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Journal articles on the topic '3CLpro'

Author: Grafiati

Published: 15 June 2024

Last updated: 31 July 2025

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1

Ziebuhr, John, Sonja Bayer, Jeff A. Cowley, and Alexander E. Gorbalenya. "The 3C-Like Proteinase of an Invertebrate Nidovirus Links Coronavirus and Potyvirus Homologs." Journal of Virology 77, no. 2 (2003): 1415–26. http://dx.doi.org/10.1128/jvi.77.2.1415-1426.2003.

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ABSTRACT Gill-associated virus (GAV), a positive-stranded RNA virus of prawns, is the prototype of newly recognized taxa (genus Okavirus, family Roniviridae) within the order Nidovirales. In this study, a putative GAV cysteine proteinase (3C-like proteinase [3CLpro]), which is predicted to be the key enzyme involved in processing of the GAV replicase polyprotein precursors, pp1a and pp1ab, was characterized. Comparative sequence analysis indicated that, like its coronavirus homologs, 3CLpro has a three-domain organization and is flanked by hydrophobic domains. The putative 3CLpro domain includ

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2

Chen, Jianzhong, Jian Wang, Wanchun Yang, Lu Zhao, and Xiaoyan Xu. "Identifying Inhibitor-SARS-CoV2-3CLpro Binding Mechanism Through Molecular Docking, GaMD Simulations, Correlation Network Analysis and MM-GBSA Calculations." Molecules 30, no. 4 (2025): 805. https://doi.org/10.3390/molecules30040805.

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The main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), known as 3CLpro, is crucial in the virus’s life cycle and plays a pivotal role in COVID-19. Understanding how small molecules inhibit 3CLpro’s activity is vital for developing anti-COVID-19 therapeutics. To this end, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to enhance the sampling of 3CLpro conformations and conducted correlation network analysis (CNA) to explore the interactions between different structural domains. Our findings indicate that a CNA-identified node in domain II

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3

Tsu, Brian V., Rimjhim Agarwal, Nandan S. Gokhale, et al. "Host-specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome." PLOS Biology 21, no. 6 (2023): e3002144. http://dx.doi.org/10.1371/journal.pbio.3002144.

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Hosts have evolved diverse strategies to respond to microbial infections, including the detection of pathogen-encoded proteases by inflammasome-forming sensors such as NLRP1 and CARD8. Here, we find that the 3CL protease (3CLpro) encoded by diverse coronaviruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), cleaves a rapidly evolving region of human CARD8 and activates a robust inflammasome response. CARD8 is required for cell death and the release of pro-inflammatory cytokines during SARS-CoV-2 infection. We further find that natural variation alters CARD8 sensing o

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4

Rawson, Jonathan M. O., Alice Duchon, Olga A. Nikolaitchik, Vinay K. Pathak, and Wei-Shau Hu. "Development of a Cell-Based Luciferase Complementation Assay for Identification of SARS-CoV-2 3CLpro Inhibitors." Viruses 13, no. 2 (2021): 173. http://dx.doi.org/10.3390/v13020173.

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The 3C-like protease (3CLpro) of SARS-CoV-2 is considered an excellent target for COVID-19 antiviral drug development because it is essential for viral replication and has a cleavage specificity distinct from human proteases. However, drug development for 3CLpro has been hindered by a lack of cell-based reporter assays that can be performed in a BSL-2 setting. Current efforts to identify 3CLpro inhibitors largely rely upon in vitro screening, which fails to account for cell permeability and cytotoxicity of compounds, or assays involving replication-competent virus, which must be performed in a

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5

Zhang, Jingjing, Yingpei Jiang, Chunxiu Wu, et al. "Development of FRET and Stress Granule Dual-Based System to Screen for Viral 3C Protease Inhibitors." Molecules 28, no. 7 (2023): 3020. http://dx.doi.org/10.3390/molecules28073020.

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3C proteases (3Cpros) of picornaviruses and 3C-like proteases (3CLpros) of coronaviruses and caliciviruses represent a group of structurally and functionally related viral proteases that play pleiotropic roles in supporting the viral life cycle and subverting host antiviral responses. The design and screening for 3C/3CLpro inhibitors may contribute to the development broad-spectrum antiviral therapeutics against viral diseases related to these three families. However, current screening strategies cannot simultaneously assess a compound’s cytotoxicity and its impact on enzymatic activity and pr

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6

Sanachai, Kamonpan, Tuanjai Somboon, Patcharin Wilasluck, et al. "Identification of repurposing therapeutics toward SARS-CoV-2 main protease by virtual screening." PLOS ONE 17, no. 6 (2022): e0269563. http://dx.doi.org/10.1371/journal.pone.0269563.

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SARS-CoV-2 causes the current global pandemic coronavirus disease 2019. Widely-available effective drugs could be a critical factor in halting the pandemic. The main protease (3CLpro) plays a vital role in viral replication; therefore, it is of great interest to find inhibitors for this enzyme. We applied the combination of virtual screening based on molecular docking derived from the crystal structure of the peptidomimetic inhibitors (N3, 13b, and 11a), and experimental verification revealed FDA-approved drugs that could inhibit the 3CLpro of SARS-CoV-2. Three drugs were selected using the bi

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7

Glab-ampai, Kittirat, Kanasap Kaewchim, Thanatsaran Saenlom, et al. "Human Superantibodies to 3CLpro Inhibit Replication of SARS-CoV-2 across Variants." International Journal of Molecular Sciences 23, no. 12 (2022): 6587. http://dx.doi.org/10.3390/ijms23126587.

