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Al-Karmalawy AA, Alnajjar R, Elmaaty AA, Binjubair FA, Al-Rashood ST, Mansour BS, Elkamhawy A, Eldehna WM, Mansour KA. Investigating the promising SARS-CoV-2 main protease inhibitory activity of secoiridoids isolated from Jasminum humile; in silico and in Vitro assessments with structure-activity relationship. J Biomol Struct Dyn 2024; 42:6941-6953. [PMID: 37505066 DOI: 10.1080/07391102.2023.2240419] [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: 04/06/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
The proteolytic enzyme 3 C-like protease (3Clpro or Mpro) is considered the most important target for SARS-CoV-2 which could be attributed to its crucial role in viral maturation and/or replication. Besides, natural phytoconstituents from plant origin are always promising lead compounds in the drug discovery area. Herein, the previously isolated and identified seven compounds from Jasminum humile (J. humile) were examined in vitro and in silico against the SARS-CoV-2 Mpro. First, the Vero E6 cells were utilized to pursue the potential of the investigated compounds (both in fractions and individual isolates) using the MTT assay. The total extract (T1) displayed the most significant activity against SARS-CoV-2 with IC50 = 29.36 µg/mL. Besides, the fractions (Fr1 and Fr3) showed good activity against the SARS-CoV-2 with IC50 values of 70.42, and 73.09 µg/mL, respectively. Then, the SARS-CoV-2 Mpro inhibitory assay was utilized to emphasize the inhibitory potential of the investigated isolates. MJN, JMD, and IJM candidates displayed prominent Mpro inhibitory potentials with IC50 = 30.44, 30.24, and 56.25 µM, respectively. Moreover, molecular docking of the identified seven compounds against the Mpro of SARS-CoV-2 showed that the five secoiridoids achieved superior results. MJN, JSM, IJM, and JMD showed higher affinities towards the Mpro target compared to the co-crystallized antagonist. Furthermore, the most active complexes (MJN, JSM, IJM, and JMD-Mpro) were subjected to MD simulations run for 150 ns and MM-GBSA calculations, compared to the co-crystallized inhibitor (O6K-Mpro). Finally, the SAR study clarified that JMD achieved the best anti-SARS-CoV-2 Mpro activity followed by MJN.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
- PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi, Libya
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Faizah A Binjubair
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sara T Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Basma S Mansour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Elkamhawy
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Khaled Ahmed Mansour
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University in Egypt, New Damietta, Egypt
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Akinosoglou K, Gogos C. Antiviral therapy for patients with COVID-19: mix and match. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(24)00407-9. [PMID: 39025097 DOI: 10.1016/s1473-3099(24)00407-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024]
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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024; 300:107456. [PMID: 38866325 PMCID: PMC11298601 DOI: 10.1016/j.jbc.2024.107456] [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: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N), and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and the N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular, and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Gregory A Voth
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA; Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, Illinois, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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Freidel MR, Vakhariya PA, Sardarni SK, Armen RS. The Dual-Targeted Fusion Inhibitor Clofazimine Binds to the S2 Segment of the SARS-CoV-2 Spike Protein. Viruses 2024; 16:640. [PMID: 38675980 PMCID: PMC11054727 DOI: 10.3390/v16040640] [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: 03/01/2024] [Revised: 03/29/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Clofazimine and Arbidol have both been reported to be effective in vitro SARS-CoV-2 fusion inhibitors. Both are promising drugs that have been repurposed for the treatment of COVID-19 and have been used in several previous and ongoing clinical trials. Small-molecule bindings to expressed constructs of the trimeric S2 segment of Spike and the full-length SARS-CoV-2 Spike protein were measured using a Surface Plasmon Resonance (SPR) binding assay. We demonstrate that Clofazimine, Toremifene, Arbidol and its derivatives bind to the S2 segment of the Spike protein. Clofazimine provided the most reliable and highest-quality SPR data for binding with S2 over the conditions explored. A molecular docking approach was used to identify the most favorable binding sites on the S2 segment in the prefusion conformation, highlighting two possible small-molecule binding sites for fusion inhibitors. Results related to molecular docking and modeling of the structure-activity relationship (SAR) of a newly reported series of Clofazimine derivatives support the proposed Clofazimine binding site on the S2 segment. When the proposed Clofazimine binding site is superimposed with other experimentally determined coronavirus structures in structure-sequence alignments, the changes in sequence and structure may rationalize the broad-spectrum antiviral activity of Clofazimine in closely related coronaviruses such as SARS-CoV, MERS, hCoV-229E, and hCoV-OC43.
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Affiliation(s)
| | | | | | - Roger S. Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, 901 Walnut St. Suite 918, Philadelphia, PA 19170, USA (P.A.V.); (S.K.S.)
