Article
Nanoscience & Nanotechnology
Guofang Zhang, Yalin Cong, Feng-Liang Liu, Jiufeng Sun, Jiantian Zhang, Guoli Cao, Lingqiang Zhou, Wenjie Yang, Qingle Song, Fangjun Wang, Ke Liu, Jing Qu, Jing Wang, Min He, Shun Feng, Didar Baimanov, Wei Xu, Rong-Hua Luo, Xin-Yan Long, Shumin Liao, Yunping Fan, Yu-Feng Li, Bai Li, Ximing Shao, Guocheng Wang, Lijing Fang, Huaiyu Wang, Xue-Feng Yu, Yan-Zhong Chang, Yuliang Zhao, Liang Li, Peng Yu, Yong-Tang Zheng, Diana Boraschi, Hongchang Li, Chunying Chen, Liming Wang, Yang Li
Summary: A biocompatible and antiviral two-dimensional nanomaterial has been reported, which can firmly adsorb the virus and inhibit viral infection through conformational changes induced by interaction with the spike protein. This study proposes CIPS as a promising nanodrug for future anti-SARS-CoV-2 therapy, and also as a decontamination agent and surface-coating material to reduce SARS-CoV-2 infectivity.
NATURE NANOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Wenyang Zhou, Chang Xu, Pingping Wang, Anastasia A. Anashkina, Qinghua Jiang
Summary: Since the outbreak of SARS-CoV-2, the viral genome has undergone multiple mutations, some of which have resulted in changes in viral infectivity and antigenicity. This review summarizes the spatiotemporal distribution of mutations in the spike protein and discusses the recent research on the impact of these mutations on viral infectivity and antigenicity. As SARS-CoV-2 continues to mutate, a systematic evaluation of mutations in the spike protein becomes crucial for the improvement of vaccine and therapeutic neutralizing antibody strategies.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Qi Zhang, Weichun Tang, Eduardo Stancanelli, Eunkyung Jung, Zulfeqhar Syed, Vijayakanth Pagadala, Layla Saidi, Catherine Z. Chen, Peng Gao, Miao Xu, Ivan Pavlinov, Bing Li, Wenwei Huang, Liqiang Chen, Jian Liu, Hang Xie, Wei Zheng, Yihong Ye
Summary: Researchers found that SARS-CoV-2 infection causes fusion of infected cells with ACE2 positive neighboring cells through cell surface heparan sulfate, forming syncytia. Using chemical genetics and 4D confocal imaging, they identified heparan sulfate as a critical factor that stimulates spike-induced cell-cell fusion. Heparan sulfate binds to spike and promotes ACE2 clustering, facilitating fusion pore formation between ACE2-expressing and spike-transfected cells. Inhibition of heparan sulfate mitigates ACE2 clustering and syncytium formation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Mijia Lu, Michelle Chamblee, Yuexiu Zhang, Chengjin Ye, Piyush Dravid, Jun-Gyu Park, K. C. Mahesh, Sheetal Trivedi, Satyapramod Murthy, Himanshu Sharma, Cole Cassady, Supranee Chaiwatpongsakorn, Xueya Liang, Jacob S. Yount, Prosper N. Boyakaa, Mark E. Peeples, Luis Martinez-Sobrido, Amit Kapoor, Jianrong Li
Summary: This study compared the immunogenicity and protective efficacy of different forms of SARS-CoV-2 S protein in mice and hamsters. The results showed that the preS-HexaPro form, with six proline substitutions, exhibited higher immunogenicity and protective efficacy, with better neutralization against multiple variants and a stronger cellular immune response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Pharmacology & Pharmacy
Shuang Liu, Yasuyuki Suzuki, Erika Takemasa, Ryusuke Watanabe, Masaki Mogi
Summary: This study investigated the role of mast cells in the response to SARS-CoV-2 viral inoculation and their contribution to host defenses. The results showed that mast cell stabilizers and chymase inhibitors have potential inhibitory effects on viral entry. Mast cell deficiency may increase the risk of viral invasion into the lower respiratory system.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2022)
Article
Multidisciplinary Sciences
Patrick J. Lenehan, Eshwan Ramudu, A. J. Venkatakrishnan, Gabriela Berner, Reid McMurry, John C. O'Horo, Andrew D. Badley, William Morice, John Halamka, Venky Soundararajan
Summary: A retrospective study compared laboratory test measurements in rehospitalized COVID-19 patients versus those not rehospitalized after viral clearance, finding that rehospitalized patients had lower hemoglobin levels and were more likely to have moderate or severe anemia. These findings suggest that anemia-related lab tests should be considered in risk assessment for COVID-19 patients.