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Broadly effective and safe anti-coronavirus agent is existentially needed. Major protease (3CLpro) is a highly conserved enzyme of betacoronaviruses. The enzyme plays pivotal role in the virus replication cycle. Thus, it is a good target of a broadly effective anti-Betacoronavirus agent. In this study, human single-chain antibodies (HuscFvs) of the SARS-CoV-2 3CLpro were generated using phage display technology. The 3CLpro-bound phages were used to infect Escherichia coli host for the production the 3CLpro-bound HuscFvs. Computerized simulation was used to guide the selection of the phage infe

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8

Ye, Gang, Xiaowei Wang, Xiaohan Tong, Yuejun Shi, Zhen F. Fu, and Guiqing Peng. "Structural Basis for Inhibiting Porcine Epidemic Diarrhea Virus Replication with the 3C-Like Protease Inhibitor GC376." Viruses 12, no. 2 (2020): 240. http://dx.doi.org/10.3390/v12020240.

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Porcine epidemic diarrhea virus (PEDV), being highly virulent and contagious in piglets, has caused significant damage to the pork industries of many countries worldwide. There are no commercial drugs targeting coronaviruses (CoVs), and few studies on anti-PEDV inhibitors. The coronavirus 3C-like protease (3CLpro) has a conserved structure and catalytic mechanism and plays a key role during viral polyprotein processing, thus serving as an appealing antiviral drug target. Here, we report the anti-PEDV effect of the broad-spectrum inhibitor GC376 (targeting 3Cpro or 3CLpro of viruses in the pico

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9

Chen, Chia-Nan, Coney P. C. Lin, Kuo-Kuei Huang, et al. "Inhibition of SARS-CoV 3C-like Protease Activity by Theaflavin-3,3'-digallate (TF3)." Evidence-Based Complementary and Alternative Medicine 2, no. 2 (2005): 209–15. http://dx.doi.org/10.1093/ecam/neh081.

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SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS). The virally encoded 3C-like protease (3CLPro) has been presumed critical for the viral replication of SARS-CoV in infected host cells. In this study, we screened a natural product library consisting of 720 compounds for inhibitory activity against 3CLPro. Two compounds in the library were found to be inhibitive: tannic acid (IC50 = 3 µM) and 3-isotheaflavin-3-gallate (TF2B) (IC50 = 7 µM). These two compounds belong to a group of natural polyphenols found in tea. We further investigated the 3CLPro-inhibitory activity o

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10

Rana, Shiwani, Prateek Kumar, Anchal Sharma, Sanjay Sharma, Rajanish Giri, and Kalyan S. Ghosh. "Identification of Naturally Occurring Antiviral Molecules for SARS-CoV-2 Mitigation." Open COVID Journal 1, no. 1 (2021): 38–46. http://dx.doi.org/10.2174/2666958702101010038.

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Aim: This study aimed to virtually screen the naturally occurring antiviral molecules for SARS-CoV-2 mitigation based on multiple molecular targets using docking and molecular dynamics simulations. Background: The coronavirus catastrophe (COVID-19) caused by a novel strain of coronavirus (SARS-CoV-2) has turned the world upside down at an unprecedented level and has been declared a pandemic by the World Health Organization. It has resulted in a huge number of infections as well as fatalities due to severe lower respiratory tract sickness. Objective: The objective of this study was the identifi

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11

Wei, Chao, Yuhua Li, Lina Guo, Zhiyu Shao, and Hua Diao. "Development of Peptidomimetic PROTACs as Potential Degraders of 3-Chymotrypsin-like Protease of SARS-CoV-2." International Journal of Molecular Sciences 26, no. 8 (2025): 3903. https://doi.org/10.3390/ijms26083903.

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3CL protease (3CLpro), a key enzyme of SARS-CoV-2 replication, is one of the most selective targets of antivirals, as no homologous protease has been recognized in the human body. As proteolysis-targeting chimeras (PROTACs) are superior to traditional inhibitors, based on the reported cereblon (CRBN) ligands thalidomide and lenalidomide, 3CLpro ligands of peptidomimetic inhibitors, and suitable linkers, we aimed to develop novel PROTACs that may trigger efficient intracellular 3CLpro degradation through a balance of hydrophilicity and lipophilicity. In brief, we designed and synthesized 5 PROT

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12

Wu, Jing, Bo Feng, Li-Xin Gao, et al. "Synthesis and Biochemical Evaluation of 8H-Indeno[1,2-d]thiazole Derivatives as Novel SARS-CoV-2 3CL Protease Inhibitors." Molecules 27, no. 10 (2022): 3359. http://dx.doi.org/10.3390/molecules27103359.