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Xue Y, Cai X, Wang Y, Ban L, Mei M, Chen S, Xu Q, Chen B, Liang S, Wang X. Utilizing network pharmacology and experimental validation to investigate the underlying mechanism of Denglao Qingguan decoction against HCoV-229E. Heliyon 2024; 10:e27829. [PMID: 38533054 PMCID: PMC10963236 DOI: 10.1016/j.heliyon.2024.e27829] [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: 08/01/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Background Denglao Qingguan decoction (DLQGD) has been extensively utilized for the treatment of colds, demonstrating significant therapeutic efficacy. Human Coronavirus 229E (HCoV-229E) is considered a crucial etiological agent of influenza. However, the specific impact and underlying mechanisms of DLQGD on HCoV-229E remain poorly understood. Methods Active ingredients and targets information of DLQGD were collected from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), literature search, and Swiss ADEM database. The Genecard database was used to collect HCoV-229E related targets. We built an "ingredient-target network" through Cytoscape. Protein - Protein interaction (PPI) networks were mapped using the String database. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were enriched using the DAVID database. Then, we used molecular docking techniques to verify the binding activity between the core compounds and the core gene targets. Finally, in vitro experiments were conducted to validate DLQGD's antiviral activity against HCoV-229E and assess its anti-inflammatory effects. Results In total, we identified 227 active components in DLQGD. 18 key targets involved in its activity against HCoV-229E. Notably, the core active ingredients including quercetin, luteolin, kaempferol, β-sitosterol, and apigenin, and the core therapeutic targets were CXCL8, RELA, MAPK14, NFKB1, and CXCL10, all associated with HCoV-229E. KEGG enrichment results included IL-17 signaling pathway, Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and so on. The core active ingredients and the core therapeutic targets and Human Aminopeptidase N (ANPEP) all showed good binding activity by molecular docking verification. In vitro, DLQGD exhibited anti-HCoV-229E activity and anti-inflammatory effects. Conclusion Our study suggests that DLQGD has both effects of anti-HCoV-229E and anti-inflammatory. The core active ingredients (quercetin, luteolin, kaempferol, β-sitosterol, apigenin) and the core therapeutic targets (CXCL8, RELA, MAPK14, NFKB1, CXCL10) may play key roles in the pharmacological action of DLQGD against HCoV-229E.
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Affiliation(s)
- Yajing Xue
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuejun Cai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yutao Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ban
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Manxue Mei
- College of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuqi Chen
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qihua Xu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Boqian Chen
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong, China
| | - Shuhua Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Institute of Integration of Traditional and Western Medicine, Guangzhou Medical University, Guangzhou, China
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Brogna C, Montano L, Zanolin ME, Bisaccia DR, Ciammetti G, Viduto V, Fabrowski M, Baig AM, Gerlach J, Gennaro I, Bignardi E, Brogna B, Frongillo A, Cristoni S, Piscopo M. A retrospective cohort study on early antibiotic use in vaccinated and unvaccinated COVID-19 patients. J Med Virol 2024; 96:e29507. [PMID: 38504586 DOI: 10.1002/jmv.29507] [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: 09/22/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
The bacteriophage behavior of SARS-CoV-2 during the acute and post-COVID-19 phases appears to be an important factor in the development of the disease. The early use of antibiotics seems to be crucial to inhibit disease progression-to prevent viral replication in the gut microbiome, and control toxicological production from the human microbiome. To study the impact of specific antibiotics on recovery from COVID-19 and long COVID (LC) taking into account: vaccination status, comorbidities, SARS-CoV-2 wave, time of initiation of antibiotic therapy and concomitant use of corticosteroids and nonsteroidal anti-inflammatory drugs (NSAIDs). A total of 211 COVID-19 patients were included in the study: of which 59 were vaccinated with mRNA vaccines against SARS-CoV-2 while 152 were unvaccinated. Patients were enrolled in three waves: from September 2020 to October 2022, corresponding to the emergence of the pre-Delta, Delta, and Omicron variants of the SARS-CoV-2 virus. The three criteria for enrolling patients were: oropharyngeal swab positivity or fecal findings; moderate symptoms with antibiotic intake; and measurement of blood oxygen saturation during the period of illness. The use of antibiotic combinations, such as amoxicillin with clavulanic acid (875 + 125 mg tablets, every 12 h) plus rifaximin (400 mg tablets every 12 h), as first choice, as suggested from the previous data, or azithromycin (500 mg tablets every 24 h), plus rifaximin as above, allows healthcare professionals to focus on the gut microbiome and its implications in COVID-19 disease during patient care. The primary outcome measured in this study was the estimated average treatment effect, which quantified the difference in mean recovery between patients receiving antibiotics and those not receiving antibiotics at 3 and 9 days after the start of treatment. In the analysis, both vaccinated and unvaccinated groups had a median illness duration of 7 days (interquartile range [IQR] 6-9 days for each; recovery crude hazard ratio [HR] = 0.94, p = 0.700). The median illness duration for the pre-Delta and Delta waves was 8 days (IQR 7-10 days), while it was shorter, 6.5 days, for Omicron (IQR 6-8 days; recovery crude HR = 1.71, p < 0.001). These results were confirmed by multivariate analysis. Patients with comorbidities had a significantly longer disease duration: median 8 days (IQR 7-10 days) compared to 7 days (IQR 6-8 days) for those without comorbidities (crude HR = 0.75, p = 0.038), but this result was not confirmed in multivariate analysis as statistical significance was lost. Early initiation of antibiotic therapy resulted in a significantly shorter recovery time (crude HR = 4.74, p < 0.001). Concomitant use of NSAIDs did not reduce disease duration and in multivariate analysis prolonged the disease (p = 0.041). A subgroup of 42 patients receiving corticosteroids for a median of 3 days (IQR 3-6 days) had a longer recovery time (median 9 days, IQR 8-10 days) compared to others (median 7 days, IQR 6-8 days; crude HR = 0.542, p < 0.001), as confirmed also by the adjusted HR. In this study, a statistically significant reduction in recovery time was observed among patients who received early antibiotic treatment. Early initiation of antibiotics played a crucial role in maintaining higher levels of blood oxygen saturation. In addition, it is worth noting that a significant number of patients who received antibiotics in the first 3 days and for a duration of 7 days, during the acute phase did not develop LC.
