1
|
Zhang Y, Tian Y, Yan A. A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024:1-33. [PMID: 39077983 DOI: 10.1080/1062936x.2024.2375513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/27/2024] [Indexed: 07/31/2024]
Abstract
The 3C-like Proteinase (3CLpro) of novel coronaviruses is intricately linked to viral replication, making it a crucial target for antiviral agents. In this study, we employed two fingerprint descriptors (ECFP_4 and MACCS) to comprehensively characterize 889 compounds in our dataset. We constructed 24 classification models using machine learning algorithms, including Support Vector Machine (SVM), Random Forest (RF), extreme Gradient Boosting (XGBoost), and Deep Neural Networks (DNN). Among these models, the DNN- and ECFP_4-based Model 1D_2 achieved the most promising results, with a remarkable Matthews correlation coefficient (MCC) value of 0.796 in the 5-fold cross-validation and 0.722 on the test set. The application domains of the models were analysed using dSTD-PRO calculations. The collected 889 compounds were clustered by K-means algorithm, and the relationships between structural fragments and inhibitory activities of the highly active compounds were analysed for the 10 obtained subsets. In addition, based on 464 3CLpro inhibitors, 27 QSAR models were constructed using three machine learning algorithms with a minimum root mean square error (RMSE) of 0.509 on the test set. The applicability domains of the models and the structure-activity relationships responded from the descriptors were also analysed.
Collapse
Affiliation(s)
- Y Zhang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Y Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| |
Collapse
|
2
|
Wyss MT, Heuer C, Herwerth M. The bumpy road of purinergic inhibitors to clinical application in immune-mediated diseases. Neural Regen Res 2024; 19:1206-1211. [PMID: 37905866 DOI: 10.4103/1673-5374.386405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/05/2023] [Indexed: 11/02/2023] Open
Abstract
ABSTRACT Purinergic signaling plays important roles throughout the body in the regulation of organ functions during and following the disruption of homeostasis. This is also reflected by the widespread expression of two families of purinergic receptors (P1 and P2) with numerous subtypes. In the last few decades, there has been increasing evidence that purinergic signaling plays an important role in the regulation of immune functions. Mainly, signals mediated by P2 receptors have been shown to contribute to immune system-mediated pathologies. Thus, interference with P2 receptors may be a promising strategy for the modulation of immune responses. Although only a few clinical studies have been conducted in isolated entities with limited success, preclinical work suggests that the use of P2 receptor inhibitors may bear some promise in various autoimmune diseases. Despite the association of P2 receptors with several disorders from this field, the use of P2 receptor antagonists in clinical therapy is still very scarce. In this narrative review, we briefly review the involvement of the purinergic system in immunological responses and clinical studies on the effect of purinergic inhibition on autoimmune processes. We then open the aperture a bit and show some preclinical studies demonstrating a potential effect of purinergic blockade on autoimmune events. Using suramin, a non-specific purinergic inhibitor, as an example, we further show that off-target effects could be responsible for observed effects in immunological settings, which may have interesting implications. Overall, we believe that it is worthwhile to further investigate this hitherto underexplored area.
Collapse
Affiliation(s)
- Matthias T Wyss
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zürich, Switzerland
| | - Christine Heuer
- Neurology Department, University Hospital of Zurich, Zürich, Switzerland
| | - Marina Herwerth
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zürich, Switzerland
- Neurology Department, University Hospital of Zurich, Zürich, Switzerland
| |
Collapse
|
3
|
Kim JH, Park YI, Hur M, Park WT, Moon YH, Huh YC, Kim TIL, Kang MH, Kang JS, Cho CW, Park J. Inhibition by components of Glycyrrhiza uralensis of 3CLpro and HCoV-OC43 proliferation. J Enzyme Inhib Med Chem 2023; 38:2242704. [PMID: 37537881 PMCID: PMC10405751 DOI: 10.1080/14756366.2023.2242704] [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] [Received: 05/26/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). 3CLpro is a key enzyme in coronavirus proliferation and a treatment target for COVID-19. In vitro and in silico, compounds 1-3 from Glycyrrhiza uralensis had inhibitory activity and binding affinity for 3CLpro. These compounds decreased HCoV-OC43 cytotoxicity in RD cells. Moreover, they inhibited viral growth by reducing the amounts of the necessary proteins (M, N, and RDRP). Therefore, compounds 1-3 are inhibitors of 3CLpro and HCoV-OC43 proliferation.