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The COVID-19 pandemic caused by SARS-CoV-2 is a global burden on human health and economy. The 3-Chymotrypsin-like cysteine protease (3CLpro) becomes an attractive target for SARS-CoV-2 due to its important role in viral replication. We synthesized a series of 8H-indeno[1,2-d]thiazole derivatives and evaluated their biochemical activities against SARS-CoV-2 3CLpro. Among them, the representative compound 7a displayed inhibitory activity with an IC50 of 1.28 ± 0.17 μM against SARS-CoV-2 3CLpro. Molecular docking of 7a against 3CLpro was performed and the binding mode was rationalized. These pre

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13

Kim, Yunjeong, Vinay Shivanna, Sanjeev Narayanan, et al. "Broad-Spectrum Inhibitors against 3C-Like Proteases of Feline Coronaviruses and Feline Caliciviruses." Journal of Virology 89, no. 9 (2015): 4942–50. http://dx.doi.org/10.1128/jvi.03688-14.

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ABSTRACTFeline infectious peritonitis and virulent, systemic calicivirus infection are caused by certain types of feline coronaviruses (FCoVs) and feline caliciviruses (FCVs), respectively, and are important infectious diseases with high fatality rates in members of the Felidae family. While FCoV and FCV belong to two distinct virus families, theCoronaviridaeand theCaliciviridae, respectively, they share a dependence on viral 3C-like protease (3CLpro) for their replication. Since 3CLpro is functionally and structurally conserved among these viruses and essential for viral replication, 3CLpro i

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14

Naumovich, Vladislav, Maria Grishina, and Vladimir Potemkin. "Establishment of models for reliability evaluation of 3CLpro ligand-receptor complexes with different binding sites." Future Medicinal Chemistry 14, no. 7 (2022): 501–10. http://dx.doi.org/10.4155/fmc-2021-0271.

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Aim: Recent research shows that 3CLpro enzyme of SARS-CoV-2 is a significant target against COVID-19. Drug modeling allows the design of inhibitors of 3CLpro, but the accuracy of those methods remains unclear. Therefore, it is important to determine the trustworthiness of the designed ligand–receptor complexes. Method & materials: The authors built models for the reliability evaluation of 3CLpro complexes with ligands using an in-house developed AlteQ approach and complementarity principles. The models were based on 145 experimentally found 3CLpro complexes with ligands for five different

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15

Zhang, Yue, Huijie Chen, Mengmeng Zou, et al. "Hypericin Inhibit Alpha-Coronavirus Replication by Targeting 3CL Protease." Viruses 13, no. 9 (2021): 1825. http://dx.doi.org/10.3390/v13091825.

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The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3C

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16

Ahmad, Bilal, Maria Batool, Qurat ul Ain, Moon Suk Kim, and Sangdun Choi. "Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations." International Journal of Molecular Sciences 22, no. 17 (2021): 9124. http://dx.doi.org/10.3390/ijms22179124.

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The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoamide, lopinavir, and ritonavir to the coronavirus 3-chymotrypsin-like-protease (3CLpro) by means of docking and molecular dynamic (MD) simulations. The analysis of MD trajectories of 3CLpro with PF-07321332, α-ketoamide, lopinavir, and ritonavir revealed that 3CLpro–PF-07321332 and 3CLpro–α-ketoamide complexes remained stable compared with 3CLpro–ri

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17

Lu, Xiao Tao, Amy C. Sims, and Mark R. Denison. "Mouse Hepatitis Virus 3C-Like Protease Cleaves a 22-Kilodalton Protein from the Open Reading Frame 1a Polyprotein in Virus-Infected Cells and In Vitro." Journal of Virology 72, no. 3 (1998): 2265–71. http://dx.doi.org/10.1128/jvi.72.3.2265-2271.1998.

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ABSTRACT The 3C-like proteinase (3CLpro) of mouse hepatitis virus (MHV) is predicted to cleave at least 11 sites in the 803-kDa gene 1 polyprotein, resulting in maturation of proteinase, polymerase, and helicase proteins. However, most of these cleavage sites have not been experimentally confirmed and the proteins have not been identified in vitro or in virus-infected cells. We used specific antibodies to identify and characterize a 22-kDa protein (p1a-22) expressed from gene 1 in MHV A59-infected DBT cells. Processing of p1a-22 from the polyprotein began immediately after translation, but som

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18

Shen, Hao, Shiqi Liu, Limin Shang, et al. "Discovery of Small-Molecule Inhibitors Against Norovirus 3CLpro Using Structure-Based Virtual Screening and FlipGFP Assay." Viruses 17, no. 6 (2025): 814. https://doi.org/10.3390/v17060814.

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Norovirus, a major cause of acute gastroenteritis, possesses a single-stranded positive-sense RNA genome. The viral 3C-like cysteine protease (3CLpro) plays a critical role in processing the viral polyprotein into mature non-structural proteins, a step essential for viral replication. Targeting 3CLpro has emerged as a promising strategy for developing small-molecule inhibitors against Norovirus. In this study, we employed a combination of virtual screening and the FlipGFP assay to identify potential inhibitors targeting the 3CLpro of Norovirus genotype GII.4. A library of approximately 58,800

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19

Ibrahim, Mahmoud A. A., Alaa H. M. Abdelrahman, Dina E. M. Mohamed, et al. "Chetomin, a SARS-CoV-2 3C-like Protease (3CLpro) Inhibitor: In Silico Screening, Enzyme Docking, Molecular Dynamics and Pharmacokinetics Analysis." Viruses 15, no. 1 (2023): 250. http://dx.doi.org/10.3390/v15010250.

