1
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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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2
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Velma G, Shen Z, Holberg C, Fu J, Soleymani F, Cooper L, Ramos OL, Indukuri D, Musku SR, Rychetsky P, Slilaty S, Li Z, Ratia K, Rong L, Schenten D, Xiong R, J Thatcher GR. Non-Covalent Inhibitors of SARS-CoV-2 Papain-Like Protease (PLpro): In Vitro and In Vivo Antiviral Activity. J Med Chem 2024; 67:13681-13702. [PMID: 39102360 PMCID: PMC11345844 DOI: 10.1021/acs.jmedchem.4c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
The SARS-CoV-2 papain-like protease (PLpro), essential for viral processing and immune response disruption, is a promising target for treating acute infection of SARS-CoV-2. To date, there have been no reports of PLpro inhibitors with both submicromolar potency and animal model efficacy. To address the challenge of PLpro's featureless active site, a noncovalent inhibitor library with over 50 new analogs was developed, targeting the PLpro active site by modulating the BL2-loop and engaging the BL2-groove. Notably, compounds 42 and 10 exhibited strong antiviral effects and were further analyzed pharmacokinetically. 10, in particular, showed a significant lung accumulation, up to 12.9-fold greater than plasma exposure, and was effective in a mouse model of SARS-CoV-2 infection, as well as against several SARS-CoV-2 variants. These findings highlight the potential of 10 as an in vivo chemical probe for studying PLpro inhibition in SARS-CoV-2 infection.
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Affiliation(s)
- Ganga
Reddy Velma
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Zhengnan Shen
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Cameron Holberg
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Jiqiang Fu
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Farinaz Soleymani
- Department
of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
| | - Laura Cooper
- Department
of Microbiology, College of Medicine, University
of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Omar Lozano Ramos
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Divakar Indukuri
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Soumya Reddy Musku
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Pavel Rychetsky
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Steve Slilaty
- Sunshine
Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Zuomei Li
- Sunshine
Biopharma Inc, 333 Las Olas Way, CU4 Suite 433, Fort Lauderdale 33301, Florida, United States
| | - Kiira Ratia
- Research
Resources Center, University of Illinois
at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Lijun Rong
- Department
of Microbiology, College of Medicine, University
of Illinois at Chicago (UIC), Chicago 60612, Illinois, United States
| | - Dominik Schenten
- Department
of Immunology, College of Medicine, University
of Arizona, Tucson 85721, Arizona, United States
| | - Rui Xiong
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
| | - Gregory R. J Thatcher
- Department
of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, University of Arizona, Tucson 85721, Arizona, United States
- Department
of Chemistry & Biochemistry, Colleges of Science and Medicine, University of Arizona, Tucson 85721, Arizona, United States
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3
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Zhang W, Xiao L, Li D, Hu Y, Yu W. New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs. J Med Chem 2024; 67:11522-11542. [PMID: 38967785 DOI: 10.1021/acs.jmedchem.4c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths, posing a serious threat to public health and safety. Rapid mutations of SARS-CoV-2 and complex interactions among multiple targets during infection pose a risk of expiry for small molecule inhibitors. This suggests that the traditional concept of "one bug, one drug" could be ineffective in dealing with the coronavirus. The dual-target drug strategy is expected to be the key to ending coronavirus infections. However, the lack of design method and improper combination of dual-targets poses obstacle to the discovery of new dual-target drugs. In this Perspective, we summarized the profiles concerning drug design methods, structure-activity relationships, and pharmacological parameters of dual-target drugs for the treatment of COVID-19. Importantly, we underscored how target combination and rational drug design illuminate the development of dual-target drugs for SARS-CoV-2.
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Affiliation(s)
- Wenyi Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lecheng Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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4
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Schäfer A, Debnath S, Tränkle J, Mohr T, Kappes MM. Acriflavine Is More than It Seems: Resolving Optical Properties of Multiple Isomeric Constituents at 5 K. J Phys Chem Lett 2024; 15:7295-7301. [PMID: 38980149 DOI: 10.1021/acs.jpclett.4c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Ion mobility spectrometry at room temperature was combined with vibrationally resolved electronic spectroscopy of mass-selected ions at 5 K to study the well-known cationic fluorophore acriflavine. One- and two-color photodepletion action spectra recorded in gas-phase (by helium tagging) as well as dispersed fluorescence spectra obtained in neon matrix (after soft-landing deposition) indicate that the primary cation mass electrosprayed from solution comprises two isomers with different optical properties. Theory at the TD-DFT level allowed full spectral assignment. The results have implications for the preparation of novel thin film photonic materials by low-energy ion beam deposition.
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Affiliation(s)
- Alexander Schäfer
- Institute of Physical Chemistry II, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sreekanta Debnath
- Institute of Physical Chemistry II, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Jana Tränkle
- Institute of Physical Chemistry II, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Theresa Mohr
- Institute of Physical Chemistry II, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry II, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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5
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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6
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Teruel N, Borges VM, Najmanovich R. Surfaces: a software to quantify and visualize interactions within and between proteins and ligands. Bioinformatics 2023; 39:btad608. [PMID: 37788107 PMCID: PMC10568369 DOI: 10.1093/bioinformatics/btad608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/23/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023] Open
Abstract
SUMMARY Computational methods for the quantification and visualization of the relative contribution of molecular interactions to the stability of biomolecular structures and complexes are fundamental to understand, modulate and engineer biological processes. Here, we present Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics. AVAILABILITY AND IMPLEMENTATION All scripts are available at https://github.com/NRGLab/Surfaces. Surface's documentation is available at https://surfaces-tutorial.readthedocs.io/en/latest/index.html.
