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Alqaaf M, Nasution AK, Karim MB, Rumman MI, Sedayu MH, Supriyanti R, Ono N, Altaf-Ul-Amin M, Kanaya S. Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins. Sci Rep 2025; 15:200. [PMID: 39747174 PMCID: PMC11697186 DOI: 10.1038/s41598-024-83637-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 12/16/2024] [Indexed: 01/04/2025] Open
Abstract
The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into host cells. Utilizing the Protein Data Bank Japan (PDBJ) and BindingDB databases, we isolated 204 S-glycoprotein sequences and conducted a clustering analysis to identify similarities and differences among them. We subsequently identified 33,722 binding molecules (BMs) by matching them with the sequences of 204 S-glycoproteins and compared them with 52,107 secondary metabolites (SMs) from the KNApSAcK database to identify potential inhibitors. We conducted docking and drug-likeness property analyses to identify several SMs with potential as drug candidates based on binding energy (BE), no Lipinski's rule violation (LV), psychochemical properties within the pink area of the bioavailability radar, and a bioavailability score (BAS) not less than 0.55. Fourteen SMs were predicted through computational analysis as potential candidates for inhibiting the three major types of S proteins. Our study provides a foundation for further experimental validation of these compounds as potential therapeutic agents against SARS-CoV-2.
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Affiliation(s)
- Muhammad Alqaaf
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Ahmad Kamal Nasution
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mohammad Bozlul Karim
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mahfujul Islam Rumman
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Muhammad Hendrick Sedayu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Department of Electrical Engineering, Jenderal Soedirman University, Purbalingga, 53371, Central Java, Indonesia
| | - Retno Supriyanti
- Department of Electrical Engineering, Jenderal Soedirman University, Purbalingga, 53371, Central Java, Indonesia
| | - Naoaki Ono
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Md Altaf-Ul-Amin
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Shigehiko Kanaya
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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Han Y, Katayama S, Futakuchi M, Nakamichi K, Wakabayashi Y, Sakamoto M, Nakayama J, Semba K. Targeting c-Jun Is a Potential Therapy for Luminal Breast Cancer Bone Metastasis. Mol Cancer Res 2023; 21:908-921. [PMID: 37310848 DOI: 10.1158/1541-7786.mcr-22-0695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/30/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
Luminal breast cancer has the highest bone metastasis frequency among all breast cancer subtypes; however, its metastatic mechanism has not been elucidated because of a lack of appropriate models. We have previously developed useful bone metastatic cell lines of luminal breast cancer using MCF7 cells. In this study, we characterized bone metastatic MCF7-BM cell lines and identified c-Jun as a novel bone metastasis marker of luminal breast cancer. The protein level of c-Jun was upregulated in MCF7-BM cells compared with that in parental cells, and its deficiency resulted in the suppression of tumor cell migration, transformation, and reduced osteolytic ability. In vivo, dominant-negative c-Jun exhibited smaller bone metastatic lesions and a lower metastatic frequency. Histologic analysis revealed that c-Jun expression was heterogeneous in bone metastatic lesions, whereas c-Jun overexpression mediated a vicious cycle between MCF7-BM cells and osteoclasts by enhancing calcium-induced migration and releasing the osteoclast activator BMP5. Pharmacological inhibition of c-Jun by the Jun amino-terminal kinase (JNK) inhibitor JNK-IN-8 effectively suppressed tumorigenesis and bone metastasis in MCF7-BM cells. Furthermore, c-Jun downstream signals were specifically correlated with the clinical prognosis of patients with the luminal subtype of breast cancer. Our results illustrate the potential benefits of a therapy that targets c-Jun to prevent bone metastasis in luminal breast cancer. IMPLICATIONS c-Jun expression mediates bone metastasis in luminal breast cancer by forming a vicious cycle in the bone microenvironment, which reveals potential strategies for subtype-specific bone metastasis therapy.
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Affiliation(s)
- Yuxuan Han
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Shota Katayama
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Mitsuru Futakuchi
- Department of Pathological Diagnostics, Yamagata University, Yamagata, Japan
| | - Kazuya Nakamichi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yutaro Wakabayashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Mai Sakamoto
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Jun Nakayama
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Translational Research Center, Fukushima Medical University, Fukushima, Japan
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Molecular Research and Treatment of Breast Cancer. Int J Mol Sci 2022; 23:ijms23179617. [PMID: 36077013 PMCID: PMC9455640 DOI: 10.3390/ijms23179617] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is the leading cause of cancer-related deaths in the female population [...]
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