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Wang F, Yang G, Yan L. Crystal Structures of Fusion Cores from CCoV-HuPn-2018 and SADS-CoV. Viruses 2024; 16:272. [PMID: 38400047 PMCID: PMC10893436 DOI: 10.3390/v16020272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 02/25/2024] Open
Abstract
Cross-species spillover to humans of coronaviruses (CoVs) from wildlife animal reservoirs poses marked and global threats to human and animal health. Recently, sporadic infection of canine coronavirus-human pneumonia-2018 (CCoV-HuPn-2018) in hospitalized patients with pneumonia genetically related to canine and feline coronavirus were identified. In addition, swine acute diarrhea syndrome coronavirus (SADS-CoV) had the capability of broad tropism to cultured cells including from humans. Together, the transmission of Alphacoronaviruses that originated in wildlife to humans via intermediate hosts was responsible for the high-impact emerging zoonosis. Entry of CoV is mainly mediated by Spike and formation of a typical six helix bundle (6-HB) structure in the postfusion state of Spike is pivotal. Here, we present the complete fusion core structures of CCoV-HuPn-2018 and SADS-CoV from Alphacoronavirus at 2.10 and 2.59 Å, respectively. The overall structure of the CCoV-HuPn-2018 fusion core is similar to Alphacoronavirus like HCoV-229E, while SADS-CoV is analogous to Betacoronavirus like SARS-CoV-2. Collectively, we provide a structural basis for the development of pan-CoV small molecules and polypeptides based on the HR1-HR2 complex, concerning CCoV-HuPn-2018 and SADS-CoV.
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Affiliation(s)
- Fulian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China;
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China;
| | - Lei Yan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China;
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2
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Sun L, Zhou A, Zhang F. Crystallization and crystallographic studies of a novel chickpea 11S globulin. Acta Crystallogr F Struct Biol Commun 2022; 78:324-329. [PMID: 36048082 PMCID: PMC9435671 DOI: 10.1107/s2053230x22007919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Chickpea is a crop that is known as a source of high-quality proteins. CL-AI, which belongs to the 11S globulin and cupin superfamily, was initially identified in chickpea seeds. CL-AI has recently been shown to inhibit various types of α-amylases. To determine its molecular mechanism, the crystal structure of CL-AI was solved at a final resolution of 2.2 Å. Structural analysis indicated that each asymmetric unit contains three molecules with threefold symmetry and a head-to-tail association, and each molecule is divided into an α-chain and a β-chain. CL-AI has high structural similarity to other 11S globulins and canonical metal-dependent enzyme-related cupin proteins, whereas its stimilarity to α-amylase inhibitor from Phaseolus vulgaris is quite low. The structure presented here will provide insight into the function of CL-AI.
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Affiliation(s)
- Linan Sun
- Department of Dermatology, People’s Hospital of SND, Suzhou, Jiangsu 215129, People’s Republic of China
| | - Aiwu Zhou
- Key Laboratory of Cell Differentiation and Apoptosis of The Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People’s Republic of China
| | - Fei Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of The Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People’s Republic of China
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3
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Li N, Yang H, Liu K, Zhou L, Huang Y, Cao D, Li Y, Sun Y, Yu A, Du Z, Yu F, Zhang Y, Wang B, Geng M, Li J, Xiong B, Xu S, Huang X, Liu T. Structure-Based Discovery of a Series of NSD2-PWWP1 Inhibitors. J Med Chem 2022; 65:9459-9477. [PMID: 35704853 DOI: 10.1021/acs.jmedchem.2c00709] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Overexpression, point mutations, or translocations of protein lysine methyltransferase NSD2 occur in many types of cancer cells. Therefore, it was recognized as onco-protein and considered as a promising anticancer drug target. NSD2 consists of multiple domains including a SET catalytic domain and two PWWP domains binding to methylated histone proteins. Here, we reported our efforts to develop a series of NSD2-PWWP1 inhibitors, and further structure-based optimization resulted in a potent inhibitor 38, which has high selectivity toward the NSD2-PWWP1 domain. The detailed biological evaluation revealed that compound 38 can bind to NSD2-PWWP1 and then affect the expression of genes regulated by NSD2. The current discovery will provide a useful chemical probe to the future research in understanding the specific regulation mode of NSD2 by PWWP1 recognition and pave the way to develop potential drugs targeting NSD2 protein.