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Affiliation(s)
- Natália Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal H3T 1J4, Canada
| | - Vinicius Magalhães Borges
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, USA
| | - Rafael Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal H3T 1J4, Canada
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7
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Dabrowska A, Botwina P, Barreto-Duran E, Kubisiak A, Obloza M, Synowiec A, Szczepanski A, Targosz-Korecka M, Szczubialka K, Nowakowska M, Pyrc K. Reversible rearrangement of the cellular cytoskeleton: A key to the broad-spectrum antiviral activity of novel amphiphilic polymers. Mater Today Bio 2023; 22:100763. [PMID: 37600352 PMCID: PMC10433002 DOI: 10.1016/j.mtbio.2023.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
The battle against emerging viral infections has been uneven, as there is currently no broad-spectrum drug available to contain the spread of novel pathogens throughout the population. Consequently, the pandemic outbreak that occurred in early 2020 laid bare the almost empty state of the pandemic box. Therefore, the development of novel treatments with broad specificity has become a paramount concern in this post-pandemic era. Here, we propose copolymers of poly (sodium 2-(acrylamido)-2-methyl-1-propanesulfonate) (PAMPS) and poly (sodium 11-(acrylamido)undecanoate (AaU), both block (PAMPS75-b-PAaUn) and random (P(AMPSm-co-AaUn)) that show efficacy against a broad range of alpha and betacoronaviruses. Owing to their intricate architecture, these polymers exhibit a highly distinctive mode of action, modulating nano-mechanical properties of cells and thereby influencing viral replication. Through the employment of confocal and atomic force microscopy techniques, we discerned perturbations in actin and vimentin filaments, which correlated with modification of cellular elasticity and reduction of glycocalyx layer. Intriguingly, this process was reversible upon polymer removal from the cells. To ascertain the applicability of our findings, we assessed the efficacy and underlying mechanism of the inhibitors using fully differentiated human airway epithelial cultures, wherein near-complete abrogation of viral replication was documented. Given their mode of action, these polymers can be classified as biologically active nanomaterials that exploit a highly conserved molecular target-cellular plasticity-proffering the potential for truly broad-spectrum activity while concurrently for drug resistance development is minimal.
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Affiliation(s)
- Agnieszka Dabrowska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Pawel Botwina
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Emilia Barreto-Duran
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Agata Kubisiak
- Department of Physics of Nanostructures and Nanotechnology, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Lojasiewicza 11, 30-348, Cracow, Poland
| | - Magdalena Obloza
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Aleksandra Synowiec
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Lojasiewicza 11, 30-348, Cracow, Poland
| | - Artur Szczepanski
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Marta Targosz-Korecka
- Department of Physics of Nanostructures and Nanotechnology, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Lojasiewicza 11, 30-348, Cracow, Poland
| | - Krzysztof Szczubialka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
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8
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Brian Chia CS, Pheng Lim S. A Patent Review on SARS Coronavirus Papain-Like Protease (PL pro ) Inhibitors. ChemMedChem 2023; 18:e202300216. [PMID: 37248169 DOI: 10.1002/cmdc.202300216] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 6.6 million fatalities by 31 December 2022. So far, only three antiviral drugs have been granted emergency use authorisation or approved by the FDA. The SARS-CoV-2 papain-like protease (PLpro ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis although no inhibitors have yet been approved. This patent review discusses coronavirus PLpro inhibitors reported in patents published between 1 January 2003 to 2 March 2023, giving an overview on the inhibitors that have generated commercial interest, especially amongst drug companies.
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Affiliation(s)
- C S Brian Chia
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
| | - Siew Pheng Lim
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
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9
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El-Masry AA, Zeid AM. Acriflavine: an efficient green fluorescent probe for sensitive analysis of aceclofenac in pharmaceutical formulations. BMC Chem 2023; 17:93. [PMID: 37533016 PMCID: PMC10394782 DOI: 10.1186/s13065-023-00979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/21/2023] [Indexed: 08/04/2023] Open
Abstract
Acriflavine is a multipurpose drug that shows antibacterial, antiviral, antimalarial, and antifungal activities. The remarkable native fluorescence of acriflavine is exploited in analytical chemistry field as an efficient probe for analysis of pharmaceutical and biological compounds. The fluorescent probe action of acriflavine is based on the remarkable fluorescence turning-off via formation of ion-pair complexes with acidic drugs at a specific pH. Herein, the acidic drug aceclofenac is analysed for the first time using acriflavine as a fluorescent probe. Aceclofenac can form an ion-pair complex with acriflavine at pH 8.5, and hence it partially turns off the fluorescence intensity of acriflavine over a concentration range of 1-20 µg/mL. The fluorescence quenching was monitored at 502 nm following an excitation at 265 or 451 nm. The reaction stoichiometry between acriflavine and aceclofenac was found to be 1:1 using limiting logarithmic method. The type of quenching was confirmed to be static using Stern-Volmer plot. The method showed low values of quantitation limit (0.89 µg/mL) and detection limit (0.29 µg/mL). Moreover, the method was linear (r = 0.9999), accurate, precise (RSD < 1.7%), robust, and specific. The proposed method was successfully employed to analyse aceclofenac in its dosage forms with high %recovery (98-101%). Additionally, GAPI and AGREE approaches were used to guarantee the suggested techniques' greenness, and the findings showed an excellent level of greenness.