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The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to over 6 million deaths. The 3C-like protease (3CLpro) enzyme of the SARS-CoV-2 virus is an attractive druggable target for exploring therapeutic drug candidates to combat COVID-19 due to its key function in viral replication. Marine natural products (MNPs) have attracted considerable attention as alternative sources of antiviral drug candidates. In looking for potential 3CLpro inhibitors, the MNP database (>14,000 molecules) was virtually screene

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20

Fakih, Taufik Muhammad, and Dwi Syah Fitra Ramadhan. "Prediction of SARS-CoV-2 3C-like protease (3CLpro) crystal structure to provide COVID-19 inhibitor design through computational studies." Biogenesis: Jurnal Ilmiah Biologi 9, no. 2 (2021): 213–19. http://dx.doi.org/10.24252/bio.v9i2.24520.

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Infectious diseases have lately become pandemic, posing a threat to global public health with the introduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously provisionally named 2019 novel coronavirus or 2019-nCoV). Technological advancements have increased the possibility of discovering natural inhibitor candidates capable of preventing and controlling COVID-19 infections. The SARS-CoV-2 3C-like protease (3CLpro) is critical for SARS-CoV-2 replication and is a prospective therapeutic target. This study aims to identify, evaluate, and explore the 3CLpro macromolecu

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21

Ma, Ling, Yongli Xie, Mei Zhu, et al. "Identification of Darunavir Derivatives for Inhibition of SARS-CoV-2 3CLpro." International Journal of Molecular Sciences 23, no. 24 (2022): 16011. http://dx.doi.org/10.3390/ijms232416011.

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The effective antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed around the world. The 3C-like protease (3CLpro) of SARS-CoV-2 plays a pivotal role in virus replication; it also has become an important therapeutic target for the infection of SARS-CoV-2. In this work, we have identified Darunavir derivatives that inhibit the 3CLpro through a high-throughput screening method based on a fluorescence resonance energy transfer (FRET) assay in vitro. We found that the compounds 29# and 50# containing polyphenol and caffeine derivatives as the

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22

Valipour, Mehdi, Silvia Di Giacomo, Antonella Di Sotto, and Hamid Irannejad. "Discovery of Chalcone-Based Hybrid Structures as High Affinity and Site-Specific Inhibitors against SARS-CoV-2: A Comprehensive Structural Analysis Based on Various Host-Based and Viral Targets." International Journal of Molecular Sciences 24, no. 10 (2023): 8789. http://dx.doi.org/10.3390/ijms24108789.

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Previous studies indicated that natural-based chalcones have significant inhibitory effects on the coronavirus enzymes 3CLpro and PLpro as well as modulation of some host-based antiviral targets (HBATs). In this study, a comprehensive computational and structural study was performed to investigate the affinity of our compound library consisting of 757 chalcone-based structures (CHA-1 to CHA-757) for inhibiting the 3CLpro and PLpro enzymes and against twelve selected host-based targets. Our results indicated that CHA-12 (VUF 4819) is the most potent and multi-target inhibitor in our chemical li

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23

Guijarro-Real, Carla, Mariola Plazas, Adrián Rodríguez-Burruezo, Jaime Prohens, and Ana Fita. "Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CLPro) Activity." Foods 10, no. 7 (2021): 1503. http://dx.doi.org/10.3390/foods10071503.

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Antiviral treatments inhibiting Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication may represent a strategy complementary to vaccination to fight the ongoing Coronavirus disease 19 (COVID-19) pandemic. Molecules or extracts inhibiting the SARS-CoV-2 chymotripsin-like protease (3CLPro) could contribute to reducing or suppressing SARS-CoV-2 replication. Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. Methanolic extracts were evaluated in vitro for inhibiti

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Jukič, Marko, Blaž Škrlj, Gašper Tomšič, Sebastian Pleško, Črtomir Podlipnik, and Urban Bren. "Prioritisation of Compounds for 3CLpro Inhibitor Development on SARS-CoV-2 Variants." Molecules 26, no. 10 (2021): 3003. http://dx.doi.org/10.3390/molecules26103003.

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COVID-19 represents a new potentially life-threatening illness caused by severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 pathogen. In 2021, new variants of the virus with multiple key mutations have emerged, such as B.1.1.7, B.1.351, P.1 and B.1.617, and are threatening to render available vaccines or potential drugs ineffective. In this regard, we highlight 3CLpro, the main viral protease, as a valuable therapeutic target that possesses no mutations in the described pandemically relevant variants. 3CLpro could therefore provide trans-variant effectiveness that is supported by st

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Huynh, Thi Ngoc Thanh, Thi Thanh Thu Tran, Thi My Hanh Pham, and Kha Quang Quach. "Study on the interaction mechanism of penciclovir drug on 3CLpro of SAR-COV-2 by simulation methods." Dong Thap University Journal of Science 12, no. 5 (2023): 42–47. http://dx.doi.org/10.52714/dthu.12.5.2023.1070.