Article
Chemistry, Multidisciplinary
Mengdan Wu, Wei Li, Sheng Lin, Jiaqi Fan, Lele Cui, Yijuan Xiang, Kaiyu Li, Linwei Tang, Yanping Duan, Zimin Chen, Fanli Yang, Weiwei Shui, Guangwen Lu, Ying Lai
Summary: The study finds that thrombin protease (Thr) cleavage at the S2' site accelerates membrane fusion of SARS-CoV-2 more strongly than PreScission (3C) protease cleavage at the S1/S2 site. Additionally, mutations at the RBD_ACE2 interface show a positive correlation between binding affinity and fusion probability. Furthermore, spike protein drives membrane fusion in the absence of ACE2, and the appropriate distance between membranes is critical for spike-mediated fusion.
Article
Virology
Qiong Wang, Sheng-Bao Ye, Zhi-Jian Zhou, A-Ling Song, Xi Zhu, Jia-Mei Peng, Rui-Min Liang, Chen-Hui Yang, Xiao-Wei Yu, Xun Huang, Jie Yu, Ye Qiu, Xing-Yi Ge
Summary: In order to control the COVID-19 pandemic, various SARS-CoV-2 vaccines have been developed. However, the rapid mutations of the SARS-CoV-2 spike protein may reduce the protective efficacy of existing vaccines, which mainly depends on neutralizing antibodies targeting the spike protein. This study screened prevalent spike mutations and assessed the susceptibility of SARS-CoV-2 variants to the immune sera of Sinovac CoronaVac and ZF2001 vaccines. The results showed that some SARS-CoV-2 variants were significantly resistant to neutralization, indicating reduced protective efficacy of the vaccines and potential increased infectivity.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Materials Science, Multidisciplinary
Werner E. G. Mueller, Heinz C. Schroeder, Meik Neufurth, Xiaohong Wang
Summary: This review explores the use of inorganic polyphosphate (polyP) as a potential novel agent against COVID-19, focusing on its ability to block the binding of the virus to cells through electrostatic interaction. Additionally, polyP upregulates the expression of mucin genes in epithelial cells, potentially reinforcing the defense barrier against virus infiltration.
Article
Medicine, Research & Experimental
Byoung Kwon Park, Jinsoo Kim, Sangkyu Park, Dongbum Kim, Minyoung Kim, Kyeongbin Baek, Joon-Yong Bae, Man-Seong Park, Won-Keun Kim, Younghee Lee, Hyung-Joo Kwon
Summary: This study identified a direct interaction between the S protein and the N protein of MERS-CoV during virus assembly in infected cells, and demonstrated that Spike CD peptides of MERS-CoV inhibit this interaction. Additionally, cell penetration by synthetic Spike CD peptides inhibits viral plaque formation in MERS-CoV-infected cells.
Article
Multidisciplinary Sciences
Hin Chu, Huiping Shuai, Yuxin Hou, Xi Zhang, Lei Wen, Xiner Huang, Bingjie Hu, Dong Yang, Yixin Wang, Chaemin Yoon, Bosco Ho-Yin Wong, Cun Li, Xiaoyu Zhao, Vincent Kwok-Man Poon, Jian-Piao Cai, Kenneth Kak-Yuen Wong, Man-Lung Yeung, Jie Zhou, Rex Kwok-Him Au-Yeung, Shuofeng Yuan, Dong-Yan Jin, Kin-Hang Kok, Stanley Perlman, Jasper Fuk-Woo Chan, Kwok-Yung Yuen
Summary: The study demonstrates that in Middle East respiratory syndrome coronavirus (MERS-CoV) infection, the protein kinase R-like endoplasmic reticulum kinase (PERK) signaling mediates apoptotic signals, and inhibiting PERK signaling or intrinsic apoptosis can alleviate MERS pathogenesis.