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Affiliation(s)
- Amal A El-Masry
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Abdallah M Zeid
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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10
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Akinsulie OC, Shahzad S, Ogunleye SC, Oladapo IP, Joshi M, Ugwu CE, Gbadegoye JO, Hassan FO, Adeleke R, Afolabi Akande Q, Adesola RO. Crosstalk between hypoxic cellular micro-environment and the immune system: a potential therapeutic target for infectious diseases. Front Immunol 2023; 14:1224102. [PMID: 37600803 PMCID: PMC10434535 DOI: 10.3389/fimmu.2023.1224102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/26/2023] [Indexed: 08/22/2023] Open
Abstract
There are overwhelming reports on the promotional effect of hypoxia on the malignant behavior of various forms of cancer cells. This has been proposed and tested exhaustively in the light of cancer immunotherapy. However, there could be more interesting functions of a hypoxic cellular micro-environment than malignancy. There is a highly intricate crosstalk between hypoxia inducible factor (HIF), a transcriptional factor produced during hypoxia, and nuclear factor kappa B (NF-κB) which has been well characterized in various immune cell types. This important crosstalk shares common activating and inhibitory stimuli, regulators, and molecular targets. Impaired hydroxylase activity contributes to the activation of HIFs. Inflammatory ligands activate NF-κB activity, which leads to the expression of inflammatory and anti-apoptotic genes. The eventual sequelae of the interaction between these two molecular players in immune cells, either bolstering or abrogating functions, is largely cell-type dependent. Importantly, this holds promise for interesting therapeutic interventions against several infectious diseases, as some HIF agonists have helped prevent immune-related diseases. Hypoxia and inflammation are common features of infectious diseases. Here, we highlighted the role of this crosstalk in the light of functional immunity against infection and inflammation, with special focus on various innate and adaptive immune cells. Particularly, we discussed the bidirectional effects of this crosstalk in the regulation of immune responses by monocytes/macrophages, dendritic cells, neutrophils, B cells, and T cells. We believe an advanced understanding of the interplay between HIFs and NF-kB could reveal novel therapeutic targets for various infectious diseases with limited treatment options.
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Affiliation(s)
- Olalekan Chris Akinsulie
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Sammuel Shahzad
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Seto Charles Ogunleye
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Ifeoluwa Peace Oladapo
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Melina Joshi
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | - Charles Egede Ugwu
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, United States
| | - Joy Olaoluwa Gbadegoye
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Fasilat Oluwakemi Hassan
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Richard Adeleke
- College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Qudus Afolabi Akande
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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11
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Shiraishi Y, Shimada I. NMR Characterization of the Papain-like Protease from SARS-CoV-2 Identifies the Conformational Heterogeneity in Its Inhibitor-Binding Site. J Am Chem Soc 2023. [PMID: 37478405 DOI: 10.1021/jacs.3c04115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Papain-like protease (PLpro) from severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a prime target for the development of antivirals for Coronavirus disease 2019 (COVID-19). However, drugs that target the PLpro protein have not yet been approved. In order to gain insights into the development of a PLpro inhibitor, conformational dynamics of PLpro in complex with GRL0617, the most well-characterized PLpro inhibitor, were investigated using nuclear magnetic resonance (NMR) spectroscopy in solution. Although mutational analyses demonstrated that the L162 sidechain interaction is responsible for the affinity for GRL0617, NMR analyses revealed that L162 in the inhibitor-binding pocket underwent conformational exchange and was not fixed in the conformation in which it formed a contact with ortho-methyl group of GRL0617. The identified conformational dynamics would provide a rationale for the binding mechanism of a covalent inhibitor designed based on GRL0617.
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Affiliation(s)
- Yutaro Shiraishi
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ichio Shimada
- Laboratory for Dynamic Structure of Biomolecules, RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima 739-8528, Japan
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12
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Piorecka K, Kurjata J, Gostynski B, Kazmierski S, Stanczyk WA, Marcinkowska M, Janaszewska A, Klajnert-Maculewicz B. Is acriflavine an efficient co-drug in chemotherapy? RSC Adv 2023; 13:21421-21431. [PMID: 37465576 PMCID: PMC10350790 DOI: 10.1039/d3ra02608f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is a global health problem being the second worldwide cause of deaths right after cardiovascular diseases. The main methods of cancer treatment involve surgery, radiation and chemotherapy with an emphasis on the latter. Thus development of nanochemistry and nanomedicine in a search for more effective and safer cancer treatment is an important area of current research. Below, we present interaction of doxorubicin and acriflavine and the cytotoxicity of these drug nano-complexes towards cervical cancer (HeLa) cells. Experimental results obtained from NMR measurements and fluorescence spectroscopy show that the drugs' interaction was due to van der Waals forces, formation of hydrogen bonds and π-π stacking. Quantum molecular simulations confirmed the experimental results with regard to existing π-π stacking. Additionally it was shown that, at the level of theory applied (DFT, triple zeta basis set), the stacking interactions comprise the most preferable interactions (the lowest ΔG ca. -12 kcal mol-1) both between the molecules forming the acriflavine system and between the other component - another drug (doxorubicin) dimer. Biological tests performed on HeLa cells showed high cytotoxicity of the complexes, comparable to free drugs (ACF and DOX), both after 24 and 48 hours of incubation. For non-cancerous cells, a statistically significant difference in the cytotoxicity of drugs and complexes was observed in the case of a short incubation period. The results of the uptake study showed significantly more efficient cellular uptake of acriflavine than doxorubicin, whether administered alone or in combination with an anthracycline. The mechanism determining the selective uptake of acriflavine and ACF : DOX complexes towards non-cancer and cancer cells should be better understood in the future, as it may be of key importance in the design of complexes with toxic anti-cancer drugs.