Collapse
Affiliation(s)
- Jang Hoon Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Yea-In Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| | - Mok Hur
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Woo Tae Park
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Youn-Ho Moon
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Yun-Chan Huh
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Tae IL Kim
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Min Hye Kang
- Department of Herbal Crop Research, National Institute of Horticultural & Herbal Science, RDA, Eumsung, Republic of Korea
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Chong Woon Cho
- College of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
| |
Collapse
|
4
|
Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
Collapse
Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, 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
- Department of Pharmacology and Chemical Biology, 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.
| |
Collapse
|
5
|
Ahuja R, Kaur A, Kumari G, Kumar A, Kumar S, Roy AK, Majumdar T. Enhanced expression and solubility of main protease (Mpro) of SARS-CoV-2 from E. coli. Protein Expr Purif 2023; 211:106337. [PMID: 37453569 DOI: 10.1016/j.pep.2023.106337] [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] [Received: 05/16/2023] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a essential enzyme that facilitates viral transcription and replication. Furthermore, the conservation of Mpro across different variants and its non-overlapping nature with human proteases make it an appealing target for therapeutic interventions against SARS-CoV-2. Multiple inhibitors specifically target Mpro to mitigate the infection caused by SARS-CoV-2. In the current study, successful cloning and expression of SARS-CoV-2 Mpro were achieved using two E. coli hosts, namely BL21-DE3 and BL21-DE3-RIL. By optimizing the conditions for induction, the expression of Mpro in the soluble fraction of E. coli was improved. Subsequently, Mpro was purified using affinity chromatography, yielding significantly higher quantities from the BL21-DE3-RIL strain compared to the BL21-DE3 strain, with the former producing nearly twice as much as the latter. The purified Mpro was further characterized by mass spectrometry, fluorescence spectroscopy and circular dichroism (CD). Through fluorescence quenching studies, it was discovered that both GC376 and chitosan, which are inhibitors of Mpro, induced structural changes in the purified Mpro protein. This indicates that the protein retained its functional activity even after being expressed in a bacterial host. Further, FRET-based assay highlighted that the enzymatic activity of Mpro was significantly reduced in presence of both GC376 and chitosan. Consequently, the utilization of optimal conditions and the BL21-DE3-RIL bacterial host facilitates the cost-effective production of Mpro on a large scale, enabling high yields. This production approach can be applied for the screening of potent therapeutic drugs, making it a valuable resource for drug development endeavors.
Collapse
Affiliation(s)
- Rahul Ahuja
- National Institute of Immunology, New Delhi, 110067, India.
| | | | - Geetika Kumari
- National Institute of Immunology, New Delhi, 110067, India
| | - Amit Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - Santosh Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - Atul Kumar Roy
- National Institute of Immunology, New Delhi, 110067, India
| | | |
Collapse
|
6
|
Boniardi I, Corona A, Basquin J, Basquin C, Milia J, Nagy I, Tramontano E, Zinzula L. Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function. Virus Res 2023; 336:199221. [PMID: 37704176 PMCID: PMC10514558 DOI: 10.1016/j.virusres.2023.199221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.
Collapse
Affiliation(s)
- Irene Boniardi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - István Nagy
- Center of Research and Development, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy.
| | - Luca Zinzula
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
| |
Collapse
|
7
|
Eberle RJ, Coronado MA, Gering I, Sommerhage S, Korostov K, Stefanski A, Stühler K, Kraemer-Schulien V, Blömeke L, Bannach O, Willbold D. Tau protein aggregation associated with SARS-CoV-2 main protease. PLoS One 2023; 18:e0288138. [PMID: 37603556 PMCID: PMC10441795 DOI: 10.1371/journal.pone.0288138] [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: 03/16/2023] [Accepted: 06/20/2023] [Indexed: 08/23/2023] Open
Abstract
The primary function of virus proteases is the proteolytic processing of the viral polyprotein. These enzymes can also cleave host cell proteins, which is important for viral pathogenicity, modulation of cellular processes, viral replication, the defeat of antiviral responses and modulation of the immune response. It is known that COVID-19 can influence multiple tissues or organs and that infection can damage the functionality of the brain in multiple ways. After COVID-19 infections, amyloid-β, neurogranin, tau and phosphorylated tau were detected extracellularly, implicating possible neurodegenerative processes. The present study describes the possible induction of tau aggregation by the SARS-CoV-2 3CL protease (3CLpro) possibly relevant in neuropathology. Further investigations demonstrated that tau was proteolytically cleaved by the viral protease 3CL and, consequently, generated aggregates. However, more evidence is needed to confirm that COVID-19 is able to trigger neurodegenerative diseases.