Article
Multidisciplinary Sciences
Ryuta Uraki, Maki Kiso, Shun Iida, Masaki Imai, Emi Takashita, Makoto Kuroda, Peter J. Halfmann, Samantha Loeber, Tadashi Maemura, Seiya Yamayoshi, Seiichiro Fujisaki, Zhongde Wang, Mutsumi Ito, Michiko Ujie, Kiyoko Iwatsuki-Horimoto, Yuri Furusawa, Ryan Wright, Zhenlu Chong, Seiya Ozono, Atsuhiro Yasuhara, Hiroshi Ueki, Yuko Sakai-Tagawa, Rong Li, Yanan Liu, Deanna Larson, Michiko Koga, Takeya Tsutsumi, Eisuke Adachi, Makoto Saito, Shinya Yamamoto, Masao Hagihara, Keiko Mitamura, Tetsuro Sato, Masayuki Hojo, Shin-ichiro Hattori, Kenji Maeda, Riccardo Valdez, Moe Okuda, Jurika Murakami, Calvin Duong, Sucheta Godbole, Daniel C. Douek, Ken Maeda, Shinji Watanabe, Aubree Gordon, Norio Ohmagari, Hiroshi Yotsuyanagi, Michael S. Diamond, Hideki Hasegawa, Hiroaki Mitsuya, Tadaki Suzuki, Yoshihiro Kawaoka
Summary: The replicative ability and pathogenicity of Omicron BA.2 variant is similar to that of BA.1 in rodents, but it shows less pathogenicity compared to early SARS-CoV-2 strains. There is a marked reduction in the neutralizing activity of plasma from individuals who had recovered from COVID-19 and vaccine recipients against BA.2 variant.
Article
Immunology
Alina Baum, Christos A. Kyratsous
Summary: Christos Kyratsous and Alina Baum from Regeneron Pharmaceuticals discuss the development of antibody therapeutics targeting the spike protein of SARS-CoV-2.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Julian Valero, Laia Civit, Daniel M. Dupont, Denis Selnihhin, Line S. Reinert, Manja Idorn, Brett A. Israels, Aleksandra M. Bednarz, Claus Bus, Benedikt Asbach, David Peterhoff, Finn S. Pedersen, Victoria Birkedal, Ralf Wagner, Soren R. Paludan, Jorgen Kjems
Summary: A special RNA aptamer with high affinity to the receptor binding domain of SARS-CoV-2 spike protein has been discovered, preventing its interaction with the host receptor and efficiently blocking viral infection. Trimerized version of the aptamer enhances binding affinity, showing potential for widespread use in detecting and treating SARS-CoV-2 and emerging variants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Kishore Vaddadi, Chaitanya Gandikota, Chaoqun Huang, Yurong Liang, Lin Liu
Summary: MicroRNAs (miRNAs) regulate viral replication and host tropism by interacting with the viral genome or modulating host factors. Experimental validation showed that miR-15a, miR-153, miR-298, miR-508, miR-1909, and miR-3130 can effectively reduce SARS-CoV-2 replication and S-protein levels, and these miRNAs target conserved regions in the viral RNA genome among variants.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Microbiology
Wenying Gao, Liuli Wang, Xiaohui Ju, Simin Zhao, Zhaolong Li, Manman Su, Jiancheng Xu, Peihui Wang, Qiang Ding, Guoyue Lv, Wenyan Zhang
Summary: This study reveals the regulation of ORF9b protein in SARS-CoV-2 and its interaction with the host. The findings suggest that targeting USP29 may be an effective strategy to combat SARS-CoV-2 infection.