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Affiliation(s)
- Carlo Brogna
- Craniomed Group Srl. Research Facility, Bresso, Italy
| | - Luigi Montano
- Andrology Unit and Service of Lifestyle Medicine in Uro-Andrology, Local Health Authority (ASL), Salerno, Italy
| | | | | | - Gianluca Ciammetti
- Otorhinolaryngology Unit, Hospital Ferdinando Veneziale Isernia, Regional Health Authority of Molise, Italy
| | | | - Mark Fabrowski
- Department of Emergency Medicine, Royal Sussex County Hospital, University Hospitals Sussex, Brighton, UK
| | - Abdul M Baig
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Iapicca Gennaro
- Pineta Grande Hospital Group, Department of Urology, Santa Rita Clinic, Atripalda, Italy
| | | | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Avellino, Italy
| | | | | | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Naples, Italy
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [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: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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Miyazaki K, Kanno H, Yamada S, Sagehashi Y, Matsumoto S, Takahashi S, Kim Y, Namiki K, Fujii S. Clinical Features and Treatment of Patients Infected With SARS-CoV-2 Omicron Variant While Hospitalized Due to Stroke: A Single Center Study in Japan. Cureus 2024; 16:e54760. [PMID: 38523985 PMCID: PMC10961056 DOI: 10.7759/cureus.54760] [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] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND AND OBJECTIVE In December 2019, COVID-19 spread rapidly across the globe. Throughout the pandemic, SARS-CoV-2 repeatedly mutated, transitioning from the alpha variant to the omicron variant. The severity and mortality of COVID-19 have been linked to age, sex, and the presence of underlying diseases (respiratory, cerebrovascular, cardiovascular, metabolic, and immune diseases, as well as cancer). The clinical features of patients infected with COVID-19 following a stroke, however, are fully unknown. Therefore, it is significant to explore the appropriate treatment for these patients based on their clinical features. METHODS Of the 6175 patients who visited Asahi Hospital (Tokyo, Japan) between November 2022 and February 2023, 206 were admitted. Of these 206 patients, the 44 that contracted COVID-19 while hospitalized for strokes were retrospectively analyzed. RESULTS Six (13.6%) of these patients died; four expired due to coagulopathy associated with ischemic heart failure and recurrent ischemic cerebrovascular disease. The mean D-dimer level increased to 3.53 in the deceased patients, while it was 1.64 in all patients. The platelet count was low in three of the deceased patients, while it was high in two patients. The severity of COVID-19 was significantly correlated with a high modified Rankin Scale (mRS) score and a high National Institute of Health Stroke Scale (NIHSS) score. The timing of vaccination is inversely correlated with COVID-19 severity. CONCLUSION Patients with COVID-19 after a stroke have high mortality rates due to coagulopathy. Stroke patients with high mRS scores and high NIHSS scores are more likely to develop severe COVID-19. Anticoagulant therapy should be administered to COVID-19 patients with high mRS scores following a stroke.