Collapse
Affiliation(s)
- Raphael Josef Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Mônika Aparecida Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Ian Gering
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Simon Sommerhage
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Karolina Korostov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory (MPL), BMFZ, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory (MPL), BMFZ, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Victoria Kraemer-Schulien
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Lara Blömeke
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Oliver Bannach
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- attyloid GmbH, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| |
Collapse
|
8
|
Wu G, Zhou H, Lv D, Zheng R, Wu L, Yu S, Kai J, Xu N, Gu L, Hong N, Shentu J. Phase I, Single-Dose Study to Assess the Pharmacokinetics and Safety of Suramin in Healthy Chinese Volunteers. Drug Des Devel Ther 2023; 17:2051-2061. [PMID: 37457890 PMCID: PMC10349579 DOI: 10.2147/dddt.s416325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose Suramin is a multifunctional molecule with a wide range of potential applications, including parasitic and viral diseases, as well as cancer. Methods A double-blinded, randomized, placebo-controlled single ascending dose study was conducted to investigate the safety, tolerability, and pharmacokinetics of suramin in healthy Chinese volunteers. A total of 36 healthy subjects were enrolled. All doses of suramin sodium and placebo were administered as a 30-minute infusion. Blood and urine samples were collected at the designated time points for pharmacokinetic analysis. Safety was assessed by clinical examinations and adverse events. Results After a single dose, suramin maximum plasma concentration (Cmax) and area under the plasma concentration-time curve from time zero to the time of the last measurable concentration (AUClast) increased in a dose-proportional manner. The plasma half-life (t1/2) was dose-independent, average 48 days (range 28-105 days). The cumulative percentages of the dose excreted in urine over 7 days were less than 4%. Suramin can be detected in urine samples for longer periods (more than 140 days following infusion). Suramin was generally well tolerated. Treatment-emergent adverse events (TEAEs) were generally mild in severity. Conclusion The PK and safety profiles of suramin in Chinese subjects indicated that 10 mg/kg or 15 mg/kg could be an appropriate dose in a future multiple-dose study.
Collapse
Affiliation(s)
- Guolan Wu
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Polytechnic Institute, Zhejiang University, Hangzhou, People’s Republic of China
| | - Huili Zhou
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Duo Lv
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ruling Zheng
- The Fifth Affiliated Hospital, College of Medicine, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lihua Wu
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Songxia Yu
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jiejing Kai
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Nana Xu
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Lie Gu
- Hainan Honz Pharmaceutical Co. Ltd, Haikou, Hainan, People’s Republic of China
| | - Nanfang Hong
- Hainan Honz Pharmaceutical Co. Ltd, Haikou, Hainan, People’s Republic of China
| | - Jianzhong Shentu
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| |
Collapse
|
9
|
Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
Collapse
Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
| |
Collapse
|
10
|
Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules 2023; 28:molecules28062534. [PMID: 36985506 PMCID: PMC10051649 DOI: 10.3390/molecules28062534] [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: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (Kd = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (Kd = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2.