Article
Virology
Lulu Han, Yi Zheng, Jian Deng, Mei-Ling Nan, Yang Xiao, Meng-Wei Zhuang, Jing Zhang, Wei Wang, Chengjiang Gao, Pei-Hui Wang
Summary: A characteristic feature of COVID-19 is the dysregulated immune response and overwhelming inflammatory cytokine storm. This study demonstrates that the ORF10 protein of SARS-CoV-2 interacts with STING, impairing the cGAS-STING signaling pathway and weakening the innate antiviral immunity.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Immunology
Yao Ma, Mei Luo, Yusheng Deng, Xiaoman Yang, Xionglue Wang, Guozhong Chen, Zixin Qin, Yun Deng, Meiling Nan, Yang Chen, Peihui Wang, Hong Wei, Lijuan Han, Xiaodong Fang, Zhi Liu
Summary: The gut microbiome of COVID-19 patients has been found to be related to viral load, disease severity, and immune dysfunction. In this study, a high-throughput screening system was established to investigate the role of gut microbiota in anti-infection against SARS-CoV-2. Unexpectedly, antibiotic treatment led to the appearance of substances with activity inhibition of the target protein Nsp15 in the intestine. Further analysis revealed that these substances were primarily bile acids that accumulated as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yadi Zhou, Yuan Liu, Shagun Gupta, Mauricio Paramo, Yuan Hou, Chengsheng Mao, Yuan Luo, Julius Judd, Shayne Wierbowski, Marta Bertolotti, Mriganka Nerkar, Lara Jehi, Nir Drayman, Vlad Nicolaescu, Haley Gula, Savas Tay, Glenn Randall, Peihui Wang, John T. Lis, Cedric Feschotte, Serpil C. Erzurum, Feixiong Cheng, Haiyuan Yu
Summary: Studying the interaction between viral and host proteins can help discover therapies for viral infections. In this study, a comprehensive network of interactions between SARS-CoV-2 and human proteins was generated using high-throughput techniques, validating known host factors and identifying new ones. The network showed the highest overlap with differentially expressed genes in COVID-19 patients and revealed an interaction between a viral protein and a human transcription factor. Additionally, network-based screening of FDA-approved or investigational drugs identified several candidates with significant proximity to SARS-CoV-2 host factors, including a drug called carvedilol which showed clinical benefits and antiviral properties.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiao Liang, Jun Xiao, Xuzichao Li, Yujie Liu, Yao Lu, Yanan Wen, Zexing Li, Xing Che, Yongjian Ma, Xingyan Zhang, Yi Zhang, Deng Jian, Peihui Wang, Chenghao Xuan, Guimei Yu, Long Li, Heng Zhang
Summary: The E3 ligase TRIM7 plays a critical role in viral infection and pathogenesis. The association between TRIM7 and its substrates is determined by the C-terminal glutamine residue of 2C peptides. New substrates of TRIM7, including norovirus and SARS-CoV-2 proteins, have been identified. Crystal structures of TRIM7 in complex with peptides from SARS-CoV-2 proteins reveal a common recognition mode.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kaixin He, Tingting Wan, Decai Wang, Ji Hu, Tingyue Zhou, Wanyin Tao, Zheng Wei, Qiao Lu, Rongbin Zhou, Zhigang Tian, Richard A. Flavell, Shu Zhu
Summary: In this study, it was found that intestinal epithelial cells (IECs) induce protective immunity against pathogens while maintaining immune tolerance to food by accumulating a less recognized 13-kD N-terminal fragment of GSDMD. This fragment translocates to the nucleus and induces the transcription of CIITA and MHCII molecules, which in turn induces the Tr1 cells in the upper small intestine. Disrupted food tolerance phenotype was observed in mice treated with a caspase-3/7 inhibitor, mice with GSDMD mutation resistant to caspase-3/7 cleavage, mice with MHCII deficiency in IECs, and mice with Tr1 deficiency. The study suggests that differential cleavage of GSDMD acts as a regulatory hub controlling immunity versus tolerance in the small intestine.