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Affiliation(s)
| | - Hiroshi Kanno
- Department of Neurosurgery, Asahi Hospital, Tokyo, JPN
| | | | | | | | | | - Yongson Kim
- Department of Neurosurgery, Asahi Hospital, Tokyo, JPN
| | - Keiko Namiki
- Department of Pharmacy, Asahi Hospital, Tokyo, JPN
| | - Satoshi Fujii
- Department of Neurosurgery, Asahi Hospital, Tokyo, JPN
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Zhao F, Xiang Z, Han J, Pan J, Qu Y, Fan K, Wu Z, Xu D, Yu Y, Shen Z, Su C. Simultaneous quantification of nirmatrelvir/ritonavir in human serum by LC-HRMS. J Pharm Biomed Anal 2024; 237:115796. [PMID: 37839266 DOI: 10.1016/j.jpba.2023.115796] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
In December 2021, the U.S. Food and Drug Administration (FDA) granted emergency authorization for Paxlovid® as an antiviral treatment for COVID-19. Paxlovid® is composed of two tablets, nirmatrelvir and ritonavir. Dose adjustment is necessary in cases of renal insufficiency. The aim of present study is to establish a LC-HRMS method for simultaneous determination of nirmatrelvir/ritonavir in human serum for therapeutic drug monitoring. Internal standard saquinavir was added in 25 μL human serum samples, and then the samples were precipitated with methanol. The analytes were separated by gradient elution on a C18 column, using a mobile phase of 0.1 % formic acid-water and methanol, at a flow rate of 0.4 mL/min. The injection volume was 2 μL, and the analysis time was 5 min. The determination of the analytes was performed by electrospray ionization in positive mode by full mass monitoring. The detected ions of nirmatrelvir, ritonavir and saquinavir were m/z 500.24792, 721.32004 and 671.39155, respectively. The linear concentration range for nirmatrelvir was 78.13-20000 ng mL-1, for ritonavir was 15.63-4000 ng mL-1 (r2>0.9900). The accuracy ranged from 87.45 %∼104.63 %, and the intra-day and inter-day precision RSD was <15 %. The recovery of nirmatrelvir ranged from 98.72 %∼109.83 %, and that of ritonavir was 95.41∼112.36 %. The matrix effect of nirmatrelvir was 88.31∼97.73 %, and that of ritonavir was 85.17∼103.05 %. This method was used to measure the trough concentrations of nirmatrelvir/ritonavir in 17 patients. The trough concentration of nirmatrelvir was 1331.7-8352.5 ng/mL, and that of ritonavir was 53.4-1325.5 ng mL-1, with large individual differences. The method is simple, sensitive, specific, and reproducible, and can be used for monitoring the blood concentration and pharmacokinetic study of nirmatrelvir/ritonavir in COVID-19 patients.
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Affiliation(s)
- Fenglun Zhao
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Zheng Xiang
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Junping Han
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Jie Pan
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Yuchen Qu
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Kai Fan
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Zhiqiang Wu
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Delai Xu
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Yunli Yu
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Zhu Shen
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.
| | - Cunjin Su
- Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.
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De SK. Recent Discovery of Peptidomimetics for the Treatment of Coronavirus (COVID-19), Human Coronavirus, and Enteroviruses. Curr Med Chem 2024; 31:1289-1295. [PMID: 37143268 DOI: 10.2174/0929867330666230504150758] [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: 12/11/2022] [Revised: 03/18/2023] [Accepted: 03/24/2023] [Indexed: 05/06/2023]
Abstract
This patent describes the synthesis of compounds, methods, and compositions for preventing, treating, and/or curing Covid-19, human coronavirus, and enterovirus infections. Some peptidomimetic compounds are very potent and could be a game changer in new treatment therapy for COVID-19.
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Affiliation(s)
- Surya K De
- Department of Chemistry, Conju-Probe, San Diego, California, USA
- Bharath University, Chennai, Tamil Nadu, 600126, India
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11
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Ali S, Bolinger AA, Zhou J. Highlights on Fluorine-containing Drugs Approved by U.S. FDA in 2023. Curr Top Med Chem 2024; 24:843-849. [PMID: 38445700 DOI: 10.2174/0115680266300245240223070242] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Fluorine continues to show its potential applications in drug discovery and development, as reflected by twelve drugs being fluorinated out of the fifty-five approved by the FDA in 2023. This concise review highlights the discovery of each of these fluorine-containing drugs in the past year, including its brand name, date of approval, composition, sponsors, indication, and mechanism of action. The relevant future trend is also briefly discussed.
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Affiliation(s)
- Saghir Ali
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, 77555, United States
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, 77555, United States
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Kosonocky CW, Feller AL, Wilke CO, Ellington AD. Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches. PATTERNS (NEW YORK, N.Y.) 2023; 4:100865. [PMID: 38106612 PMCID: PMC10724362 DOI: 10.1016/j.patter.2023.100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/09/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023]
Abstract
Chemical similarity searches are a widely used family of in silico methods for identifying pharmaceutical leads. These methods historically relied on structure-based comparisons to compute similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend previous implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing search results from nine queries with diverse targets. We find that the method identifies molecules with similar patent-derived functionality to the query, as determined by our validated LLM-assisted patent summarization pipeline. Further, many of these functionally similar molecules have different structures and scaffolds from the query, making them unlikely to be found with traditional chemical similarity searches. This method may serve as a new tool for the discovery of novel molecular structural classes that achieve target functionality.
