Article
Multidisciplinary Sciences
Lin Lin, Da-Yuan Chen, Christina Scartelli, Huanzhang Xie, Glenn Merrill-Skoloff, Moua Yang, Lijun Sun, Mohsan Saeed, Robert Flaumenhaft
Summary: This study screened 1,019 plant-based flavonoids and identified compounds that can inhibit the SARS-CoV-2 main protease. The most potent inhibitors were apigenin and a galloylated pinocembrin analog called PGHG.
Article
Environmental Sciences
Perumal Arumugam Desingu, K. Nagarajan, Kuldeep Dhama
Summary: The origin of SARS-CoV-2 is still debated, but this study reveals that it has acquired a novel spike protein S1-N-terminal domain (S1-NTD). Analysis shows that SARS-CoV/SARS-CoV-2 S1-NTDs are closely related to OC43 and HKU1, while the complete spike protein has a closer relationship with MERS-CoV. Different types of S1-NTDs were identified in SARS-CoV-2-related viruses and SARS-CoV-related viruses. This study provides insights into the evolution and relationships of these viruses.
ENVIRONMENTAL RESEARCH
(2022)
Article
Chemistry, Medicinal
Bin Tan, Michael Sacco, Haozhou Tan, Kan Li, Ryan Joyce, Xiujun Zhang, Yu Chen, Jun Wang
Summary: In the study, reactive warheads, including Jun11119R (vinyl sulfonamide warhead), Jun10221R (propiolamide warhead), Jun1112R (4-chlorobut-2-ynamide warhead), Jun10541R (nitrile warhead), and Jun10963R (dually activated nitrile warhead), were identified as potent Mpro inhibitors. Jun10541R and Jun10963R also showed strong antiviral activity against SARS-CoV-2 in Calu-3 cells, with EC50 values of 2.92 and 6.47 μM, respectively. X-ray crystal structures of Mpro with Jun10541R and Jun10221 demonstrated covalent modification of Cys145. These Mpro inhibitors with diverse reactive warheads hold promise for further development.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Abdul Mateen Khan, Atia-tul-Wahab, Saba Farooq, Asmat Ullah, M. Iqbal Choudhary
Summary: This study evaluated 156 drugs and natural compounds against SARS-CoV-2 Main protease (Mpro) using STD-NMR spectroscopy, and identified 10 drugs that interact with Mpro. The antiviral activity of these drugs was determined through enzyme kinetics studies. This study demonstrates the importance of drug repurposing in addressing emerging and neglected diseases, and successfully applies STD-NMR spectroscopy combined with plaque reduction assay for rapid identification of potential antiviral agents.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Spectroscopy
Jinwen Li, Yantao Zhang, Huimin Pang, Shu Jie Li
Summary: Heparin interacts with SARS-CoV-2's M-pro and inhibits its activity, potentially playing a role in inhibiting the viral infection.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Biochemistry & Molecular Biology
Sin-Yee Fung, Kam-Leung Siu, Huayue Lin, Man Lung Yeung, Dong-Yan Jin
Summary: Both SARS-CoV and SARS-CoV-2 use NSPS proteins to antagonize IFN production, with variants like G15S and K90R retaining this antagonistic property.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Virology
Lukas van de Sand, Maren Bormann, Mira Alt, Leonie Schipper, Christiane Silke Heilingloh, Eike Steinmann, Daniel Todt, Ulf Dittmer, Carina Elsner, Oliver Witzke, Adalbert Krawczyk
Summary: The global pandemic of SARS-CoV-2 has had a significant impact on millions of people worldwide, highlighting the urgent need for novel antiviral compounds. The study demonstrated the antiviral activity of glycyrrhizin against SARS-CoV-2 and uncovered its mechanism of action by inhibiting the viral main protease. This suggests that glycyrrhizin-containing products, like licorice root tea, could benefit those infected with SARS-CoV-2 and warrants further investigation for clinical use in treating COVID-19 patients.
Article
Pharmacology & Pharmacy
Zhen Xu, Yunting Zou, Xi Gao, Miao-Miao Niu, Jindong Li, Lu Xue, Su Jiang
Summary: Four novel RBD/Mpro dual-targeting peptides with high binding affinities have been discovered, showing potential in inhibiting SARS-CoV-2 pseudovirus infection.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Subodh Kumar Samrat, Jimin Xu, Xuping Xie, Eleonora Gianti, Haiying Chen, Jing Zou, Jason G. Pattis, Khaled Elokely, Hyun Lee, Zhong Li, Michael L. Klein, Pei-Yong Shi, Jia Zhou, Hongmin Li
Summary: In this study, researchers screened a drug library and identified JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro. They demonstrated the antiviral activity of these compounds through cell-based assays and characterized their mechanisms of action and binding sites.
