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Nshogoza G, Liu Y, Gao J, Liu M, Moududee SA, Ma R, Li F, Zhang J, Wu J, Shi Y, Ruan K. NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43. Int J Mol Sci 2019; 20:ijms20133230. [PMID: 31262091 PMCID: PMC6651732 DOI: 10.3390/ijms20133230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 01/10/2023] Open
Abstract
The TDP-43 is originally a nuclear protein but translocates to the cytoplasm in the pathological condition. TDP-43, as an RNA-binding protein, consists of two RNA Recognition Motifs (RRM1 and RRM2). RRMs are known to involve both protein-nucleotide and protein-protein interactions and mediate the formation of stress granules. Thus, they assist the entire TDP-43 protein with participating in neurodegenerative and cancer diseases. Consequently, they are potential therapeutic targets. Protein-observed and ligand-observed nuclear magnetic resonance (NMR) spectroscopy were used to uncover the small molecule inhibitors against the tandem RRM of TDP-43. We identified three hits weakly binding the tandem RRMs using the ligand-observed NMR fragment-based screening. The binding topology of these hits is then depicted by chemical shift perturbations (CSP) of the 15N-labeled tandem RRM and RRM2, respectively, and modeled by the CSP-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK). These hits mainly bind to the RRM2 domain, which suggests the druggability of the RRM2 domain of TDP-43. These hits also facilitate further studies regarding the hit-to-lead evolution against the TDP-43 RRM domain.
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Affiliation(s)
- Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yaqian Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Mingqing Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Sayed Ala Moududee
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- CAS, Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
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Xie C, He C, Jiang Y, Yu H, Cheng L, Nshogoza G, Ala MS, Tian C, Wu J, Shi Y, Li F. Structural insights into the recognition of phosphorylated Hop1 by Mek1. Acta Crystallogr D Struct Biol 2018; 74:1027-1038. [PMID: 30289413 DOI: 10.1107/s2059798318011993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022]
Abstract
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition. It was further found that in Schizosaccharomyces pombe Mek1 FHA binds both pT15 in its N-terminal SQ/TQ cluster domain (SCD) and pT270 in the Hop1 SCD. The results revealed the structural basis for the preferential recognition of phosphorylated Hop1 by Mek1 in S. cerevisiae and facilitate the understanding of the interaction between the S. pombe Mek1 FHA domain and its binding targets.
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Affiliation(s)
- Changlin Xie
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Hailong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Lin Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Moududee Sayed Ala
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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Xu D, Li B, Gao J, Liu Z, Niu X, Nshogoza G, Zhang J, Wu J, Su XC, He W, Ma R, Yang D, Ruan K. Ligand Proton Pseudocontact Shifts Determined from Paramagnetic Relaxation Dispersion in the Limit of NMR Intermediate Exchange. J Phys Chem Lett 2018; 9:3361-3367. [PMID: 29864276 DOI: 10.1021/acs.jpclett.8b01443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Delineation of protein-ligand interaction modes is key for rational drug discovery. The availability of complex crystal structures is often limited by the aqueous solubility of the compounds, while lead-like compounds with micromolar affinities normally fall into the NMR intermediate exchange regime, in which severe line broadening to beyond the detection of interfacial resonances limits NMR applications. Here, we developed a new method to retrieve low-populated bound-state 1H pseudocontact shifts (PCSs) using paramagnetic relaxation dispersion (RD). We evaluated using a 1H PCS-RD approach in a BRM bromodomain lead-like inhibitor to filter molecular docking poses using multiple intermolecular structural restraints. Considering the universal presence of proton atoms in druglike compounds, our work will have wide application in structure-guided drug discovery even under an extreme condition of NMR intermediate exchange and low aqueous solubility of ligands.
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Affiliation(s)
- Difei Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Bin Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Jia Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
- Center of Medical Physics and Technology, Hefei Institute of Physical Science , Cancer Hospital Chinese Academy of Science , Hefei , Anhui 230031 , PR China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai , 201210 , PR China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , PR China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Nankai University , Tianjin , 300071 , PR China
| | - Wei He
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences , Tsinghua University , Beijing , 100084 , PR China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , Singapore , 117543 , Singapore
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230027 , PR China
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Liu J, Zhang S, Liu M, Liu Y, Nshogoza G, Gao J, Ma R, Yang Y, Wu J, Zhang J, Li F, Ruan K. Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. FEBS J 2018; 285:2091-2103. [DOI: 10.1111/febs.14469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Jiuyang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Shuya Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Mingqing Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yaqian Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jia Gao
- Center of Medical Physics and Technology Hefei Institute of Physical Science Chinese Academy of Science Hefei China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yang Yang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
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