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Since the outbreak of SAR-CoV-2 infections in Wuhan (China), researched communication is on race to investigate the specific antiviral drug for Covid-19 treatment. 3CLpro main protease is chosen as a protein target because of its high value in preventing the SAR-CoV-2 viral replications. In this study, we hereby aim to clarify the efficiency of Penciclovir in inhibiting the mechanic of 3CLpro target of SAR-CoV-2. Using docking simulation and molecular dynamic simulation (SMD), the interaction of Penciclovir with 3CLpro target was investigated. The results show that Penciclovir strongly interac

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Chen, Lili, Shuai Chen, Chunshan Gui, Jianhua Shen, Xu Shen, and Hualiang Jiang. "Discovering Severe Acute Respiratory Syndrome Coronavirus 3CL Protease Inhibitors: Virtual Screening, Surface Plasmon Resonance, and Fluorescence Resonance Energy Transfer Assays." Journal of Biomolecular Screening 11, no. 8 (2006): 915–21. http://dx.doi.org/10.1177/1087057106293295.

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An integrated system has been developed for discovering potent inhibitors of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CLpro) by virtual screening correlating with surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) technologies-based assays. The authors screened 81,287 small molecular compounds against SPECS database by virtual screening; 256 compounds were subsequently selected for biological evaluation. Through SPR technology-based assay, 52 from these 256 compounds were discovered to show binding to SARS-CoV 3CLpro. The enzymati

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Hamill, Pamela, Derek Hudson, Richard Y. Kao, et al. "Development of a red-shifted fluorescence-based assay for SARS-coronavirus 3CL protease: identification of a novel class of anti-SARS agents from the tropical marine sponge Axinella corrugata." Biological Chemistry 387, no. 8 (2006): 1063–74. http://dx.doi.org/10.1515/bc.2006.131.

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Abstract SARS-coronavirus (SARS-CoV) encodes a main protease, 3CLpro, which plays an essential role in the viral life cycle and is currently the prime target for discovering new anti-coronavirus agents. In this article, we report our success in developing a novel red-shifted (RS) fluorescence-based assay for 3CLpro and its application for identifying small-molecule anti-SARS agents from marine organisms. We have synthesised and characterised the first generation of a red-shifted internally quenched fluorogenic substrate (RS-IQFS) for 3CLpro based on resonance energy transfer between the donor

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Jo, Seri, Hwa Young Kim, Dong Hae Shin, and Mi-Sun Kim. "Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro." International Journal of Molecular Sciences 23, no. 9 (2022): 5268. http://dx.doi.org/10.3390/ijms23095268.

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3CLpro of SARS-CoV-2 is a promising target for developing anti-COVID19 agents. In order to evaluate the catalytic activity of 3CLpros according to the presence or absence of the dimerization domain, two forms had been purified and tested. Enzyme kinetic studies with a FRET method revealed that the catalytic domain alone presents enzymatic activity, despite it being approximately 8.6 times less than that in the full domain. The catalytic domain was crystallized and its X-ray crystal structure has been determined to 2.3 Å resolution. There are four protomers in the asymmetric unit. Intriguingly,

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Garland, Gavin D., Robert F. Harvey, Thomas E. Mulroney, et al. "Development of a colorimetric assay for the detection of SARS-CoV-2 3CLpro activity." Biochemical Journal 479, no. 8 (2022): 901–20. http://dx.doi.org/10.1042/bcj20220105.

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Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes the 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts an in vitro colorimetric gold nanoparticle (AuNP) based protease assay to specifically detect the activity of SARS-CoV-2 3CLpro as a purified recombinant protein and as a cellular protein exogenously expressed in HEK293T human cells. We also demons

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30

Li, Zhonghua, Hua Cao, Yufang Cheng, et al. "Inhibition of Porcine Epidemic Diarrhea Virus Replication and Viral 3C-Like Protease by Quercetin." International Journal of Molecular Sciences 21, no. 21 (2020): 8095. http://dx.doi.org/10.3390/ijms21218095.

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For the last decade, porcine epidemic diarrhea virus (PEDV) variant strains have caused severe damage to the global pig industry. Until now, no effective antivirals have been developed for the therapeutic treatment of PEDV infection. In the present study, we found that quercetin significantly suppressed PEDV infection at noncytotoxic concentrations. A molecular docking study indicated that quercetin might bind the active site and binding pocket of PEDV 3C-like protease (3CLpro). Surface plasmon resonance (SPR) analysis revealed that quercetin exhibited a binding affinity to PEDV 3CLpro. Based

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31

Fitriana, Adita Silvia, and Sri Royani. "Molecular Docking Study of Chalcone Derivatives as Potential Inhibitors of SARS-CoV-2 Main Protease." Indo. J. Chem. Res. 9, no. 3 (2022): 150–62. http://dx.doi.org/10.30598//ijcr.2022.9-fit.

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SARS-CoV-2 main protease is a potential target for the development of AntiCOVID-19. Several chalcones have inhibitory activity against 3CLpro SARS-CoV and 3CLpro MERS-CoV. This study aims to predict the potential of chalcones in inhibiting 3CLpro SARS-CoV-2, which plays a role in the viral replication process. In silico research carried the prediction through molecular docking toward proteins with PDB ID 6LU7 and 6Y2F. Compound K27 has a docking score more negative than lopinavir. This result indicates that compound K27 is predicted to inhibit the SARS-CoV-2 replication.