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Affiliation(s)
- Clayton W. Kosonocky
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
| | - Aaron L. Feller
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
| | - Claus O. Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78705, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78705, USA
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13
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Bello SO, Imam MU, Bello MB, Yunusa A, Ahmed Adamu A, Shuaibu A, Igumbor EU, Habib ZG, Popoola MA, Ochu CL, Yahaya Bello A, Deeni YY, Okoye I. Erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin inhibit cytopathic effect, papain-like protease, and M PRO enzymes of SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1273982. [PMID: 38089816 PMCID: PMC10711598 DOI: 10.3389/fcimb.2023.1273982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023] Open
Abstract
Background Although tremendous success has been achieved in the development and deployment of effective COVID-19 vaccines, developing effective therapeutics for the treatment of those who do come down with the disease has been with limited success. To repurpose existing drugs for COVID-19, we previously showed, qualitatively, that erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin inhibit SARS-COV-2-induced cytopathic effect (CPE) in Vero cells. Aim This study aimed to quantitatively explore the inhibition of SARS-CoV-2-induced CPE by erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin and to determine the effect of these drugs on SARS-CoV-2 papain-like protease and 3CL protease (MPRO) enzymes. Methods Neutral red (3-amino-7-dimethylamino-2-methyl-phenazine hydrochloride) cell viability assay was used to quantify CPE after infecting pre-treated Vero cells with clinical SARS-Cov-2 isolates. Furthermore, SensoLyte® 520 SARS-CoV-2 papain-like protease and SensoLyte® 520 SARS-CoV-2 MPRO activity assay kits were used to evaluate the inhibitory activity of the drugs on the respective enzymes. Results Erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin dose-dependently inhibit SARS-CoV-2-induced CPE in Vero cells, with inhibitory concentration-50 (IC50) values of 3.27 µM, 4.23 µM, 9.29 µM, 3.19 µM, and 84.31 µM, respectively. Furthermore, erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin dose-dependently inhibited SARS-CoV-2 papain-like protease with IC50 values of 0.94 µM, 0.88 µM, 1.14 µM, 1.07 µM, and 1.51 µM, respectively, and inhibited the main protease (MPRO) with IC50 values of 1.35 µM, 1.25 µM, 7.36 µM, 1.15 µM, and 2.44 µM, respectively. Conclusion The IC50 for all the drugs, except ivermectin, was at the clinically achievable plasma concentration in humans, which supports a possible role for the drugs in the management of COVID-19. The lack of inhibition of CPE by ivermectin at clinical concentrations could be part of the explanation for its lack of effectiveness in clinical trials.
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Affiliation(s)
- Shaibu Oricha Bello
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Medical Biochemistry, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Adamu Ahmed Adamu
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Abdulmalik Shuaibu
- Centre for Advanced Medical Research and Training, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Ehimario Uche Igumbor
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
- School of Public Health, University of the Western Cape, Cape Town, South Africa
| | - Zaiyad Garba Habib
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
- Department of Medicine, University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Mustapha Ayodele Popoola
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
| | - Chinwe Lucia Ochu
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
- Nigerian Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Aishatu Yahaya Bello
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Yusuf Yahaya Deeni
- Nigerian COVID-19 Research Coalition, Nigerian Institute of Medical Research Institute, Lagos, Nigeria
- Department of Microbiology and Biotechnology, Federal University of Dutse, Dutse, Nigeria
- Centre for Environmental and Public Health Research and Development, Kano, Nigeria
| | - Ifeoma Okoye
- University of Nigeria Centre for Clinical Trials, University of Nigeria Teaching Hospital, Enugu, Nigeria
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14
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Zheng B, Tazare J, Nab L, Green AC, Curtis HJ, Mahalingasivam V, Herrett EL, Costello RE, Eggo RM, Speed V, Bacon SC, Bates C, Parry J, Cockburn J, Hester F, Harper S, Schaffer AL, Hulme WJ, Mehrkar A, Evans SJ, MacKenna B, Goldacre B, Douglas IJ, Tomlinson LA. Comparative effectiveness of nirmatrelvir/ritonavir versus sotrovimab and molnupiravir for preventing severe COVID-19 outcomes in non-hospitalised high-risk patients during Omicron waves: observational cohort study using the OpenSAFELY platform. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100741. [PMID: 37927438 PMCID: PMC10624988 DOI: 10.1016/j.lanepe.2023.100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023]
Abstract