Collapse
|
11
|
Albino SL, da Silva Moura WC, dos Reis MML, Sousa GLS, da Silva PR, de Oliveira MGC, Borges TKDS, Albuquerque LFF, de Almeida SMV, de Lima MDCA, Kuckelhaus SAS, Nascimento IJDS, Junior FJBM, da Silva TG, de Moura RO. ACW-02 an Acridine Triazolidine Derivative Presents Antileishmanial Activity Mediated by DNA Interaction and Immunomodulation. Pharmaceuticals (Basel) 2023; 16:204. [PMID: 37259353 PMCID: PMC9967605 DOI: 10.3390/ph16020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 03/11/2024] Open
Abstract
The present study proposed the synthesis of a novel acridine derivative not yet described in the literature, chemical characterization by NMR, MS, and IR, followed by investigations of its antileishmanial potential. In vitro assays were performed to assess its antileishmanial activity against L. amazonensis strains and cytotoxicity against macrophages through MTT assay and annexin V-FITC/PI, and the ability to perform an immunomodulatory action using CBA. To investigate possible molecular targets, its interaction with DNA in vitro and in silico targets were evaluated. As results, the compound showed good antileishmanial activity, with IC50 of 6.57 (amastigotes) and 94.97 (promastigotes) µg mL-1, associated with non-cytotoxicity to macrophages (CC50 > 256.00 µg mL-1). When assessed by flow cytometry, 99.8% of macrophages remained viable. The compound induced an antileishmanial effect in infected macrophages and altered TNF-α, IL-10 and IL-6 expression, suggesting a slight immunomodulatory activity. DNA assay showed an interaction with the minor grooves due to the hyperchromic effect of 47.53% and Kb 1.17 × 106 M-1, and was sustained by docking studies. Molecular dynamics simulations and MM-PBSA calculations propose cysteine protease B as a possible target. Therefore, this study demonstrates that the new compound is a promising molecule and contributes as a model for future works.
Collapse
Affiliation(s)
- Sonaly Lima Albino
- Programa de Pós Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Willian Charles da Silva Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Malu Maria Lucas dos Reis
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | - Gleyton Leonel Silva Sousa
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, Brazil
| | - Pablo Rayff da Silva
- Programa de Pós Graduação em Produtos Naturais, Sintéticos e Bioativos, Universidade Federal da Paraiba, João Pessoa 58051-900, Brazil
| | | | - Tatiana Karla dos Santos Borges
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | - Lucas Fraga Friaça Albuquerque
- Laboratório de Imunologia Celular, Área de Patologia, Faculdade de Medicina, Campus Darcy Ribeiro, Brasília 70910-900, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica, Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Selma Aparecida Souza Kuckelhaus
- Área de Morfologia, Faculdade de Medicina—UnB, Universidade de Brasília, Campus Darcy Ribeiro/Asa Norte, Brasília 70910-900, Brazil
| | - Igor José dos Santos Nascimento
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| | | | | | - Ricardo Olímpio de Moura
- Laboratório de Desenvolvimento e Síntese de Fármacos, Departamento de Farmácia, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
- Programa de Pós Graduação em Ciências Farmacêuticas, Universidade Estadual da Paraíba, Campina Grande 58429-500, Brazil
| |
Collapse
|
12
|
Eberle R, Sevenich M, Gering I, Scharbert L, Strodel B, Lakomek NA, Santur K, Mohrlüder J, Coronado MA, Willbold D. Discovery of All-d-Peptide Inhibitors of SARS-CoV-2 3C-like Protease. ACS Chem Biol 2023; 18:315-330. [PMID: 36647580 PMCID: PMC9942092 DOI: 10.1021/acschembio.2c00735] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
During the replication process of SARS-CoV-2, the main protease of the virus [3-chymotrypsin-like protease (3CLpro)] plays a pivotal role and is essential for the life cycle of the pathogen. Numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat COVID-19. We describe a novel and efficient next-generation sequencing (NGS) supported phage display selection strategy for the identification of a set of SARS-CoV-2 3CLpro targeting peptide ligands that inhibit the 3CL protease, in a competitive or noncompetitive mode, in the low μM range. From the most efficient l-peptides obtained from the phage display, we designed all-d-peptides based on the retro-inverso (ri) principle. They had IC50 values also in the low μM range and in combination, even in the sub-micromolar range. Additionally, the combination with Rutinprivir decreases 10-fold the IC50 value of the competitive inhibitor. The inhibition modes of these d-ri peptides were the same as their respective l-peptide versions. Our results demonstrate that retro-inverso obtained all-d-peptides interact with high affinity and inhibit the SARS-CoV-2 3CL protease, thus reinforcing their potential for further development toward therapeutic agents. The here described d-ri peptides address limitations associated with current l-peptide inhibitors and are promising lead compounds. Further optimization regarding pharmacokinetic properties will allow the development of even more potent d-peptides to be used for the prevention and treatment of COVID-19.