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Affiliation(s)
- Kinga Piorecka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Jan Kurjata
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Bartłomiej Gostynski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Slawomir Kazmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Wlodzimierz A Stanczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Sienkiewicza 112 Lodz 90-363 Poland
| | - Monika Marcinkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
| | - Anna Janaszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
| | - Barbara Klajnert-Maculewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz 141/143 Pomorska St. 90-236 Lodz Poland
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13
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Pang X, Xu W, Liu Y, Li H, Chen L. The research progress of SARS-CoV-2 main protease inhibitors from 2020 to 2022. Eur J Med Chem 2023; 257:115491. [PMID: 37244162 DOI: 10.1016/j.ejmech.2023.115491] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication and transcription and represents an attractive drug target for fighting COVID-19. Many SARS-CoV-2 Mpro inhibitors have been reported, including covalent and noncovalent inhibitors. The SARS-CoV-2 Mpro inhibitor PF-07321332 (Nirmatrelvir) designed by Pfizer has been put on the market. This paper briefly introduces the structural characteristics of SARS-CoV-2 Mpro and summarizes the research progress of SARS-CoV-2 Mpro inhibitors from the aspects of drug repurposing and drug design. These information will provide a basis for the drug development of treating the infection of SARS-CoV-2 and even other coronaviruses in the future.
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Affiliation(s)
- Xiaojing Pang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Wei Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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14
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Luo J, Zhang Z, Zhao S, Gao R. A Comparison of Etiology, Pathogenesis, Vaccinal and Antiviral Drug Development between Influenza and COVID-19. Int J Mol Sci 2023; 24:ijms24076369. [PMID: 37047339 PMCID: PMC10094131 DOI: 10.3390/ijms24076369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Influenza virus and coronavirus, two kinds of pathogens that exist widely in nature, are common emerging pathogens that cause respiratory tract infections in humans. In December 2019, a novel coronavirus SARS-CoV-2 emerged, causing a severe respiratory infection named COVID-19 in humans, and raising a global pandemic which has persisted in the world for almost three years. Influenza virus, a seasonally circulating respiratory pathogen, has caused four global pandemics in humans since 1918 by the emergence of novel variants. Studies have shown that there are certain similarities in transmission mode and pathogenesis between influenza and COVID-19, and vaccination and antiviral drugs are considered to have positive roles as well as several limitations in the prevention and control of both diseases. Comparative understandings would be helpful to the prevention and control of these diseases. Here, we review the study progress in the etiology, pathogenesis, vaccine and antiviral drug development for the two diseases.
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15
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Boivin L, Harvey PD. Virus Management Using Metal-Organic Framework-Based Technologies. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 36892577 DOI: 10.1021/acsami.3c00922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The eradication and isolation of viruses are two concurrent approaches to protect ourselves from viral infections and diseases. The quite versatile porous materials called metal-organic frameworks (MOFs), have recently emerged as efficient nanosized tools to manage viruses, and several strategies to accomplish these tasks have been developed. This review describes these strategies employing nanoscale MOFs against SARS-CoV-2, HIV-1, tobacco mosaic virus, etc., which include the sequestration by host-guest penetration inside pores, mineralization, design of a physical barrier, controlled delivery of organic and inorganic antiviral drugs or bioinhibitors, photosensitization of singlet oxygen, and direct contact with inherently cytotoxic MOFs.
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Affiliation(s)
- Léo Boivin
- Département de Chimie, Université de Sherbrooke, Québec J1K 2R1, Canada
| | - Pierre D Harvey
- Département de Chimie, Université de Sherbrooke, Québec J1K 2R1, Canada
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16
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Bioinformatics analysis based on high-throughput sequencing data to identify hub genes related to different clinical types of COVID-19. Funct Integr Genomics 2023; 23:71. [PMID: 36856850 PMCID: PMC9975444 DOI: 10.1007/s10142-023-00998-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
This article aims to explore hub genes related to different clinical types of cases with COVID-19 and predict the therapeutic drugs related to severe cases. The expression profile of GSE166424 was divided into four data sets according to different clinical types of COVID-19 and then calculated the differential expression genes (DEGs). The specific genes of four clinical types of COVID-19 were obtained by Venn diagram and conducted enrichment analysis, protein-protein interaction (PPI) networks analysis, screening hub genes, and ROC curve analysis. The hub genes related to severe cases were verified in GSE171110, their RNA-specific expression tissues were obtained from the HPA database, and potential therapeutic drugs were predicted through the DGIdb database. There were 536, 266, 944, and 506 specific genes related to asymptomatic infections, mild, moderate, and severe cases, respectively. The hub genes of severe specific genes were AURKB, BRCA1, BUB1, CCNB1, CCNB2, CDC20, CDC6, KIF11, TOP2A, UBE2C, and RPL11, and also differentially expressed in GSE171110 (P < 0.05), and their AUC values were greater than 0.955. The RNA tissue specificity of AURKB, CDC6, KIF11, UBE2C, CCNB2, CDC20, TOP2A, BUB1, and CCNB1 specifically enhanced on lymphoid tissue; CCNB2, CDC20, TOP2A, and BUB1 specifically expressed on the testis. Finally, 55 drugs related to severe COVID-19 were obtained from the DGIdb database. Summary, AURKB, BRCA1, BUB1, CCNB1, CCNB2, CDC20, CDC6, KIF11, TOP2A, UBE2C, and RPL11 may be potential diagnostic biomarkers for severe COVID-19, which may affect immune and male reproductive systems. 55 drugs may be potential therapeutic drugs for severe COVID-19.