Background Timely evidence of the comparative effectiveness between COVID-19 therapies in real-world settings is needed to inform clinical care. This study aimed to compare the effectiveness of nirmatrelvir/ritonavir versus sotrovimab and molnupiravir in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients during Omicron waves. Methods With the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform. Patient-level primary care data were obtained from 24 million people in England and were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death, covering a period where both nirmatrelvir/ritonavir and sotrovimab were first-line treatment options in community settings (February 10, 2022-November 27, 2022). Molnupiravir (third-line option) was used as an exploratory comparator to nirmatrelvir/ritonavir, both of which were antivirals. Cox proportional hazards model stratified by area was used to compare the risk of 28-day COVID-19 related hospitalisation/death across treatment groups. Findings A total of 9026 eligible patients treated with nirmatrelvir/ritonavir (n = 5704) and sotrovimab (n = 3322) were included in the main analysis. The mean age was 52.7 (SD = 14.9) years and 93% (8436/9026) had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 55/9026 (0.61%) COVID-19 related hospitalisations/deaths were observed (34/5704 [0.60%] treated with nirmatrelvir/ritonavir and 21/3322 [0.63%] with sotrovimab). After adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, we observed no significant difference in outcome risk between nirmatrelvir/ritonavir and sotrovimab users (HR = 0.89, 95% CI: 0.48-1.63; P = 0.698). Results from propensity score weighted model also showed non-significant difference between treatment groups (HR = 0.82, 95% CI: 0.45-1.52; P = 0.535). The exploratory analysis comparing nirmatrelvir/ritonavir users with 1041 molnupiravir users (13/1041 [1.25%] COVID-19 related hospitalisations/deaths) showed an association in favour of nirmatrelvir/ritonavir (HR = 0.45, 95% CI: 0.22-0.94; P = 0.033). Interpretation In routine care of non-hospitalised high-risk adult patients with COVID-19 in England, no substantial difference in the risk of severe COVID-19 outcomes was observed between those who received nirmatrelvir/ritonavir and sotrovimab between February and November 2022, when Omicron subvariants BA.2, BA.5, or BQ.1 were dominant. Funding UK Research and Innovation, Wellcome Trust, UK Medical Research Council, National Institute for Health and Care Research, and Health Data Research UK.
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Affiliation(s)
- Bang Zheng
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - John Tazare
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Linda Nab
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Amelia Ca Green
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Helen J Curtis
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | | | - Emily L Herrett
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Ruth E Costello
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Rosalind M Eggo
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Victoria Speed
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Sebastian Cj Bacon
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | | | - John Parry
- TPP, TPP House, 129 Low Lane, Horsforth, Leeds LS18 5PX, UK
| | | | - Frank Hester
- TPP, TPP House, 129 Low Lane, Horsforth, Leeds LS18 5PX, UK
| | - Sam Harper
- TPP, TPP House, 129 Low Lane, Horsforth, Leeds LS18 5PX, UK
| | - Andrea L Schaffer
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - William J Hulme
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Amir Mehrkar
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Stephen Jw Evans
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Brian MacKenna
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Ben Goldacre
- Nuffield Department of Primary Care Health Sciences, Bennett Institute for Applied Data Science, University of Oxford, Oxford OX2 6GG, UK
| | - Ian J Douglas
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Laurie A Tomlinson
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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15
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Zhang AH, Diao ZL, Wang G, Guan YM, Liu YJ, Tian DL, Zhao YC, Huang HD, Liu WH. Nirmatrelvir/ritonavir use in patients with COVID-19 on hemodialysis: a case series. Diagn Microbiol Infect Dis 2023; 107:115969. [PMID: 37677996 PMCID: PMC10129908 DOI: 10.1016/j.diagmicrobio.2023.115969] [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: 02/09/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 09/09/2023]
Abstract
Patients undergoing hemodialysis (HD) are particularly vulnerable to coronavirus disease 2019 (COVID-19) and are at increased risk of developing severe infection. However, given the exclusion of such patients from clinical trials, there are limited data regarding the effectiveness of the antiviral drug nirmatrelvir/ritonavir (N/R) in patients on HD. We prescribed N/R to 4 patients on HD with COVID-19 after obtaining informed consent. Their clinical symptoms were improved at approximately 3 days after N/R administration. The viral load was reduced after approximately 10 days. The main adverse effects were nausea and vomiting. Rational dosage adjustment obtained good tolerance but did not influence the efficacy. These results suggest that N/R may be a promising agent for patients on HD with COVID-19.
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Affiliation(s)
- Ai-Hua Zhang
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Zong-Li Diao
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Gang Wang
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Yi-Ming Guan
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Ying-Jie Liu
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Dong-Li Tian
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Yu-Chao Zhao
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China
| | - Hong-Dong Huang
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China.
| | - Wen-Hu Liu
- Renal Division, Capital Medical University Affiliated Beijing Friendship Hospital, Beijing, China.
