JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
·
2025
·
IF 5.4
Man Liu,Li Zhao,Xupeng Huang,Zhenhao Tang,Yihang Zhong,Mengrong Yan,Shun Liu,Shunjing Wang,Zeyun Sun,Zixuan Rao,Linyi Yu,Yuying Fang,Wei Zhang,Hongbo Zhang,Wei Peng
The COVID-19 pandemic underscores the urgent need to develop broad-spectrum antivirals against coronaviruses (CoVs) to prepare for future outbreaks. In this study, we presented a systematic approach to developing broad-spectrum Mpro inhibitors, with a focus on high-risk CoVs. We optimised S-217622 as a lead compound, with the goal of enhancing conserved interactions within the S1, S2, and S3/S4 pockets of Mpro, leading to significantly improved inhibitory potency against representative CoVs. Compound 25 exhibited submicromolar activity across all ten CoVs, with IC50 values below 0.1 μM for six of them. The X-ray co-crystal structure of SARS-CoV-2 Mpro in complex with compound 25 revealed the structural basis of conserved interactions contributing to its broad-spectrum activity. This study demonstrates the feasibility of reinforcing conserved interactions to develop Mpro inhibitors with broad-spectrum activity and provides valuable strategies for combating future pandemics caused by unknown CoVs.
研究领域:
病毒学
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药物开发
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结构生物学
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DOI
PubMed
高影响因子
Pharmaceuticals
·
2023
·Vol. 16
·期 5
·767
·
IF 4.6
Jie Chen,Xiang Zhou,Lifeng Fu,Haiyu Xu
Drugs that cure COVID-19 have been marketed; however, this disease continues to ravage the world without becoming extinct, and thus, drug discoveries are still relevant. Since Mprohas known advantages as a drug target, such as the conserved nature of the active site and the absence of homologous proteins in the body, it receives the attention of many researchers. Meanwhile, the role of traditional Chinese medicine (TCM) in the control of epidemics in China has also led to a focus on natural products, with the hope of finding some promising lead molecules through screening. In this study, we selected a commercial library of 2526 natural products from plants, animals and microorganisms with known biological activity for drug discovery, which had previously been reported for compound screening of the SARS CoV-2 S protein, but had not been tested on Mpro. This library contains compounds from a variety of Chinese herbs, includingLonicerae Japonicae Flos,Forsythiae FructusandScutellariae Radix, which are derived from traditional Chinese medicine prescriptions that have been shown to be effective against COVID-19. We used the conventional FRET method for the initial screening. After two rounds of selection, the remaining 86 compounds were divided into flavonoids, lipids, phenylpropanoids, phenols, quinones, alkaloids, terpenoids and steroids according to the skeleton structures, with inhibition rates greater than 70%. The top compounds in each group were selected to test the effective concentration ranges; the IC50values were as follows: (−)–gallocatechin gallate (1.522 ± 0.126 μM), ginkgolic acid C15:1 (9.352 ± 0.531 μM), hematoxylin (1.025 ± 0.042 μM), fraxetin (2.486 ± 0.178 μM), wedelolactone (1.003 ± 0.238 μM), hydroxytyrosol acetate (3.850 ± 0.576 μM), vanitiolide (2.837 ± 0.225 μM), β,β–dimethylacrylalkannin (2.731 ± 0.308 μM), melanin (7.373 ± 0.368 μM) and cholesteryl sodium sulfate (2.741 ± 0.234μM). In the next step, we employed two biophysical techniques, SPR and nanoDSF, to obtain KD/Kobsvalues: hematoxylin (0.7 μM), (−)–gallocatechin gallate (126 μM), ginkgolic acid C15:1 (227 μM), wedelolactone (0.9770 μM), β,β–dimethylacrylalkannin (1.9004 μM,), cholesteryl sodium sulfate (7.5950 μM) and melanin (11.5667 μM), which allowed better assessments of the binding levels. Here, seven compounds were the winners. Then, molecular docking experiments were specially performed by AutoDock Vina to analyze the mode of interactions within Mproand ligands. We finally formulated the present in silico study to predict pharmacokinetic parameters as well as drug-like properties, which is presumably the step that tells humans whether the compounds are drug-like or not. Moreover, hematoxylin, melanin, wedelolactone, β,β–dimethylacrylalkannin and cholesteryl sodium sulfate are in full compliance with the “Lipinski” principle and possess reasonable ADME/T properties, they have a greater potential of being lead compounds. The proposed five compounds are also the first to be found to have potential inhibitory effects on SARS CoV-2 Mpro. We hope that the results in this manuscript may serve as benchmarks for the above potentials.Keywords:SARS CoV-2 Mpro;natural products;high-throughput screening;lead compounds;in silico study
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DOI
PubMed
高影响因子
ANALYST
·
2024
·
IF 3.6
Lei Han,Bing Wang,Kunhui Sun,Muqadas Sitara,Meifang Li,Ping Wang,Ning Chen,Xie-an Yu,Jiangwei Tian
The main protease of SARS-CoV-2 (SARS-CoV-2 Mpro) plays a critical role in the replication and life cycle of the virus. Currently, how to screen SARS-CoV-2 Mpro inhibitors from complex traditional Chinese medicine (TCM) is the bottleneck for exploring the pharmacodynamic substances of TCM against SARS-CoV-2. In this study, a simple, cost-effective, rapid, and selective fluorescent sensor (TPE-S-TLG sensor) was designed with an AIE (aggregation-induced emission) probe (TPE-Ph-In) and the SARS-CoV-2 Mpro substrate (S-TLG). The TPE-S-TLG sensor was characterized using UV-Vis absorption spectroscopy, fluorescence spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), zeta potential, and Fourier transform infrared (FTIR) spectroscopy techniques. The limit of detection of this method to detect SARS-CoV-2 Mpro was measured to be 5 ng mL−1. Furthermore, the TPE-S-TLG sensor was also successfully applied to screen Mpro inhibitors from Xuebijing injection using the separation and collection of the HPLC-fully automatic partial fraction collector (HPLC-FC). Six active compounds, including protocatechualdehyde, chlorogenic acid, hydroxysafflower yellow A, caffeic acid, isoquercetin, and pentagalloylglucose, were identified using UHPLC-Q-TOF/MS that could achieve 90% of the Mpro inhibition rate for the Xuebijing injection. Accordingly, the strategy can be broadly applied in the detection of disease-related proteases as well as screening active substances from TCM.