ANTIVIRAL RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Weijuan Shang, Wenhao Dai, Cheng Yao, Ling Xu, Xiangming Tao, Haixia Su, Jian Li, Xiong Xie, Yechun Xu, Min Hu, Dong Xie, Hualiang Jiang, Leike Zhang, Hong Liu
Summary: FB2001 is a promising therapeutic agent in COVID-19 treatment that exhibits potent antiviral activity against various SARS-CoV-2 variants and shows improvement in pathological symptoms in the lungs and brains. It can be combined with remdesivir for better clinical outcomes. This drug candidate has been approved for Phase II/III clinical trial due to its good safety and tolerability.
ANTIVIRAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Preeti Dhaka, Ankur Singh, Shweta Choudhary, Rama Krishna Peddinti, Pravindra Kumar, Gaurav Kumar Sharma, Shailly Tomar
Summary: This study identifies potential antiviral molecules against SARS-CoV-2 by targeting the RNA-binding site in the N-terminal domain of the nucleocapsid protein. Twelve high-affinity molecules that bind to the RNA binding site are identified using a structure-based repurposing approach. Two compounds, Telmisartan and BMS-189453, show potential antiviral activity against SARS-CoV-2.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Multidisciplinary Sciences
Xiaodong Luan, Xinming Li, Yufan Li, Gengchen Su, Wanchao Yin, Yi Jiang, Ning Xu, Feng Wang, Wang Cheng, Ye Jin, Leike Zhang, H. Eric Xu, Yi Xue, Shuyang Zhang
Summary: This study presents the crystal structures of the N-terminal domain (NTD) and C-terminal domain (CTD) of the nucleocapsid (N) protein of SARS-CoV-2, as well as the NTD-RNA complex. The findings reveal a tetramer organization of the NTD and identify a unique RNA binding mode in the NTD-RNA complex. In addition, a small molecule inhibitor, ceftriaxone sodium, is shown to block RNA binding to the NTD and inhibit RNP complex formation. These results provide insights for the development of antiviral drugs targeting the N protein.
Article
Biology
Manish Manish, Smriti Mishra, Ayush Anand, Naidu Subbarao
Summary: This study utilized various computational methods and found that theaflavin digallate can strongly interact with the main protease of SARS-CoV-2, suggesting its potential as a drug candidate for inhibiting the virus.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Svetlana V. Belenkaya, Iuliia A. Merkuleva, Olga I. Yarovaya, Varvara Yu. Chirkova, Elena A. Sharlaeva, Daniil V. Shanshin, Ekaterina A. Volosnikova, Sergey Z. Vatsadze, Mikhail V. Khvostov, Nariman F. Salakhutdinov, Dmitriy N. Shcherbakov
Summary: Despite the long history and knowledge of E. coli, obtaining soluble recombinant proteins in this system can still be problematic. However, we have successfully used the 3CL protease from SARS-CoV-2 virus to transfer the target protein into the periplasmic space of E. coli. This protease showed higher catalytic efficiency compared to other commonly used proteases and can effectively work in E. coli cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yao Zhao, Yan Zhu, Xiang Liu, Zhenming Jin, Yinkai Duan, Qi Zhang, Chengyao Wu, Lu Feng, Xiaoyu Du, Jinyi Zhao, Maolin Shao, Bing Zhang, Xiuna Yang, Lijie Wu, Xiaoyun Ji, Luke W. Guddat, Kailin Yang, Zihe Rao, Haitao Yang
Summary: This study determines the high-resolution structures of SARS-CoV-2 M-Pro in different states, revealing the conformational changes that occur during substrate processing. The study also demonstrates the enzyme's specificity for certain sequences and provides a foundation for the development of new anti-SARS-CoV-2 drugs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Xiao Xu, Tian Li, Zhongxing Xu, Hejia Wei, Ruoyun Lin, Bin Xia, Feng Liu, Na Li
ANALYTICAL CHEMISTRY
(2015)
Article
Biochemistry & Molecular Biology
Hejia Wei, Lei Wang, Xiaobai Ren, Wenyu Yu, Jian Lin, Changwen Jin, Bin Xia
Article
Oncology
Pengfei Ding, Xin Zhang, Shujuan Jin, Bo Duan, Pengxiang Chu, Yufei Zhang, Zhi-Nan Chen, Bin Xia, Fei Song
Article
Biochemistry & Molecular Biology
Bingjie Ouyang, Lei Wang, Shuo Wan, Yang Luo, Lu Wang, Jian Lin, Bin Xia
JOURNAL OF BIOMOLECULAR NMR
(2013)
Letter
Multidisciplinary Sciences
Lei Chen, Feng-Jiao Xin, Jue Wang, Jicheng Hu, Yuan-Yuan Zhang, Shuo Wan, Lu-Sha Cao, Chang Lu, Peng Li, S. Frank Yan, Dietbert Neumann, Uwe Schlattner, Bin Xia, Zhi-Xin Wang, Jia-Wei Wu