Collapse
Affiliation(s)
- Raphael
J. Eberle
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Marc Sevenich
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany,Priavoid
GmbH, Merowingerplatz
1, 40225Düsseldorf, Germany
| | - Ian Gering
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Lara Scharbert
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Birgit Strodel
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Nils A. Lakomek
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Karoline Santur
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany
| | - Jeannine Mohrlüder
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Mônika A. Coronado
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,
| | - Dieter Willbold
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany,Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, Universitätsstraße
1, 40225Düsseldorf, Germany,
| |
Collapse
|
13
|
Sargsyan K, Mazmanian K, Lim C. A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2. Sci Rep 2023; 13:502. [PMID: 36627366 PMCID: PMC9831016 DOI: 10.1038/s41598-023-27649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Alterations in viral fitness cannot be inferred from only mutagenesis studies of an isolated viral protein. To-date, no systematic analysis has been performed to identify mutations that improve virus fitness and reduce drug efficacy. We present a generic strategy to evaluate which viral mutations might diminish drug efficacy and applied it to assess how SARS-CoV-2 evolution may affect the efficacy of current approved/candidate small-molecule antivirals for Mpro, PLpro, and RdRp. For each drug target, we determined the drug-interacting virus residues from available structures and the selection pressure of the virus residues from the SARS-CoV-2 genomes. This enabled the identification of promising drug target regions and small-molecule antivirals that the virus can develop resistance. Our strategy of utilizing sequence and structural information from genomic sequence and protein structure databanks can rapidly assess the fitness of any emerging virus variants and can aid antiviral drug design for future pathogens.
Collapse
Affiliation(s)
- Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.
| |
Collapse
|
14
|
Mucke HA. Drug Repurposing Patent Applications July–September 2022. Assay Drug Dev Technol 2022; 20:359-366. [DOI: 10.1089/adt.2022.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
15
|
Xu X, Chen Y, Lu X, Zhang W, Fang W, Yuan L, Wang X. An update on inhibitors targeting RNA-dependent RNA polymerase for COVID-19 treatment: Promises and challenges. Biochem Pharmacol 2022; 205:115279. [PMID: 36209840 PMCID: PMC9535928 DOI: 10.1016/j.bcp.2022.115279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The highly transmissible variants of SARS-CoV-2, the causative pathogen of the COVID-19 pandemic, bring new waves of infection worldwide. Identification of effective therapeutic drugs to combat the COVID-19 pandemic is an urgent global need. RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication, is the most promising target for antiviral drug research since it has no counterpart in human cells and shows the highest conservation across coronaviruses. This review summarizes recent progress in studies of RdRp inhibitors, focusing on interactions between these inhibitors and the enzyme complex, based on structural analysis, and their effectiveness. In addition, we propose new possible strategies to address the shortcomings of current inhibitors, which may guide the development of novel efficient inhibitors to combat COVID-19.
Collapse
Affiliation(s)
- Xiaoying Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Yuheng Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xinyu Lu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wanlin Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wenxiu Fang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Luping Yuan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Xiaoyan Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China.
| |
Collapse
|
16
|
Alzyoud L, Ghattas MA, Atatreh N. Allosteric Binding Sites of the SARS-CoV-2 Main Protease: Potential Targets for Broad-Spectrum Anti-Coronavirus Agents. Drug Des Devel Ther 2022; 16:2463-2478. [PMID: 35941927 PMCID: PMC9356625 DOI: 10.2147/dddt.s370574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 12/23/2022] Open
Abstract
The current pandemic caused by the COVID-19 disease has reached everywhere in the world and has affected every aspect of our lives. As of the current data, the World Health Organization (WHO) has reported more than 300 million confirmed COVID-19 cases worldwide and more than 5 million deaths. Mpro is an enzyme that plays a key role in the life cycle of the SARS-CoV-2 virus, and it is vital for the disease progression. The Mpro enzyme seems to have several allosteric sites that can hinder the enzyme catalytic activity. Furthermore, some of these allosteric sites are located at or nearby the dimerization interface which is essential for the overall Mpro activity. In this review paper, we investigate the potential of the Mpro allosteric site to act as a drug target, especially since they interestingly appear to be resistant to mutation. The work is illustrated through three subsequent sections: First, the two main categories of Mpro allosteric sites have been explained and discussed. Second, a total of six pockets have been studied and evaluated for their druggability and cavity characteristics. Third, the experimental and computational attempts for the discovery of new allosteric inhibitors have been illustrated and discussed. To sum up, this review paper gives a detailed insight into the feasibility of developing new Mpro inhibitors to act as a potential treatment for the COVID-19 disease.