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Hegyi, Annette, Agnes Friebe, Alexander E. Gorbalenya, and John Ziebuhr. "Mutational analysis of the active centre of coronavirus 3C-like proteases." Journal of General Virology 83, no. 3 (2002): 581–93. http://dx.doi.org/10.1099/0022-1317-83-3-581.

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Formation of the coronavirus replication–transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CLpro, was determined. Comparative sequence analyses revealed that FIPV 3CLpro and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational an

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Saquib, Quaiser, Ahmed H. Bakheit, Sarfaraz Ahmed, Sabiha M. Ansari, Abdullah M. Al-Salem, and Abdulaziz A. Al-Khedhairy. "Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CLPro and PLPro) by Molecular Docking and Dynamic Simulation Studies." Molecules 29, no. 5 (2024): 998. http://dx.doi.org/10.3390/molecules29050998.

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We provide promising computational (in silico) data on phytochemicals (compounds 1–10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1–10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1–10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversib

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Komissarov, Alexey, Maria Karaseva, Marina Roschina, Sergey Kostrov, and Ilya Demidyuk. "The SARS-CoV-2 main protease doesn’t induce cell death in human cells in vitro." PLOS ONE 17, no. 5 (2022): e0266015. http://dx.doi.org/10.1371/journal.pone.0266015.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19) which has extremely rapidly spread worldwide. In order to develop the effective antiviral therapies, it is required to understand the molecular mechanisms of the SARS-CoV-2 pathogenesis. The main protease, or 3C-like protease (3CLpro), plays the essential role in the coronavirus replication that makes the enzyme a promising therapeutic target. Viral enzymes are known to be multifunctional. Particularly, 3CLpro of SARS-CoV was shown to induce apoptosis in addition to its main functio

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Zhang, Shilei, Jingfeng Wang, and Genhong Cheng. "Protease cleavage of RNF20 facilitates coronavirus replication via stabilization of SREBP1." Proceedings of the National Academy of Sciences 118, no. 37 (2021): e2107108118. http://dx.doi.org/10.1073/pnas.2107108118.

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COVID-19, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), has presented a serious risk to global public health. The viral main protease Mpro (also called 3Clpro) encoded by NSP5 is an enzyme essential for viral replication. However, very few host proteins have been experimentally validated as targets of 3Clpro. Here, through bioinformatics analysis of 300 interferon stimulatory genes (ISGs) based on the prediction method NetCorona, we identify RNF20 (Ring Finger Protein 20) as a novel target of 3Clpro. We have also provided evidence that 3Clpro, but not the mutant 3ClproC145A wi

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Duarte Filho, Luiz Antonio Miranda de Souza, Cintia Emi Yanaguibashi Leal, Pierre-Edouard Bodet, et al. "The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy." Marine Drugs 22, no. 6 (2024): 244. http://dx.doi.org/10.3390/md22060244.

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Brown seaweeds of the Fucus genus represent a rich source of natural antiviral products. In this study, a Fucus ceranoides hydroalcoholic extract (FCHE) was found to inhibit 74.2 ± 1.3% of the proteolytic activity of the free SARS-CoV-2 3CL protease (3CLpro), an enzyme that plays a pivotal role in polyprotein processing during coronavirus replication and has been identified as a relevant drug discovery target for SARS- and MERS-CoVs infections. To purify and identify 3CLpro ligands with potential inhibitory activity using a one-step approach, we immobilized the enzyme onto magnetic microbeads

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Rajeswari, Kalepu, W. Jun Chen, A. Aashika, et al. "Binding Interaction Analysis of Phytoconstituents of Commiphora mukul with 3CLPro and PlPro Enzymes of SARS-CoV-2 Virus." ECS Transactions 107, no. 1 (2022): 7509–30. http://dx.doi.org/10.1149/10701.7509ecst.

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The SARS-CoV-2 belongs to a family of coronaviruses, responsible for the COVID-19 pandemic. The Chymotrypsin-like protease (3CLpro) and Papain-like protease (PLPro), two important enzymes of the SARS-CoV-2, play a key role in translating the viral RNA genome into functional proteins. This study aimed to evaluate and analyze the binding interactions of phytochemicals of oleoresin of Commiphora mukul plant with 3CLPro and PLPro enzymes of SARS-CoV-2 virus. Docking studies were performed on 3CLPro and PLPro with 30 phytoconstituents using AutoDock Vina. A total of 12 compounds were shortlisted ba

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Wang, Yaxin, Binghong Xu, Sen Ma, et al. "Discovery of SARS-CoV-2 3CLPro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein–Ligand Interactions." International Journal of Molecular Sciences 23, no. 4 (2022): 2392. http://dx.doi.org/10.3390/ijms23042392.

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As the etiological agent for the coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges the ongoing efforts of vaccine development and drug design. Due to the accumulating cases of breakthrough infections, there are urgent needs for broad-spectrum antiviral medicines. Here, we designed and examined five new tetrapeptidomimetic anti-SARS-CoV-2 inhibitors targeting the 3C-Like protease (3CLPro), which is highly conserved among coronaviruses and essential for viral replications. We significantly improved the efficacy of a ketoamide lead compound based on

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Olubiyi, Olujide O., Maryam Olagunju, Monika Keutmann, Jennifer Loschwitz, and Birgit Strodel. "High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2." Molecules 25, no. 14 (2020): 3193. http://dx.doi.org/10.3390/molecules25143193.

