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Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro

Can Jin, Bo Feng, Rongjuan Pei, Yaqi Ding, Meixia Li, Xia Chen, Zhenyun Du, Yangxiao Ding, Chunfan Huang, Bo Zhang, Xinwen Chen, Yi Zang, Jia Li, Kan Ding
doi: https://doi.org/10.1101/2021.10.27.466067
Can Jin
1College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu Province 210029, China
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Bo Feng
3National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. of China
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Rongjuan Pei
5State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
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Yaqi Ding
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Meixia Li
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Xia Chen
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Zhenyun Du
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Yangxiao Ding
8Shanghai High School International Division, No.989, Baise Road, Shanghai, China, 200231
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Chunfan Huang
1College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu Province 210029, China
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Bo Zhang
5State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
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Xinwen Chen
5State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
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Yi Zang
3National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. of China
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Jia Li
3National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. of China
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
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Kan Ding
1College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing, Jiangsu Province 210029, China
2Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research
4University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, P. R. China
6Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science. SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong, China, 528400
7Henan Polysaccharide Research Center, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
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  • For correspondence: dingkan@simm.ac.cn
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Abstract

To date, COVID-19 is still a severe threat to public health, hence specific effective therapeutic drugs development against SARS-CoV-2 is urgent needed. 3CLpro and PLpro and RdRp are the enzymes required for the SARS-CoV-2 RNA synthesis. Therefore, binding to the enzyme may interfere the enzyme function. Before, we found that sulfated polysaccharide binding to 3CLpro might block the virus replication. Hence, we hypothesize that negative charged pectin glycan may also impede the virus replication. Here we show that 922 crude polysaccharide from Syzygium aromaticum may near completely block SARS-CoV-2 replication. The inhibition rate was 99.9% (EC50 : 0.90 μM). Interestingly, 922 can associates with 3CLpro, PLpro and RdRp. We further show that the homogeneous glycan 922211 from 922 may specifically attenuate 3CL protease activity. The IC50s of 922 and 922211 against 3CLpro are 4.73 ± 1.05 µM and 0.18 ± 0.01 µM, respectively. Monosaccharide composition analysis reveals that 922211 with molecular weight of 78.7 kDa is composed of rhamnose, galacturonic acid, galactose and arabinose in the molar ratio of 8.21 : 37.81 : 3.58 : 4.49. The structure characterization demonstrated that 922211 is a homogalacturonan linked to RG-I pectin polysaccharide. The linear homogalacturonan part in the backbone may be partly methyl esterified while RG-I type part bearing 1, 4-linked α-GalpA, 1, 4-linked α-GalpAOMe and 1, 2, 4-linked α-Rhap. There are four branches attached to C-1 or C4 position of Rhamnose glycosyl residues on the backbone. The branches are composed of 1, 3-linked β-Galp, terminal (T)-linked β-Galp, 1, 5-linked α-Araf, T-linked α-Araf, 4-linked α-GalpA and/or 4-linked β-GalpA. The above results suggest that 922 and 922211 might be a potential novel leading compound for anti-SARS-CoV-2 new drug development.

Competing Interest Statement

The authors have declared no competing interest.

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Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro
Can Jin, Bo Feng, Rongjuan Pei, Yaqi Ding, Meixia Li, Xia Chen, Zhenyun Du, Yangxiao Ding, Chunfan Huang, Bo Zhang, Xinwen Chen, Yi Zang, Jia Li, Kan Ding
bioRxiv 2021.10.27.466067; doi: https://doi.org/10.1101/2021.10.27.466067
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Novel pectin from crude polysaccharide of Syzygium aromaticum against SARS-CoV-2 activities by targeting 3CLpro
Can Jin, Bo Feng, Rongjuan Pei, Yaqi Ding, Meixia Li, Xia Chen, Zhenyun Du, Yangxiao Ding, Chunfan Huang, Bo Zhang, Xinwen Chen, Yi Zang, Jia Li, Kan Ding
bioRxiv 2021.10.27.466067; doi: https://doi.org/10.1101/2021.10.27.466067

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