Article
Biochemistry & Molecular Biology
Bo Duan, Pengfei Ding, Timothy R. Hughes, William Wiley Navarre, Jun Liu, Bin Xia
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Yangjie Liao, Bo Duan, Yufei Zhang, Xinmin Zhang, Bin Xia
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Qian Huang, Bo Duan, Xianzhi Dong, Shilong Fan, Bin Xia
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biophysics
Qiran Zhai, Chen Lin, Bo Duan, Jun Liu, Lu Zhang, Bin Xia
Summary: WhiB4 protein, a member of the WhiB-like protein family, plays a crucial role in the survival and pathology of Mycobacterium tuberculosis. Acting as a transcription factor, WhiB4 regulates genes involved in redox balance, central metabolism, and respiration. It exists in different forms under different redox environments, including a dimeric holo form with iron-sulfur cluster, multimeric disulfide-linked oxidized apo forms, and a monomeric reduced apo form.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)
Article
Chemistry, Multidisciplinary
Bo Duan, Dihong Fu, Chaoqun Zhang, Pengfei Ding, Xianzhi Dong, Bin Xia
Summary: The study reveals the molecular mechanisms of how TCF and GEF protein families selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structures of the C-clamp domains in HDBP1 and TCF1E were determined, showing a unique zinc finger fold and specific DNA recognition motifs. CpG base pairs play a central role in the binding mechanism, with multiple hydrogen bonds formed between specific residues in the C-clamp domain and the DNA backbone, highlighting the importance of unmethylated CpG binding proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Biochemistry & Molecular Biology
Bo Duan, Pengfei Ding, William Wiley Navarre, Jun Liu, Bin Xia
Summary: Horizontal gene transfer (HGT) is a major driving force for bacterial evolution, with xenogeneic silencers playing a crucial role in recognizing and suppressing foreign genes to maintain genomic stability. The diversity in DNA recognition mechanisms of xenogeneic silencers leads to clear characteristics in DNA sequence preferences, correlated with different host genomic features. Xenogeneic silencers also act as a selective force against GC to AT mutational bias in bacterial genomes and help maintain host genomic AT contents at relatively low levels.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Zhiliang Yuan, Zhi Qu, Bo Duan, Tianyi Wang, Jiajun Xu, Bin Xia
Summary: The C-terminal domain of M-pro-C can form a 3D domain-swapped dimer and amyloid fibrils under non-denaturing and 3D domain-swappable conditions, respectively. Positive correlations between domain swapping dimerization rates and amyloid fibrillation were found, but not essential, as mutants incapable of 3D domain swapping could still form fibrils. The unpacking of the protofibril core region during 3D domain swapping accelerates the amyloid fibrillation process.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Qian Huang, Bo Duan, Zhi Qu, Shilong Fan, Bin Xia
Summary: GapR, a nucleoid-associated protein found in Caulobacter crescentus, plays a crucial role in DNA replication, transcription, and cell division. It stimulates gyrase and topo IV to relax supercoils by binding to overtwisted DNA, facilitating the movement of replication and transcription machines. GapR forms a dimer-of-dimers structure in solution, with an open or closed conformation, and has intrinsic DNA binding preference towards AT-rich overtwisted DNA.
Article
Microbiology
Chen Lin, Yuting Tang, Yuchen Wang, Junli Zhang, Yeyu Li, Shuqin Xu, Bin Xia, Qiran Zhai, Yao Li, Lu Zhang, Jun Liu
Summary: WhiB4 plays a critical role in the disease progression and reactivation of Mycobacterium marinum infection. Targeting WhiB4 may be a promising strategy for the development of novel therapeutics to prevent the reactivation of latent tuberculosis infection.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Zhe Guan, Tiantian Cai, Zhongmin Liu, Yunfeng Dou, Xuesong Hu, Peng Zhang, Xin Sun, Hongwei Li, Yao Kuang, Qiran Zhai, Hao Ruan, Xuanxuan Li, Zeyang Li, Qihui Zhu, Jingeng Mai, Qining Wang, Luhua Lai, Jianguo Ji, Haiguang Liu, Bin Xia, Taijiao Jiang, Shu-Jin Luo, Hong-Wei Wang, Can Xie