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17
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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18
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Tkaczyk-Wlizło A, Mitrowska K. Occurrence and ecotoxicological risk assessment of pharmacologically active dyes in the environmental water of Poland. CHEMOSPHERE 2023; 313:137432. [PMID: 36460146 DOI: 10.1016/j.chemosphere.2022.137432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The interest in the fate of pharmacologically active substances (PASs) in the aquatic environment continually increases. However, little is known about pharmacologically active dyes (PADs) as contaminants of water bodies. PADs are used in medicine, but due to their colouring properties are also applied in the textile, cosmetic and food industries. Their large-scale production and widespread applications have caused these dyes permeate to the aquatic environment. The pharmacological activity and toxicological properties of some of these dyes, caused their occurrence in water should be monitored. Up to now, PADs such as crystal violet, malachite green, methylene blue, rhodamine B, have been determined in the water of Greater China and Iran. However, there is no data on whether PADs pose an environmental problem for water bodies in Poland. Thus, different water samples were collected and analysed by the UPLC-MS/MS method allowing the determination of 20 PADs. The tests showed that dyes such as crystal violet, methyl violet 2 B and rhodamine B were found in 2 out of 36 water reservoirs (0.0122-0.0594 μgL-1). The environmental risk assessment indicated that determined dyes for most model organisms did not pose a risk. Only the presence of methyl violet 2 B (0.0571 μgL-1) was related to a low risk for rohu carp, and crystal violet (0.0122-0.0209 μgL-1) showed a moderate risk for medaka fish. The occurrence of PADs was tested on a larger scale in the water samples collected from different water reservoirs in Poland. Based on obtained results, 96.3% of water samples collected from different water bodies (94.5%) were free from dyes. Thus, it could be stated that generally environmental water of Poland is contaminated with PADs at a low level. On the other hand, the presence of dyes in two samples indicates that PADs permeate the water environment, and their occurrence should be monitored.
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Affiliation(s)
- Angelika Tkaczyk-Wlizło
- Department of Pharmacology and Toxicology, National Veterinary Research Institute (PIWet), Al. Partyzantow 57, 24-100, Pulawy, Poland; Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Kamila Mitrowska
- Department of Pharmacology and Toxicology, National Veterinary Research Institute (PIWet), Al. Partyzantow 57, 24-100, Pulawy, Poland.
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19
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Biobran/MGN-3, an Arabinoxylan Rice Bran, Protects against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An In Vitro and In Silico Study. Nutrients 2023; 15:nu15020453. [PMID: 36678324 PMCID: PMC9866808 DOI: 10.3390/nu15020453] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19), poses a serious global public health threat for which there is currently no satisfactory treatment. This study examines the efficacy of Biobran/MGN-3 against SARS-CoV-2. Biobran is an arabinoxylan rice bran that has been shown to significantly inhibit the related influenza virus in geriatric subjects. Here, Biobran's anti-SARS-CoV-2 activity was assessed using MTT and plaque reduction assays, RT-PCR, ELISA techniques, and measurements of SARS-CoV-2-related gene expression and protein levels. For Vero E6 cells infected with SARS-CoV-2, Biobran reduced the viral load by 91.9% at a dose of 100 μg/mL, it reduced viral counts (PFU/mL) by 90.6% at 50 μg/mL, and it exhibited a significant selectivity index (EC50/IC50) of 22.5. In addition, Biobran at 10 μg/mL inhibited papain-like proteinase (PLpro) by 87% and ACE2 SARS-CoV-2 S-protein RBD by 90.5%, and it significantly suppressed SARS-CoV-2 gene expression, down-regulating E-gene and RdRp gene expression by 93% each at a dose of 50 μg/mL and inhibiting the E-protein by 91.3%. An in silico docking study was also performed to examine the protein-protein interaction (PPI) between SARS-CoV-2 RBD and DC-SIGN as well as between serine carboxypeptidase and papain-like protease PLpro. Serine carboxypeptidase, an active ingredient in Biobran, was found to interfere with the binding of SARS-CoV-2 to its receptor DC-SIGN on Vero cells, thus preventing the cell entry of SARS-CoV-2. In addition, it impairs the viral replication cycle by binding to PLpro. We conclude that Biobran possesses potent antiviral activity against SARS-CoV-2 in vitro and suggest that Biobran may be able to prevent SARS-CoV-2 infection. This warrants further investigation in clinical trials.
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20
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Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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21
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Miwa K, Guo Y, Hata M, Hirano Y, Yamamoto N, Hoshino T. In Silico Identification of Inhibitory Compounds for SARS-Cov-2 Papain-Like Protease. Chem Pharm Bull (Tokyo) 2023; 71:897-905. [PMID: 38044142 DOI: 10.1248/cpb.c23-00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Virtual screening with high-performance computers is a powerful and cost-effective technique in drug discovery. A chemical database is searched to find candidate compounds firmly bound to a target protein, judging from the binding poses and/or binding scores. The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) infectious disease has spread worldwide for the last three years, causing severe slumps in economic and social activities. SARS-Cov-2 has two viral proteases: 3-chymotrypsin-like (3CL) and papain-like (PL) protease. While approved drugs have already been released for the 3CL protease, no approved agent is available for PL protease. In this work, we carried out in silico screening for the PL protease inhibitors, combining docking simulation and molecular mechanics calculation. Docking simulations were applied to 8,820 molecules in a chemical database of approved and investigational compounds. Based on the binding poses generated by the docking simulations, molecular mechanics calculations were performed to optimize the binding structures and to obtain the binding scores. Based on the binding scores, 57 compounds were selected for in vitro assay of the inhibitory activity. Five inhibitory compounds were identified from the in vitro measurement. The predicted binding structures of the identified five compounds were examined, and the significant interaction between the individual compound and the protease catalytic site was clarified. This work demonstrates that computational virtual screening by combining docking simulation with molecular mechanics calculation is effective for searching candidate compounds in drug discovery.