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We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, 3CLpro of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. From our screening of over one million compounds including approved drugs, investigational drugs, natural products, and organic compounds, and a rescreening protocol incorporating enzyme dynamics via ensemble docking, we have been able to identify a range of prospective 3CLpro inhibitors. Importantly, some of the identified compounds had previously been reported to exhibi

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Yang, Cheng-Wei, Yung-Ning Yang, Po-Huang Liang, et al. "Novel Small-Molecule Inhibitors of Transmissible Gastroenteritis Virus." Antimicrobial Agents and Chemotherapy 51, no. 11 (2007): 3924–31. http://dx.doi.org/10.1128/aac.00408-07.

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ABSTRACT We used swine testicle (ST) cells infected with transmissible gastroenteritis virus (TGEV) and an indirect immunofluorescent assay with antibodies against TGEV spike and nucleocapsid proteins to screen small-molecule compounds that inhibit TGEV replication. Analogues of initial hits were collected and subjected to a 3CL protease (3CLpro) inhibition assay with recombinant 3CLpro and a fluorogenic peptide substrate. A series of benzothiazolium compounds were found to have inhibitory activity against TGEV 3CLpro and to exert anti-TGEV activities in terms of viral protein and RNA replicat

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Knez, Damijan, Matic Proj, Krištof Bozovičar та Stanislav Gobec. "α-Heteroarylthiomethyl ketones: Small molecule inhibitors of 3CL^pro". Acta Pharmaceutica 75, № 2 (2025): 283–97. https://doi.org/10.2478/acph-2025-0023.

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Abstract The main protease 3CLpro of the SARS-CoV-2 virus is a well--established therapeutic target for the treatment of COVID-19. In this study, we screened an in-house compound library and identified a series of α-heteroarylthiomethyl ketones as inhibitors of 3CLpro. Among these, analogues 31 and 33 emerged as the most interesting candidates with IC 50 values of 95.4 ± 3.1 and 95.0 ± 6.9 µmol L– 1, respectively. Preliminary in vitro studies suggest a potential covalent mode of inhibition, although further studies are required to confirm this mechanism. These findings provide a new chemical s

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Sobhy, Remah, Asad Nawaz, Mohammad Fikry, et al. "In-Silico Evaluation of 10 Structurally Different Glucosinolates on the Key Enzyme of SARS-CoV-2." Science of Advanced Materials 14, no. 1 (2022): 162–74. http://dx.doi.org/10.1166/sam.2022.4190.

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The novel coronavirus (2019-nCoV) triggered a worldwide rise in the prevalence of the coronavirus outbreak (COVID-19) and surfaced as a universal wellbeing matter. Analogous with SARS-CoV and MERS-CoV, the main 3-chymotrypsin-alike cysteine protease (3CLPro) virus enzyme that manages the replications of 2019-nCoV and regulates its existence span, possibly will be considered like a medication break through focus. In this study, the binding potential of 10 glucosinolates (Glu) having a variety of structures was studied with the catalytic dyad remains of 2019-nCoV-3CLPro by molecular cutting deve

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Du, Weian, Liang Zhao, Rong Wu, et al. "Predicting drug–Protein interaction with deep learning framework for molecular graphs and sequences: Potential candidates against SAR-CoV-2." PLOS ONE 19, no. 5 (2024): e0299696. http://dx.doi.org/10.1371/journal.pone.0299696.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 disease, which represents a new life-threatening disaster. Regarding viral infection, many therapeutics have been investigated to alleviate the epidemiology such as vaccines and receptor decoys. However, the continuous mutating coronavirus, especially the variants of Delta and Omicron, are tended to invalidate the therapeutic biological product. Thus, it is necessary to develop molecular entities as broad-spectrum antiviral drugs. Coronavirus replication is controlled by the viral 3-chymotrypsin-like cysteine

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Haniyya, M. Ulfah, A. Riswoko, L. Mulyawati, T. Ernawati, and I. Helianti. "Production of recombinant SARS-CoV-2 3CL-protease: The key for the development of protease inhibitors screening kit in search of potential herb cure for COVID-19." IOP Conference Series: Earth and Environmental Science 976, no. 1 (2022): 012051. http://dx.doi.org/10.1088/1755-1315/976/1/012051.

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Abstract Coronavirus disease-19 (COVID-19) pandemic caused millions of deaths and socio-economics damage worldwide. Corresponding to this, many studies on antiviral drugs exploration are rising to investigate the potential of drug compounds that can repress the replication of the SARS-CoV-2 virus by targeting its main protease named 3-chymotrypsin like protease (3CLpro). Without 3CLpro splicing, polyproteins of SARS-CoV-2 will not function to form new virions. We conducted an in silico thermodynamic study, and found several already known compounds from natural sources such as lovastatin, quini

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Ziebuhr, John, and Stuart G. Siddell. "Processing of the Human Coronavirus 229E Replicase Polyproteins by the Virus-Encoded 3C-Like Proteinase: Identification of Proteolytic Products and Cleavage Sites Common to pp1a and pp1ab." Journal of Virology 73, no. 1 (1999): 177–85. http://dx.doi.org/10.1128/jvi.73.1.177-185.1999.