Collapse
Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- Correspondence: Mohammad A Ghattas; Noor Atatreh, Email ;
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
17
|
Fagnani L, Nazzicone L, Bellio P, Franceschini N, Tondi D, Verri A, Petricca S, Iorio R, Amicosante G, Perilli M, Celenza G. Protocetraric and Salazinic Acids as Potential Inhibitors of SARS-CoV-2 3CL Protease: Biochemical, Cytotoxic, and Computational Characterization of Depsidones as Slow-Binding Inactivators. Pharmaceuticals (Basel) 2022; 15:ph15060714. [PMID: 35745633 PMCID: PMC9227325 DOI: 10.3390/ph15060714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
The study investigated the inhibitory activity of protocetraric and salazinic acids against SARS-CoV-2 3CLpro. The kinetic parameters were determined by microtiter plate-reading fluorimeter using a fluorogenic substrate. The cytotoxic activity was tested on murine Sertoli TM4 cells. In silico analysis was performed to ascertain the nature of the binding with the 3CLpro. The compounds are slow-binding inactivators of 3CLpro with a Ki of 3.95 μM and 3.77 μM for protocetraric and salazinic acid, respectively, and inhibitory efficiency kinact/Ki at about 3 × 10−5 s−1µM−1. The mechanism of inhibition shows that both compounds act as competitive inhibitors with the formation of a stable covalent adduct. The viability assay on epithelial cells revealed that none of them shows cytotoxicity up to 80 μM, which is well below the Ki values. By molecular modelling, we predicted that the catalytic Cys145 makes a nucleophilic attack on the carbonyl carbon of the cyclic ester common to both inhibitors, forming a stably acyl-enzyme complex. The computational and kinetic analyses confirm the formation of a stable acyl-enzyme complex with 3CLpro. The results obtained enrich the knowledge of the already numerous biological activities exhibited by lichen secondary metabolites, paving the way for developing promising scaffolds for the design of cysteine enzyme inhibitors.
Collapse
Affiliation(s)
- Lorenza Fagnani
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Lisaurora Nazzicone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
- Correspondence: (P.B.); (D.T.)
| | - Nicola Franceschini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
- Correspondence: (P.B.); (D.T.)
| | - Andrea Verri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
| | - Sabrina Petricca
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Roberto Iorio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy; (L.F.); (L.N.); (N.F.); (S.P.); (R.I.); (G.A.); (M.P.); (G.C.)
| |
Collapse
|
18
|
Peng H, Ding C, Jiang L, Tang W, Liu Y, Zhao L, Yi Z, Ren H, Li C, He Y, Zheng X, Tang H, Chen Z, Qi Z, Zhao P. Discovery of potential anti-SARS-CoV-2 drugs based on large-scale screening in vitro and effect evaluation in vivo. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1181-1197. [PMID: 34962614 PMCID: PMC8713546 DOI: 10.1007/s11427-021-2031-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis. Clinical candidates with high efficacy, ready availability, and that do not develop resistance are in urgent need. Despite that screening to repurpose clinically approved drugs has provided a variety of hits shown to be effective against SARS-CoV-2 infection in cell culture, there are few confirmed antiviral candidates in vivo. In this study, 94 compounds showing high antiviral activity against SARS-CoV-2 in Vero E6 cells were identified from 2,580 FDA-approved small-molecule drugs. Among them, 24 compounds with low cytotoxicity were selected, and of these, 17 compounds also effectively suppressed SARS-CoV-2 infection in HeLa cells transduced with human ACE2. Six compounds disturb multiple processes of the SARS-CoV-2 life cycle. Their prophylactic efficacies were determined in vivo using Syrian hamsters challenged with SARS-CoV-2 infection. Seven compounds reduced weight loss and promoted weight regain of hamsters infected not only with the original strain but also the D614G variant. Except for cisatracurium, six compounds reduced hamster pulmonary viral load, and IL-6 and TNF-α mRNA when assayed at 4 d postinfection. In particular, sertraline, salinomycin, and gilteritinib showed similar protective effects as remdesivir in vivo and did not induce antiviral drug resistance after 10 serial passages of SARS-CoV-2 in vitro, suggesting promising application for COVID-19 treatment.