研究领域:
分析化学
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药学
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病毒学
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中药学
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产品关联
DOI
PubMed
高影响因子
STAR Protocols
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2022
·
IF 0
Jing Zhang,Haohao Yan,Gangan Yan,Xiaoping Liu,Yanchang Wang,Yunyu Chen
Summary Discovery of efficacious antiviral agents targeting SARS-CoV-2 main protease (Mpro) is of the highest importance to fight against COVID-19. Here, we describe a simple protocol for high-throughput screening of Mpro inhibitors using a robust fluorescence polarization (FP) assay. Candidate Mpro inhibitors from large compound libraries could be rapidly identified by monitoring the change of millipolarization unit value. This affordable FP assay can be modified to screen antiviral agents targeting virus protease. For complete details on the use and execution of this protocol, please refer to Li et al. (2022) , Yan et al. (2021) , and Yan et al. (2022c) .
研究领域:
病毒学
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药学
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分子生物学
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DOI
PubMed
ARCHIV DER PHARMAZIE
·
2025
·Vol. 358
·期 9
·e70089
·
IF 3.6
Leyao Chen,Xinluan Lv,Xiaoyu Chang,Ruiyong Wang
The SARS-CoV-2 pandemic has spurred global efforts to develop therapeutic approaches. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and a key target for therapeutic development. In this study, 22 thiosemicarbazone derivatives were synthesized. Enzyme activity assays showed compound 3c exhibited obvious inhibition of Mpro, with an IC 50 value of 3.89 μM. The interaction mechanisms between thiosemicarbazone derivatives and Mpro were investigated using synchronous fluorescence, three-dimensional fluorescence, and circular dichroism spectroscopy. The fluorescence results indicate that static quenching is predominant. The equilibrium dissociation constant ( K d ) of 2.3 μM between 3c and Mpro was obtained by microscale thermophoresis. This K d value demonstrates the binding affinity of 3c for Mpro, consistent with the spectral results. Meanwhile, the binding modes and stability of thiosemicarbazone derivatives with Mpro were evaluated through molecular docking and molecular dynamics simulations, which also confirmed the stable binding between compound 3c and Mpro. This study provides valuable insights into the interaction mechanism between thiosemicarbazone derivatives and Mpro and provides clues for the design of Mpro inhibitors.
研究领域:
病毒学
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药物化学
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结构生物学
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分子药理学
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抗病毒治疗
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生物物理化学
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计算生物学
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产品关联
DOI
PubMed
高影响因子
ChemistrySelect
·
2025
·Vol. 10
·期 15
·e202406023
·
IF 2
Leyao Chen,Nuoya Wang,Xiaoyu Chang,Ruiyong Wang
Graphical This work investigated the inhibition of 4-thiazolidinone derivatives on SARS-CoV-2 Mpro using enzyme assays, spectroscopy, and molecular docking. Compound 3a showed the best inhibition (IC 50 = 2.36 ± 0.36 µM, K i = 1.72 µM), and the trifluoromethyl group in 3a played an important role. Hydrogen bonding and van der Waals forces were the main forces for the binding. This work provided clues for Mpro inhibitor development. Since the outbreak of COVID-19, one of the strategies used to search for potential drugs has been to screen inhibitors of SARS-CoV-2 Mpro. This work investigated the inhibitory effects of 4-thiazolidinone derivatives on main protease (Mpro) using various methods, including enzyme activity assays, enzyme kinetics, spectroscopy experiments, molecular docking simulations, microscale thermophoresis, and cytotoxicity tests. Compound 3a demonstrated the best inhibition effect among the compounds tested, with IC 50 = 2.36 ± 0.36 µM and K i = 1.72 µM. The trifluoromethyl group in 3a might enhance its inhibition ability. Interactions between the 4-thiazolidinone derivatives and Mpro resulted in fluorescence quenching primarily through static quenching. Thermodynamic analysis indicated that the interaction forces are mainly hydrogen bonds and van der Waals forces. Spectral results revealed that the 4-thiazolidinone derivatives affected the microenvironment of aromatic amino acid residues in Mpro and altered its secondary structure. Differential scanning fluorimetry was used to confirm the interaction between the 4-thiazolidinone derivatives and Mpro. Results of microscale thermophoresis indicated that the K d between 3a and Mpro was 1.56 ± 0.24 µM. Molecular docking simulations provided a more intuitive visualization of the interaction forces. This study provides clues for screening novel Mpro inhibitors.
