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Xiao H, Zhang Y, Yang X, Yu S, Chen Z, Lu A, Zhang Z, Zhang G, Zhang BT. SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102303. [PMID: 39281703 PMCID: PMC11401195 DOI: 10.1016/j.omtn.2024.102303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 08/12/2024] [Indexed: 09/18/2024]
Abstract
Mature microRNAs (miRNAs) are short, single-stranded RNAs that bind to target mRNAs and induce translational repression and gene silencing. Many miRNAs discovered in animals have been implicated in diseases and have recently been pursued as therapeutic targets. However, conventional pharmacological screening for candidate small-molecule drugs can be time-consuming and labor-intensive. Therefore, developing a computational program to assist mature miRNA-targeted drug discovery in silico is desirable. Our previous work (https://doi.org/10.1002/advs.201903451) revealed that the unique functional loops formed during Argonaute-mediated miRNA-mRNA interactions have stable structural characteristics and may serve as potential targets for small-molecule drug discovery. Developing drugs specifically targeting disease-related mature miRNAs and their target mRNAs would avoid affecting unrelated ones. Here, we present SMTRI, a convolutional neural network-based approach for efficiently predicting small molecules that target RNA secondary structural motifs formed by interactions between miRNAs and their target mRNAs. Measured on three additional testing sets, SMTRI outperformed state-of-the-art algorithms by 12.9%-30.3% in AUC and 2.0%-18.4% in accuracy. Moreover, four case studies on the published experimentally validated RNA-targeted small molecules also revealed the reliability of SMTRI.
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Affiliation(s)
- Huan Xiao
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Xin Yang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ziqi Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Zongkang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
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Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
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Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
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Yan R, Li X, Liu Y, Ye X. Design, Synthesis, and Bioassay of 2′-Modified Kanamycin A. Molecules 2022; 27:molecules27217482. [PMID: 36364310 PMCID: PMC9654810 DOI: 10.3390/molecules27217482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Chemical modification of old drugs is an important way to obtain new ones, and it has been widely used in developing new aminoglycoside antibiotics. However, many of the previous modifying strategies seem arbitrary for their lack of support from structural biological detail. In this paper, based on the structural information of aminoglycoside and its drug target, we firstly analyzed the reason that some 2′-N-acetylated products of aminoglycosides caused by aminoglycoside-modifying enzyme AAC(2′) can partially retain activity, and then we designed, synthesized, and evaluated a series of 2′-modified kanamycin A derivatives. Bioassay results showed our modifying strategy was feasible. Our study provided valuable structure–activity relationship information, which would help researchers to develop new aminoglycoside antibiotics more effectively.
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Affiliation(s)
- Ribai Yan
- National Demonstration Center for Experimental Pharmacy Education, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (R.Y.); (X.Y.)
| | - Xiaonan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuheng Liu
- Department of Medical Chemistry, College of Pharmaceutical Science, Hebei Medical University, Shijiazhuang 050017, China
| | - Xinshan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (R.Y.); (X.Y.)
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