Collapse
Affiliation(s)
- Haoran Peng
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Cuiling Ding
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Liangliang Jiang
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Wanda Tang
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Yan Liu
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Lanjuan Zhao
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hao Ren
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Chong Li
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200000, China
| | - Yanhua He
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Xu Zheng
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Hailin Tang
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China
| | - Zhihui Chen
- Department of Infectious Disease, Changhai Hospital, Shanghai, 200433, China.
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China.
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai Key Laboratory of Medical Biodefense, Shanghai, 200433, China.
| |
Collapse
|
19
|
Design of D-Amino Acids SARS-CoV-2 Main Protease Inhibitors Using the Cationic Peptide from Rattlesnake Venom as a Scaffold. Pharmaceuticals (Basel) 2022; 15:ph15050540. [PMID: 35631367 PMCID: PMC9146215 DOI: 10.3390/ph15050540] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 12/15/2022] Open
Abstract
The C30 endopeptidase (3C-like protease; 3CLpro) is essential for the life cycle of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) since it plays a pivotal role in viral replication and transcription and, hence, is a promising drug target. Molecules isolated from animals, insects, plants, or microorganisms can serve as a scaffold for the design of novel biopharmaceutical products. Crotamine, a small cationic peptide from the venom of the rattlesnake Crotalus durissus terrificus, has been the focus of many studies since it exhibits activities such as analgesic, in vitro antibacterial, and hemolytic activities. The crotamine derivative L-peptides (L-CDP) that inhibit the 3CL protease in the low µM range were examined since they are susceptible to proteolytic degradation; we explored the utility of their D-enantiomers form. Comparative uptake inhibition analysis showed D-CDP as a promising prototype for a D-peptide-based drug. We also found that the D-peptides can impair SARS-CoV-2 replication in vivo, probably targeting the viral protease 3CLpro.
Collapse
|
20
|
Sevenich M, Thul E, Lakomek NA, Klünemann T, Schubert M, Bertoglio F, van den Heuvel J, Petzsch P, Mohrlüder J, Willbold D. Phage Display-Derived Compounds Displace hACE2 from Its Complex with SARS-CoV-2 Spike Protein. Biomedicines 2022; 10:biomedicines10020441. [PMID: 35203649 PMCID: PMC8962251 DOI: 10.3390/biomedicines10020441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Severe respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly contagious beta-class coronavirus. Although vaccinations have shown high efficacy, the emergence of novel variants of concern (VOCs) has already exhibited traits of immune evasion. Thus, the development of tailored antiviral medications for patients with incomplete, inefficient, or non-existent immunization, is essential. The attachment of viral surface proteins to the cell surface is the first crucial step in the viral replication cycle, which for SARS-CoV-2 is mediated by the high affinity interaction of the viral trimeric spike with the host cell surface-located human angiotensin converting enzyme-2 (hACE2). Here, we used a novel and efficient next generation sequencing (NGS) supported phage display strategy for the selection of a set of SARS-CoV-2 receptor binding domain (RBD)-targeting peptide ligands that bind to the target protein with low µM to nM dissociation constants. Compound CVRBDL-3 inhibits the SARS-CoV-2 spike protein association to hACE2 in a concentration-dependent manner for pre- as well as post-complex formation conditions. Further rational optimization yielded a CVRBDL-3 based divalent compound, which demonstrated inhibitory efficacy with an IC50 value of 47 nM. The obtained compounds were not only efficient for the different spike constructs from the originally isolated “wt” SARS-CoV-2, but also for B.1.1.7 mutant trimeric spike protein. Our work demonstrates that phage display-derived peptide ligands are potential fusion inhibitors of viral cell entry. Moreover, we show that rational optimization of a combination of peptide sequences is a potential strategy in the further development of therapeutics for the treatment of acute COVID-19.
Collapse
Affiliation(s)
- Marc Sevenich
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (N.-A.L.)