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Affiliation(s)
- Na Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
| | - Hong Yang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Ke Liu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201210, P. R. China
| | - Liwei Zhou
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Yuting Huang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Danyan Cao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Yanlian Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Yaoliang Sun
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, #555 ZuChong Zhi Road, Shanghai 201203, P. R. China
| | - Aisong Yu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Zhiyan Du
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201210, P. R. China
| | - Ying Zhang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Bingyang Wang
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, #555 ZuChong Zhi Road, Shanghai 201203, P. R. China
| | - Meiyu Geng
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, P. R. China
| | - Bing Xiong
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,University of Chinese Academy of Sciences, NO.19A Yuquan Road, Beijing 100049, P. R. China
| | - Shilin Xu
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, #555 ZuChong Zhi Road, Shanghai 201203, P. R. China
| | - Xun Huang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.,Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Tongchao Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
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Fan S, Li D, Yan M, Feng X, Lv G, Wu G, Jin Y, Wang Y, Yang Z. The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria. Molecules 2021; 26:molecules26051451. [PMID: 33800069 PMCID: PMC7962117 DOI: 10.3390/molecules26051451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022] Open
Abstract
New drugs with novel antibacterial targets for Gram-negative bacterial pathogens are desperately needed. The protein LpxC is a vital enzyme for the biosynthesis of lipid A, an outer membrane component of Gram-negative bacterial pathogens. The ACHN-975 molecule has high enzymatic inhibitory capacity against the infectious diseases, which are caused by multidrug-resistant bacteria, but clinical research was halted because of its inflammatory response in previous studies. In this work, the structure of the recombinant UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase from Aquifex aeolicus in complex with ACHN-975 was determined to a resolution at 1.21 Å. According to the solved complex structure, ACHN-975 was docked into the AaLpxC’s active site, which occupied the site of AaLpxC substrate. Hydroxamate group of ACHN-975 forms five-valenced coordination with resides His74, His226, Asp230, and the long chain part of ACHN-975 containing the rigid alkynyl groups docked in further to interact with the hydrophobic area of AaLpxC. We employed isothermal titration calorimetry for the measurement of affinity between AaLpxC mutants and ACHN-975, and the results manifest the key residues (His74, Thr179, Tyr212, His226, Asp230 and His253) for interaction. The determined AaLpxC crystal structure in complex with ACHN-975 is expected to serve as a guidance and basis for the design and optimization of molecular structures of ACHN-975 analogues to develop novel drug candidates against Gram-negative bacteria.
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Affiliation(s)
- Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Danyang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong 276800, China;
| | - Xiao Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangxin Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Guangteng Wu
- ArNuXon Pharm-Sci Co., Ltd., Beijing 100085, China;
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; (S.F.); (D.L.); (X.F.); (G.L.); (Y.J.)
- Correspondence: (Y.W.); (Z.Y.)
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Lebugle M, Dworkowski F, Pauluhn A, Guzenko VA, Romano L, Meier N, Marschall F, Sanchez DF, Grolimund D, Wang M, David C. High-intensity x-ray microbeam for macromolecular crystallography using silicon kinoform diffractive lenses. APPLIED OPTICS 2018; 57:9032-9039. [PMID: 30461891 DOI: 10.1364/ao.57.009032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
Macromolecular crystallography often requires focused high-intensity x-ray beams for solving challenging protein structures from micrometer-sized crystals using current synchrotron radiation sources. The design of optical focusing schemes for hard x-rays showing high efficiency and flexibility in beam size is therefore continuously pursued. Here, we present an innovative solution based on a two-stage demagnification of the undulator source for photon energies from 6 keV to 19 keV, commissioned at the X10SA beamline of the Swiss Light Source, where a secondary source is imaged by two crossed silicon kinoform x-ray diffractive lenses with 75 nm outermost zone width. A source-size limited spot with a size of 4.8 μm×1.7 μm(h×v,FWHM) and flux of 7.5×1010 photons/s at 12.4 keV is demonstrated at the sample position.
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