Article
Computer Science, Software Engineering
Na Yuan, Peihui Wang, Wenlong Meng, Shuangmin Chen, Jian Xu, Shiqing Xin, Ying He, Wenping Wang
Summary: Geodesics play a crucial role in digital geometry processing, providing a way to measure the shortest distance between points on a curved surface. We address the two-point geodesic problem by formulating it as a minimization problem and introducing a specific function H(s). Our method not only guarantees the uniqueness and regularity of curve parameterization, but also demonstrates advantages in handling parameterized surfaces, meshes, point clouds, implicit surfaces, and solving the general least-cost path problem.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Virology
Jian Deng, Sheng-Nan Zheng, Yang Xiao, Mei-Ling Nan, Jing Zhang, Lulu Han, Yi Zheng, Yanying Yu, Qiang Ding, Chengjiang Gao, Pei-Hui Wang
Summary: SARS-CoV-2 NSP8 inhibits the production of type I and III interferons by targeting RIG-I/MDA5, TRIF, and STING signaling molecules. It disrupts the assembly of RIG-I/MDA5-MAVS complex, resulting in impaired phosphorylation and nuclear translocation of IRF3. NSP8 also directly interacts with TRIF and STING to suppress their signaling transduction.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Jian Deng, Yi Zheng, Sheng-Nan Zheng, Mei-Ling Nan, Lulu Han, Jing Zhang, Yunyun Jin, Ji-An Pan, Chengjiang Gao, Pei-Hui Wang
Summary: The NSP7 protein of SARS-CoV-2 inhibits the production of interferons, crucial components of antiviral immunity, by targeting multiple signaling pathways. It disrupts the normal functioning of RIG-I/MDA5, TLR3-TRIF, and cGAS-STING pathways, leading to a dampened interferon response. Additionally, NSP7 decreases immune activation and facilitates virus replication.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Yuemin Ma, Lei Ding, Zhenhai Li, Chun Zhou
Summary: TRIM72 mediates membrane damage repair through membrane fusion and exocytosis, and its oligomerization is closely linked to disulfide bond formation. The crystal structure of TRIM72 BCC-SPRY domains provides a structural foundation for further mechanistic studies and the clinical application of TRIM72. Our results also demonstrate that TRIM72 interacts with several kinds of negatively charged lipids in addition to phosphatidylserine.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Hyun-Kyu Choi, Peiwen Cong, Chenghao Ge, Aswin Natarajan, Baoyu Liu, Yong Zhang, Kaitao Li, Muaz Nik Rushdi, Wei Chen, Jizhong Lou, Michelle Krogsgaard, Cheng Zhu
Summary: Catch bonds form when T cell receptors (TCR) interact with agonist peptide-MHC (pMHC) complexes, with the lifetime of the bond increasing with applied force. In this study, the authors develop two models and analyze 55 datasets to quantitatively integrate and classify different bond behaviors and biological activities. The models can distinguish class I from class II MHCs and correlate their structural parameters with TCR/pMHC potency to trigger T cell activation, providing insights into the mechanisms of TCR mechanosensing.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Peng Zhang, Yu Liu, Chunfeng Li, Lindsay D. Stine, Pei-Hui Wang, Matthew W. Turnbull, Haodi Wu, Qing Liu
Summary: Coronavirus disease 2019 (COVID-19) is associated with adverse impacts in the cardiovascular system. This study investigated the toxic effects of SARS-CoV-2 subunits on cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) and found that the ectopic expression of S and ORF-9B subunits impaired the contractile function and altered the metabolic profiles in human cardiomyocytes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Chemistry, Physical
Xingyu Li, Zhou Fang, Dechang Li, Zhenhai Li
Summary: The main protease (M-pro) of the novel coronavirus SARS-CoV-2 plays a crucial role in virus replication and is a potential drug target for COVID-19 treatment. In this study, the interactions between M-pro and three HIV-1 protease inhibitors (Lopinavir, Saquinavir, Ritonavir) and an inhibitor PF-07321332 were studied using molecular dynamics simulations. The results showed that PF-07321332 had the highest affinity among the four simulated inhibitors and specifically bound to the catalytically activated site of M-pro. The simulations suggested that PF-07321332 could serve as an effective inhibitor with high affinity and provide insights into drug design and repositioning strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Letter
Biochemistry & Molecular Biology
Jiaxin Yang, Yan Li, Shijin Wang, Huili Li, Lili Zhang, Haichen Zhang, Pei-Hui Wang, Xiangyu Zheng, Xiao-Fang Yu, Wei Wei
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Letter
Biochemistry & Molecular Biology
Zhuanchang Wu, Xiaobo Lei, Xin Wang, Zhaoying Zhang, Yuming Li, Lifen Gao, Xiaohong Liang, Peihui Wang, Jianwei Wang, Chunhong Ma
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)