferation and differentiation. Moreover, consistent results from in vitro as well as in vivo experiments suggest that the inhibition of fat accumulation by miR-370-3p may result from the inhibition of saturated fatty acids that promote the accumulation of polyunsaturated fatty acids. In conclusion, these results suggest that miR-370-3p plays an important role in adipogenesis and fatty acid metabolism through the regulation of Mknk1. Full article
(This article belongs to the Special Issue Chemical Biology Research in Asia)
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