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Affiliation(s)
- Kazunori Miwa
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Masayuki Hata
- College of Pharmaceutical Sciences, Matsuyama University
| | | | - Norio Yamamoto
- Department of Virology, Division of Host Defense Mechanism, Tokai University School of Medicine
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University
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22
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Liang J, Zheng M, Xu W, Chen Y, Tang P, Wu G, Zou P, Li H, Chen L. Acriflavine and proflavine hemisulfate as potential antivirals by targeting M pro. Bioorg Chem 2022; 129:106185. [PMID: 36240541 PMCID: PMC9540699 DOI: 10.1016/j.bioorg.2022.106185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022]
Abstract
The evolving SARS-CoV-2 epidemic buffets the world, and the concerted efforts are needed to explore effective drugs. Mpro is an intriguing antiviral target for interfering with viral RNA replication and transcription. In order to get potential anti-SARS-CoV-2 agents, we established an enzymatic assay using a fluorogenic substrate to screen the inhibitors of Mpro. Fortunately, Acriflavine (ACF) and Proflavine Hemisulfate (PRF) with the same acridine scaffold were picked out for their good inhibitory activity against Mpro with IC50 of 5.60 ± 0.29 μM and 2.07 ± 0.01 μM, respectively. Further evaluation of MST assay and enzymatic kinetics experiment in vitro showed that they had a certain affinity to SARS-CoV-2 Mpro and were both non-competitive inhibitors. In addition, they inhibited about 90 % HCoV-OC43 replication in BHK-21 cells at 1 μM. Both compounds showed nano-molar activities against SARS-CoV-2 virus, which were superior to GC376 for anti-HCoV-43, and equivalent to the standard molecule remdesivir. Our study demonstrated that ACF and PRF were inhibitors of Mpro, and ACF has been previously reported as a PLpro inhibitor. Taken together, ACF and PRF might be dual-targeted inhibitors to provide protection against infections of coronaviruses.
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Affiliation(s)
- Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengzhu Zheng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yongkang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Piyu Tang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Guoyi Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Peng Zou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China,Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China,School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China,Corresponding authors at: Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China (H. Li and L. Chen)
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23
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Jansen-van Vuuren RD, Jedlovčnik L, Košmrlj J, Massey TE, Derdau V. Deuterated Drugs and Biomarkers in the COVID-19 Pandemic. ACS OMEGA 2022; 7:41840-41858. [PMID: 36440130 PMCID: PMC9685803 DOI: 10.1021/acsomega.2c04160] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 06/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initially identified in Wuhan (China) in December 2019, COVID-19 rapidly spread globally, resulting in the COVID-19 pandemic. Carriers of the SARS-CoV-2 can experience symptoms ranging from mild to severe (or no symptoms whatsoever). Although vaccination provides extra immunity toward SARS-CoV-2, there has been an urgent need to develop treatments for COVID-19 to alleviate symptoms for carriers of the disease. In seeking a potential treatment, deuterated compounds have played a critical role either as therapeutic agents or as internal MS standards for studying the pharmacological properties of new drugs by quantifying the parent compounds and metabolites. We have identified >70 examples of deuterium-labeled compounds associated with treatment of COVID-19. Of these, we found 9 repurposed drugs and >20 novel drugs studied for potential therapeutic roles along with a total of 38 compounds (drugs, biomarkers, and lipids) explored as internal mass spectrometry standards. This review details the synthetic pathways and modes of action of these compounds (if known), and a brief analysis of each study.
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Affiliation(s)
- Ross D. Jansen-van Vuuren
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario K7L
3N6, Canada
| | - Luka Jedlovčnik
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Thomas E. Massey
- Department
of Biomedical and Molecular Sciences, School of Medicine, Queen’s University, Botterell Hall, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada
| | - Volker Derdau
- Research
& Development, Integrated Drug Discovery, Isotope Chemistry, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst G876, Frankfurt/Main 65926, Germany
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24
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Pires De Souza GA, Le Bideau M, Boschi C, Wurtz N, Colson P, Aherfi S, Devaux C, La Scola B. Choosing a cellular model to study SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:1003608. [PMID: 36339347 PMCID: PMC9634005 DOI: 10.3389/fcimb.2022.1003608] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/03/2022] [Indexed: 08/04/2023] Open
Abstract
As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.
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Affiliation(s)
- Gabriel Augusto Pires De Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Marion Le Bideau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Céline Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Department of Biological Sciences (INSB), Centre National de la Recherche Scientifique, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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25
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Piorecka K, Kurjata J, Stanczyk WA. Acriflavine, an Acridine Derivative for Biomedical Application: Current State of the Art. J Med Chem 2022; 65:11415-11432. [PMID: 36018000 PMCID: PMC9469206 DOI: 10.1021/acs.jmedchem.2c00573] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Acriflavine (ACF) has been known for years as an antibacterial
drug. The identification of key oncogenic mechanisms has brought,
in recent years, a significant increase in studies on ACF as a multipurpose
drug that would improve the prognosis for cancer patients. ACF interferes
with the expression of the hypoxia inducible factor, thus acting on
metastatic niches of tumors and significantly enhancing the effects
of other anticancer therapies. It has been recognized as the most
potent HIF-1 inhibitor out of the 336 drugs approved by the FDA. This
work presents up-to-date knowledge about the mechanisms of action
of ACF and its related prodrug systems in the context of anticancer
and SARS-CoV-2 inhibitory properties. It explains the multitask nature
of this drug and suggests mechanisms of ACF’s action on the
coronavirus. Other recent reports on ACF-based systems as potential
antibacterial and antiviral drugs are also described.