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ABSTRACT Replicase gene expression by the human coronavirus 229E involves the synthesis of two large polyproteins, pp1a and pp1ab. Experimental evidence suggests that these precursor molecules are subject to extensive proteolytic processing. In this study, we show that a chymotrypsin-like enzyme, the virus-encoded 3C-like proteinase (3CLpro), cleaves within a common region of pp1a and pp1ab (amino acids 3490 to 4068) at four sites. trans-cleavage assays revealed that polypeptides of 5, 23, 12, and 16 kDa are processed from pp1a/pp1ab by proteolysis of the peptide bonds Q3546/S3547, Q3629/S3630

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Cheng, Jin, Yixuan Hao, Qin Shi, et al. "Discovery of Novel Chinese Medicine Compounds Targeting 3CL Protease by Virtual Screening and Molecular Dynamics Simulation." Molecules 28, no. 3 (2023): 937. http://dx.doi.org/10.3390/molecules28030937.

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The transmission and infectivity of COVID-19 have caused a pandemic that has lasted for several years. This is due to the constantly changing variants and subvariants that have evolved rapidly from SARS-CoV-2. To discover drugs with therapeutic potential for COVID-19, we focused on the 3CL protease (3CLpro) of SARS-CoV-2, which has been proven to be an important target for COVID-19 infection. Computational prediction techniques are quick and accurate enough to facilitate the discovery of drugs against the 3CLpro of SARS-CoV-2. In this paper, we used both ligand-based virtual screening and stru

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Razali, Rafida, Vijay Kumar Subbiah, and Cahyo Budiman. "Technical Data of Heterologous Expression and Purification of SARS-CoV-2 Proteases Using Escherichia coli System." Data 6, no. 9 (2021): 99. http://dx.doi.org/10.3390/data6090099.

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The SARS-CoV-2 coronavirus expresses two essential proteases: firstly, the 3Chymotrypsin-like protease (3CLpro) or main protease (Mpro), and secondly, the papain-like protease (PLpro), both of which are considered as viable drug targets for the inhibition of viral replication. In order to perform drug discovery assays for SARS-CoV-2, it is imperative that efficient methods are established for the production and purification of 3CLpro and PLpro of SARS-CoV-2, designated as 3CLpro-CoV2 and PLpro-CoV2, respectively. This article expands the data collected in the attempts to express SARS-CoV-2 pro

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Wang, Yuanyuan, Yulin Zhou, and Faez Iqbal Khan. "Molecular Insights into Structural Dynamics and Binding Interactions of Selected Inhibitors Targeting SARS-CoV-2 Main Protease." International Journal of Molecular Sciences 25, no. 24 (2024): 13482. https://doi.org/10.3390/ijms252413482.

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The SARS-CoV-2 main protease (Mpro, also known as 3CLpro) is a key target for antiviral therapy due to its critical role in viral replication and maturation. This study investigated the inhibitory effects of Bofutrelvir, Nirmatrelvir, and Selinexor on 3CLpro through molecular docking, molecular dynamics (MD) simulations, and free energy calculations. Nirmatrelvir exhibited the strongest binding affinity across docking tools (AutoDock Vina: −8.3 kcal/mol; DiffDock: −7.75 kcal/mol; DynamicBound: 7.59 to 7.89 kcal/mol), outperforming Selinexor and Bofutrelvir. Triplicate 300 ns MD simulations rev

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Rizzuti, Bruno, Laura Ceballos-Laita, David Ortega-Alarcon, et al. "Sub-Micromolar Inhibition of SARS-CoV-2 3CLpro by Natural Compounds." Pharmaceuticals 14, no. 9 (2021): 892. http://dx.doi.org/10.3390/ph14090892.

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Inhibiting the main protease 3CLpro is the most common strategy in the search for antiviral drugs to fight the infection from SARS-CoV-2. We report that the natural compound eugenol is able to hamper in vitro the enzymatic activity of 3CLpro, the SARS-CoV-2 main protease, with an inhibition constant in the sub-micromolar range (Ki = 0.81 μM). Two phenylpropene analogs were also tested: the same effect was observed for estragole with a lower potency (Ki = 4.1 μM), whereas anethole was less active. The binding efficiency index of these compounds is remarkably favorable due also to their small mo

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Morita, Takeshi, Kei Miyakawa, Sundararaj Stanleyraj Jeremiah, et al. "All-Trans Retinoic Acid Exhibits Antiviral Effect against SARS-CoV-2 by Inhibiting 3CLpro Activity." Viruses 13, no. 8 (2021): 1669. http://dx.doi.org/10.3390/v13081669.

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The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread despite the global efforts taken to control it. The 3C-like protease (3CLpro), the major protease of SARS-CoV-2, is one of the most interesting targets for antiviral drug development because it is highly conserved among SARS-CoVs and plays an important role in viral replication. Herein, we developed high throughput screening for SARS-CoV-2 3CLpro inhibitor based on AlphaScreen. We screened 91 natural product compounds and found that all-trans retinoic acid (ATRA), an FDA-approved drug, inhibited 3CLpro activity. The 3CLpro inhib

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