- Priavoid GmbH, 40225 Düsseldorf, Germany
| | - Elena Thul
- Medizinische Fakultät, Westfälische Wilhelms Universität Münster, 48149 Münster, Germany;
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (N.-A.L.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas Klünemann
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (T.K.); (J.v.d.H.)
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik—Abteilung Biotechnologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (M.S.); (F.B.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik—Abteilung Biotechnologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (M.S.); (F.B.)
| | - Joop van den Heuvel
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (T.K.); (J.v.d.H.)
| | - Patrick Petzsch
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany;
| | - Jeannine Mohrlüder
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (N.-A.L.)
- Correspondence: (J.M.); (D.W.); Tel.: +49-2461-612100 (D.W.)
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; (M.S.); (N.-A.L.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- JuStruct, Forschungszentrum Jülich, 52425 Jülich, Germany
- Correspondence: (J.M.); (D.W.); Tel.: +49-2461-612100 (D.W.)
| |
Collapse
|
21
|
Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
Collapse
Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
| |
Collapse
|
22
|
Hernández González JE, Eberle RJ, Willbold D, Coronado MA. A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease. Front Mol Biosci 2022; 8:816166. [PMID: 35187076 PMCID: PMC8852625 DOI: 10.3389/fmolb.2021.816166] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55–85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.
Collapse
Affiliation(s)
- Jorge E. Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil
- Laboratory for Molecular Modeling and Dynamics, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária Ilha do Fundão, Rio de Janeiro, Brazil
| | - Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Mônika A. Coronado
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Mônika A. Coronado,
| |
Collapse
|
23
|
Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
Collapse
Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| |
Collapse
|
24
|
Abstract
The emerging risk of viral diseases has triggered the search for preventive and therapeutic agents. Since the beginning of the COVID-19 pandemic, greater efforts have been devoted to investigating virus entry mechanisms into host cells. The feasibility of plasmonic sensing technologies for screening interactions of small molecules in real time, while providing the pharmacokinetic drug profiling of potential antiviral compounds, offers an advantageous approach over other biophysical methods. This review summarizes recent advancements in the drug discovery process of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) inhibitors using Surface Plasmon Resonance (SPR) biosensors. A variety of SPR assay formats are discussed according to the binding kinetics and drug efficacies of both natural products and repurposed drugs. Special attention has been given to the targeting of antiviral agents that block the receptor binding domain of the spike protein (RBD-S) and the main protease (3CLpro) of SARS-CoV-2. The functionality of plasmonic biosensors for high-throughput screening of entry virus inhibitors was also reviewed taking into account experimental parameters (binding affinities, selectivity, stability), potential limitations and future applications.
Collapse
|
25
|
Loas G, Le Corre P. Update on Functional Inhibitors of Acid Sphingomyelinase (FIASMAs) in SARS-CoV-2 Infection. Pharmaceuticals (Basel) 2021; 14:691. [PMID: 34358117 PMCID: PMC8308787 DOI: 10.3390/ph14070691] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 outbreak is characterized by the need of the search for curative drugs for treatment. In this paper, we present an update of knowledge about the interest of the functional inhibitors of acid sphingomyelinase (FIASMAs) in SARS-CoV-2 infection. Forty-nine FIASMAs have been suggested in the treatment of SARS-CoV-2 infection using in silico, in vitro or in vivo studies. Further studies using large-sized, randomized and double-blinded controlled clinical trials are needed to evaluate FIASMAs in SARS-CoV-2 infection as off-label therapy.
Collapse
Affiliation(s)
- Gwenolé Loas
- Department of Psychiatry, Hôpital Erasme, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
- Research Unit (ULB 266), Hôpital Erasme, Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Pascal Le Corre
- Pôle Pharmacie, Service Hospitalo-Universitaire de Pharmacie, CHU de Rennes, 35033 Rennes, France;
- Irset (Institut de Recherche en Santé, Environnement et Travail)-Inserm UMR 1085, University of Rennes, CHU Rennes, INSERM, EHESP, 35000 Rennes, France
- Laboratoire de Biopharmacie et Pharmacie Clinique, Faculté de Pharmacie, Université de Rennes 1, 35043 Rennes, France
| |
Collapse
|