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Affiliation(s)
- Kinga Piorecka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences,Sienkiewicza 112, 90-363 Lodz, Poland
| | - Jan Kurjata
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences,Sienkiewicza 112, 90-363 Lodz, Poland
| | - Wlodzimierz A Stanczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences,Sienkiewicza 112, 90-363 Lodz, Poland
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26
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Ton AT, Pandey M, Smith JR, Ban F, Fernandez M, Cherkasov A. Targeting SARS-CoV-2 Papain-Like Protease in the Post-Vaccine Era. Trends Pharmacol Sci 2022; 43:906-919. [PMID: 36114026 PMCID: PMC9399131 DOI: 10.1016/j.tips.2022.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022]
Abstract
While vaccines remain at the forefront of global healthcare responses, pioneering therapeutics against SARS-CoV-2 are expected to fill the gaps for waning immunity. Rapid development and approval of orally available direct-acting antivirals targeting crucial SARS-CoV-2 proteins marked the beginning of the era of small-molecule drugs for COVID-19. In that regard, the papain-like protease (PLpro) can be considered a major SARS-CoV-2 therapeutic target due to its dual biological role in suppressing host innate immune responses and in ensuring viral replication. Here, we summarize the challenges of targeting PLpro and innovative early-stage PLpro-specific small molecules. We propose that state-of-the-art computer-aided drug design (CADD) methodologies will play a critical role in the discovery of PLpro compounds as a novel class of COVID-19 drugs.
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Affiliation(s)
- Anh-Tien Ton
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jason R Smith
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada; Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Michael Fernandez
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada.
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Lawal B, Kuo YC, Rachmawati Sumitra M, Wu ATH, Huang HS. Identification of a novel immune-inflammatory signature of COVID-19 infections, and evaluation of pharmacokinetics and therapeutic potential of RXn-02, a novel small-molecule derivative of quinolone. Comput Biol Med 2022; 148:105814. [PMID: 35841781 PMCID: PMC9272679 DOI: 10.1016/j.compbiomed.2022.105814] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/07/2022] [Accepted: 07/03/2022] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic and respiratory infection that has enormous damage to human lives and economies. It is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), a non-pair-stranded positive-sense RNA virus. With increasing global threats and few therapeutic options, the discovery of new potential drug targets and the development of new therapy candidates against COVID-19 are urgently needed. Based on these premises, we conducted an analysis of transcriptomic datasets from SARS-CoV-2-infected patients and identified several SARS-CoV-2 infection signatures, among which TNFRSF5/PTPRC/IDO1/MKI67 appeared to be the most pertinent signature. Subsequent integrated bioinformatics analysis identified the signature as an important immunomodulatory and inflammatory signature of SARS-CoV-2 infection. It was suggested that this gene signature mediates the interplay of immune and immunosuppressive cells leading to infiltration-exclusion of effector memory T cells in the lungs, which is of translation relevance for developing novel SARS-CoV-2 drug and vaccine candidates. Consequently, we designed and synthesized a novel small-molecule quinoline derivative (RXn-02) and evaluated its pharmacokinetics in rats, revealing a peak plasma concentration (Cmax) and time to Cmax (Tmax) of 1.756 μg/mL and 0.6 h, respectively. Values of the area under the curve (AUC) (0–24 h) and AUC (0 h∼∞) were 18.90 and 71.20 μg h/mL, respectively. Drug absorption from the various regional segments revealed that the duodenum (49.84%), jejunum (47.885%), cecum (1.82%), and ileum (0.32%) were prime sites of RXn-02 absorption. No absorption was detected from the stomach, and the least was from the colon (0.19%). Interestingly, RXn-02 exhibited in vitro antiproliferative activities against hub gene hyper-expressing cell lines; A549 (IC50 = 48.1 μM), K-562 (IC50 = 100 μM), and MCF7 (IC50 = 0.047 μM) and against five cell lines originating from human lungs (IC50 range of 33.2–69.5 μM). In addition, RXn-02 exhibited high binding efficacies for targeting the TNFRSF5/PTPRC/IDO1/MK signature with binding affinities (ΔG) of −6.6, −6.0, −9.9, −6.9 kcal/mol respectively. In conclusion, our study identified a novel signature of SARS-CoV-2 pathogenesis. RXn-02 is a drug-like candidate with good in vivo pharmacokinetics and hence possesses great translational relevance worthy of further preclinical and clinical investigations for treating SARS-CoV-2 infections.
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Affiliation(s)
- Bashir Lawal
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan; School of Post-baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Maryam Rachmawati Sumitra
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 11031, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan.
| | - Hsu-Shan Huang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11490, Taiwan; School of Pharmacy, National Defense Medical Center, Taipei, 11490, Taiwan; PhD Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan.