研究领域:
病毒学
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药物化学
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分子生物学
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DOI
高影响因子
International Journal of Electrochemical Science
·
2023
·
IF 1.5
Qiongyu Zhang,Gang Liu,Lingbin Ou
This work reported an electrochemical method for the detection of SARS-CoV-2 major protease (Mpro). Specifically, ferrocene (Fc)-labeled peptide substrates were immobilized on the gold nanoparticles (AuNPs)-modified electrode. Cleavage of the peptides by Mpro led to the release of Fc tags and the decrease of the electrochemical signals. The analytical performance of the biosensor for analysis of Mpro was investigated. Inhibiting the activity of Mpro prevented the cleavage of the peptide substrates. The method was successfully used to evaluate the inhibition efficiency of a well-known inhibitor.
研究领域:
生物化学
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分析化学
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病毒学
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DOI
PubMed
高影响因子
Algal Research-Biomass Biofuels and Bioproducts
·
2025
·
IF 4.5
Qiao-Hui Zeng,Zhi-En Yao,Xian-Min Zhou,Ping Qi,Xin-An Zeng
Inhibition of the biological activity of SARS-CoV-2 main protease (Mpro) effectively prevents viral replication, thereby presenting a promising therapeutic target for Corona Virus Disease 2019 (COVID-19) intervention. This study aims to screen the Mpro inhibitory peptides from the natural nutritional supplement Spirulina platensis ( S. platensis ). Firstly, Mpro was successfully prepared by heterologous expression in E. coli and Mpro's activity was detected. Meanwhile, four distinct peptides derived from S. platensis were obtained through enzymatic hydrolysis of protein. Subsequently, highly active peptides were synthesized and their inhibition effects on Mpro were verified by in vitro experiment and computer simulations. Results showed that the extraction rate of the protein from S. platensis was 96.11 %, the activity of Mpro was 845.90 U mg −1 , the peptide MQGPNY could inhibit the activity of Mpro at the inhibition rate of 20.21 % ± 3.8 % at the concentration of 2 mmol L −1 . Furthermore, results from computer Simulation showed that the peptide MQGPNY forms four pairs of hydrogen bonds with Mpro, which are Gln189, Ser46, Thr26 and Glu166. In addition, there were ten free residues involved in hydrophobic contacts, including His164, His41, Thr24, Met49, Thr45, Thr25, Gly143, Asn142, Cys145 and Met165. The foundings could provide theoretical support for the use of protein and its hydrolysates from S. platensis in functional food and supplement formulations in the post-epidemic era.
研究领域:
生物化学
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分子生物学
·
药理学
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产品关联
DOI
高影响因子
JOURNAL OF GENERAL VIROLOGY
·
2024
·Vol. 105
·期 5
·001996
·
IF 3.6
Yuting Duan,Haichuan Li,Shuai Huang,Yaoming Li,Shuyi Chen,Lilan Xie
Transmissible gastroenteritis virus (TGEV), an enteropathogenic coronavirus, has caused huge economic losses to the pig industry, with 100% mortality in piglets aged 2 weeks and intestinal injury in pigs of other ages. However, there is still a shortage of safe and effective anti-TGEV drugs in clinics. In this study, phloretin, a naturally occurring dihydrochalcone glycoside, was identified as a potent antagonist of TGEV. Specifically, we found phloretin effectively inhibited TGEV proliferation in PK-15 cells, dose-dependently reducing the expression of TGEV N protein, mRNA, and virus titer. The anti-TGEV activity of phloretin was furthermore refined to target the internalization and replication stages. Moreover, we also found that phloretin could decrease the expression levels of proinflammatory cytokines induced by TGEV infection. In addition, we expanded the potential key targets associated with the anti-TGEV effect of phloretin to AR, CDK2, INS, ESR1, ESR2, EGFR, PGR, PPARG, PRKACA, and MAPK14 with the help of network pharmacology and molecular docking techniques. Furthermore, resistant viruses have been selected by culturing TGEV with increasing concentrations of phloretin. Resistance mutations were reproducibly mapped to the residue (S242) of main protease (Mpro). Molecular docking analysis showed that the mutation (S242F) significantly disrupted phloretin binding to Mpro, suggesting Mpromight be a potent target of phloretin. In summary, our findings indicate that phloretin is a promising drug candidate for combating TGEV, which may be helpful for developing pharmacotherapies for TGEV and other coronavirus infections.
研究领域:
病毒学
·
药理学
·
分子生物学
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DOI
PubMed
高影响因子
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