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16
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Panza F, Fiorino F, Pastore G, Fiaschi L, Tumbarello M, Medaglini D, Ciabattini A, Montagnani F, Fabbiani M. Does Nirmatrelvir/Ritonavir Influence the Immune Response against SARS-CoV-2, Independently from Rebound? Microorganisms 2023; 11:2607. [PMID: 37894265 PMCID: PMC10609571 DOI: 10.3390/microorganisms11102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Recurrence of coronavirus disease 19 (COVID-19) symptoms and SARS-CoV-2 viral load relapse have been reported in people treated with nirmatrelvir/ritonavir (NM/r). However, little is understood about the etiology of this phenomenon. Our aim was to investigate the relation between the host's immune response and viral rebound. We described three cases of COVID-19 rebound that occurred after treatment with nirmatrelvir/ritonavir (group A). In addition, we compared spike-specific antibody response and plasma cytokine/chemokine patterns of the rebound cases with those of (i) control patients treated with nirmatrelvir/ritonavir who did not show rebound (group B), and (ii) subjects not treated with any anti-SARS-CoV-2 drug (group C). The anti-spike antibodies and plasma cytokines/chemokines were similar in groups A and B. However, we observed a higher anti-BA.2 spike IgG response in patients without antiviral treatment (group C) [geometric mean titer 210,807, 5.1- and 8.2-fold higher compared to group A (p = 0.039) and group B (p = 0.032)]. Moreover, the patients receiving antiviral treatment (groups A-B) showed higher circulating levels of platelet-derived growth factor subunit B (PDGF-BB) and vascular endothelial growth Factors (VEGF) and lower levels of interleukin-9 (IL-9), interleukine-1 receptor antagonist (IL-1 RA), and regulated upon activation normal T cell expressed and presumably secreted chemokine (RANTES) when compared to group C. In conclusion, we observed lower anti-spike IgG levels and different cytokine patterns in nirmatrelvir/ritonavir-treated patients compared to those not treated with anti-SARS-CoV-2 drugs. This suggests that early antiviral treatment, by reducing viral load and antigen presentation, could mitigate the immune response against SARS-CoV-2. The clinical relevance of such observation should be further investigated in larger populations.
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Affiliation(s)
- Francesca Panza
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.P.); (L.F.); (M.T.)
- Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
| | - Fabio Fiorino
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.F.); (G.P.); (D.M.); (A.C.)
- Department of Medicine and Surgery, LUM University “Giuseppe Degennaro”, Casamassima, 70010 Bari, Italy
| | - Gabiria Pastore
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.F.); (G.P.); (D.M.); (A.C.)
| | - Lia Fiaschi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.P.); (L.F.); (M.T.)
| | - Mario Tumbarello
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.P.); (L.F.); (M.T.)
- Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.F.); (G.P.); (D.M.); (A.C.)
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.F.); (G.P.); (D.M.); (A.C.)
| | - Francesca Montagnani
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (F.P.); (L.F.); (M.T.)
- Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
| | - Massimiliano Fabbiani
- Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy;
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17
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Dutta M, Su Y, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557899. [PMID: 37745364 PMCID: PMC10516002 DOI: 10.1101/2023.09.15.557899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we find the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, lipid binding is shown to occur in the N protein C-terminal domain, which is supported by extensive in silico analysis. Anionic lipid binding occurs for both the free and N oligomeric forms suggesting N can associate with membranes in the nucleocapsid form. Herein we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to M assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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18
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Zhu KW. Deuremidevir and Simnotrelvir-Ritonavir for the Treatment of COVID-19. ACS Pharmacol Transl Sci 2023; 6:1306-1309. [PMID: 37705591 PMCID: PMC10496140 DOI: 10.1021/acsptsci.3c00134] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 09/15/2023]
Abstract
Deuremidevir hydrobromide tablets and simnotrelvir tablets/ritonavir tablets (co-packaged) were approved by the Chinese National Medical Products Administration for the treatment of mild to moderate COVID-19 in January 2023. Both formulations contain small-molecule anti-SARS-CoV-2 agents. Deuremidevir, an oral nucleoside analog, is a broad-spectrum virus replication inhibitor targeting the highly conserved RNA-dependent RNA polymerase. Simnotrelvir-ritonavir is a co-packaged combination drug consisting of simnotrelvir tablets and ritonavir tablets. Simnotrelvir is an oral antiviral agent targeting the 3-chymotrypsin-like protease, which is essential for SARS-CoV-2 viral replication. Previous clinical trials revealed that both deuremidevir and simnotrelvir-ritonavir were effective and well tolerated in the treatment of COVID-19.
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Affiliation(s)
- Ke-Wei Zhu
- Office of Pharmacovigilance, Guangzhou Baiyunshan Pharmaceutical Holding Co., Ltd.