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28
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Jodłowski PJ, Dymek K, Kurowski G, Jaśkowska J, Bury W, Pander M, Wnorowska S, Targowska-Duda K, Piskorz W, Wnorowski A, Boguszewska-Czubara A. Zirconium-Based Metal-Organic Frameworks as Acriflavine Cargos in the Battle against Coronaviruses─A Theoretical and Experimental Approach. ACS APPLIED MATERIALS & INTERFACES 2022; 14:28615-28627. [PMID: 35700479 PMCID: PMC9212192 DOI: 10.1021/acsami.2c06420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
In this study, we present a complementary approach for obtaining an effective drug, based on acriflavine (ACF) and zirconium-based metal-organic frameworks (MOFs), against SARS-CoV-2. The experimental results showed that acriflavine inhibits the interaction between viral receptor-binding domain (RBD) of spike protein and angiotensin converting enzyme-2 (ACE2) host receptor driving viral cell entry. The prepared ACF@MOF composites exhibited low (MOF-808 and UiO-66) and high (UiO-67 and NU-1000) ACF loadings. The drug release profiles from prepared composites showed different release kinetics depending on the local pore environment. The long-term ACF release with the effective antiviral ACF concentration was observed for all studied ACF@MOF composites. The density functional theory (DFT) calculations allowed us to determine that π-π stacking together with electrostatic interaction plays an important role in acriflavine adsorption and release from ACF@MOF composites. The molecular docking results have shown that acriflavine interacts with several possible binding sites within the RBD and binding site at the RBD/ACE2 interface. The cytotoxicity and ecotoxicity results have confirmed that the prepared ACF@MOF composites may be considered potentially safe for living organisms. The complementary experimental and theoretical results presented in this study have confirmed that the ACF@MOF composites may be considered a potential candidate for the COVID-19 treatment, which makes them good candidates for clinical trials.
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Affiliation(s)
- Przemysław J. Jodłowski
- Faculty
of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska, 31-155 Kraków, Poland
| | - Klaudia Dymek
- Faculty
of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska, 31-155 Kraków, Poland
| | - Grzegorz Kurowski
- Faculty
of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska, 31-155 Kraków, Poland
| | - Jolanta Jaśkowska
- Faculty
of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska, 31-155 Kraków, Poland
| | - Wojciech Bury
- Faculty
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Marzena Pander
- Faculty
of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Sylwia Wnorowska
- Department
of Medical Chemistry, Medical University
of Lublin, 4A Chodzki, 20-093 Lublin, Poland
| | | | - Witold Piskorz
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Artur Wnorowski
- Department
of Biopharmacy, Medical University of Lublin, 4A Chodzki, 20-093 Lublin, Poland
| | - Anna Boguszewska-Czubara
- Department
of Medical Chemistry, Medical University
of Lublin, 4A Chodzki, 20-093 Lublin, Poland
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29
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Tan H, Hu Y, Jadhav P, Tan B, Wang J. Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease. J Med Chem 2022; 65:7561-7580. [PMID: 35620927 PMCID: PMC9159073 DOI: 10.1021/acs.jmedchem.2c00303] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PLpro) mediates the cleavage of viral polyprotein and modulates the host's innate immune response upon viral infection, rendering it a promising antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PLpro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PLpro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PLpro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PLpro inhibitors to the clinic.
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Affiliation(s)
- Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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30
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Popowicz GM, Pyrc K, Hadian K. Vaccination versus SARS-CoV-2 Omicron: three vaccine doses win the battle. Signal Transduct Target Ther 2022; 7:140. [PMID: 35477929 PMCID: PMC9044391 DOI: 10.1038/s41392-022-01000-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Grzegorz Maria Popowicz
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.
| | - Kamyar Hadian
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Research Group Cell Signaling and Chemical Biology, Institute of Molecular Toxicology and Pharmacology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
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31
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Calleja DJ, Lessene G, Komander D. Inhibitors of SARS-CoV-2 PLpro. Front Chem 2022; 10:876212. [PMID: 35559224 PMCID: PMC9086436 DOI: 10.3389/fchem.2022.876212] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
The emergence of SARS-CoV-2 causing the COVID-19 pandemic, has highlighted how a combination of urgency, collaboration and building on existing research can enable rapid vaccine development to fight disease outbreaks. However, even countries with high vaccination rates still see surges in case numbers and high numbers of hospitalized patients. The development of antiviral treatments hence remains a top priority in preventing hospitalization and death of COVID-19 patients, and eventually bringing an end to the SARS-CoV-2 pandemic. The SARS-CoV-2 proteome contains several essential enzymatic activities embedded within its non-structural proteins (nsps). We here focus on nsp3, that harbours an essential papain-like protease (PLpro) domain responsible for cleaving the viral polyprotein as part of viral processing. Moreover, nsp3/PLpro also cleaves ubiquitin and ISG15 modifications within the host cell, derailing innate immune responses. Small molecule inhibition of the PLpro protease domain significantly reduces viral loads in SARS-CoV-2 infection models, suggesting that PLpro is an excellent drug target for next generation antivirals. In this review we discuss the conserved structure and function of PLpro and the ongoing efforts to design small molecule PLpro inhibitors that exploit this knowledge. We first discuss the many drug repurposing attempts, concluding that it is unlikely that PLpro-targeting drugs already exist. We next discuss the wealth of structural information on SARS-CoV-2 PLpro inhibition, for which there are now ∼30 distinct crystal structures with small molecule inhibitors bound in a surprising number of distinct crystallographic settings. We focus on optimisation of an existing compound class, based on SARS-CoV PLpro inhibitor GRL-0617, and recapitulate how new GRL-0617 derivatives exploit different features of PLpro, to overcome some compound liabilities.
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Affiliation(s)
- Dale J. Calleja
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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