Baiyunshan Pharmaceutical General Factory, Guangzhou 510515, China
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19
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Xu F, Huang X, Wu H, Wang X. Screening compounds for treating the diabetes and COVID-19 from Miao medicine by molecular docking and bioinformatics. ARAB J CHEM 2023; 16:105001. [PMID: 37228247 PMCID: PMC10191702 DOI: 10.1016/j.arabjc.2023.105001] [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: 12/21/2022] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Both diabetes and Corona Virus Disease 2019 (COVID-19) are seriously harmful to human health, and they are closely related. It is of great significance to find drugs that can simultaneously treat diabetes and COVID-19. Based on the theory of traditional Chinese medicine for treating COVID-19, this study first sorted out the compounds of Guizhou Miao medicine with "return to the lung channel" and "clear heat and detoxify" effects in China. The active components against COVID-19 were screened by molecular docking with SARS-CoV-2 PLpro and angiotensin-converting enzyme II as targets. Furthermore, the common target dipeptidyl peptidase 4 (DPP4) of diabetes and COVID-19 was used as a screening protein, and molecular docking was used to obtain potential components for the treatment of diabetes and COVID-19. Finally, the mechanism of potential ingredients in the treatment of diabetes and COVID-19 was explored with bioinformatics. More than 80 kinds of Miao medicine were obtained, and 584 compounds were obtained. Further, 110 compounds against COVID-19 were screened, and top 6 potential ingredients for the treatment of diabetes and COVID-19 were screened, including 3-O-β-D-Xylopyranosyl-(1-6)-β-D-glucopyranosyl-(1-6)-β-D-glucopyranosyl oleanolic acid 28-O-β-D-glucopyranosyl ester, Glycyrrhizic acid, Sequoiaflavone, 2-O-Caffeoyl maslinic acid, Pholidotin, and Ambewelamide A. Bioinformatics analysis found that their mechanism of action in treating diabetes and COVID-19 may be related to regulating the expression of DPP4, angiotensin II type 1 receptor, vitamin D receptor, plasminogen, chemokine C-C-motif receptor 6, and interleukin 2. We believe that Guizhou Miao medicine is rich in potential ingredients for the treatment of diabetes and COVID-19.
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Affiliation(s)
- Feng Xu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, PR China
| | - Xulong Huang
- Department of Pharmacy, Chengdu University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, PR China
| | - Hongmei Wu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou Province, PR China
| | - Xiangpei Wang
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Guiyang 550025, Guizhou Province, PR China
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20
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Sha A, Liu Y, Hao H. Current state-of-the-art and potential future therapeutic drugs against COVID-19. Front Cell Dev Biol 2023; 11:1238027. [PMID: 37691829 PMCID: PMC10485263 DOI: 10.3389/fcell.2023.1238027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
The novel coronavirus disease (COVID-19) continues to endanger human health, and its therapeutic drugs are under intensive research and development. Identifying the efficacy and toxicity of drugs in animal models is helpful for further screening of effective medications, which is also a prerequisite for drugs to enter clinical trials. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invades host cells mainly by the S protein on its surface. After the SARS-CoV-2 RNA genome is injected into the cells, M protein will help assemble and release new viruses. RdRp is crucial for virus replication, assembly, and release of new virus particles. This review analyzes and discusses 26 anti-SARS-CoV-2 drugs based on their mechanism of action, effectiveness and safety in different animal models. We propose five drugs to be the most promising to enter the next stage of clinical trial research, thus providing a reference for future drug development.
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Affiliation(s)
- Ailong Sha
- School of Teacher Education, Chongqing Three Gorges University, Chongqing, China
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Yi Liu
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Haiyan Hao
- School of Environmental and Chemical Engineering, Chongqing, China
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21
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Zhao Q, Zheng B, Han B, Feng P, Xia Z, Jiang H, Ying Y, Zhu J, Fei C, Xiang J, Shen L, Luo Q, Wu Y, Wusiman A, Xin C, Zhang M, Li G, Li X. Is Azvudine Comparable to Nirmatrelvir-Ritonavir in Real-World Efficacy and Safety for Hospitalized Patients with COVID-19? A Retrospective Cohort Study. Infect Dis Ther 2023; 12:2087-2102. [PMID: 37486556 PMCID: PMC10505125 DOI: 10.1007/s40121-023-00845-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/30/2023] [Indexed: 07/25/2023] Open
Abstract
INTRODUCTION Azvudine and nirmatrelvir-ritonavir are more extensively used to treat COVID-19 in China due to their earlier approval by the National Medical Products Administration. However, there has been a scarcity of research directly comparing the clinical outcomes between azvudine and nirmatrelvir-ritonavir till now. We aimed to make a head-to-head comparison of the efficacy and safety of azvudine or nirmatrelvir-ritonavir in hospitalized patients with COVID-19 in China. METHODS This retrospective cohort study was conducted using data collected from Tongde Hospital of Zhejiang Province between December 2022 and January 2023. All-cause mortality, risk of progressing to a critical condition, proportion with nucleic-acid negative conversion (PNANC), time to first nucleic-acid negative conversion (TFNANC), length of hospital stay and incidence of adverse events were systematically assessed as outcomes. Multi-model regression analysis, propensity-score-matching analysis, subgroup analysis and several sensitivity analyses were applied to compare these outcomes. RESULTS This study included a total of 1571 hospitalized patients with COVID-19, among whom 272 received nirmatrelvir-ritonavir and 156 received azvudine. We found no significant differences in all-cause mortality (HR 1.41; 95% CI 0.56-3.56; P = 0.471), risk of progressing to critical COVID-19 (HR 1.67; 95% CI 0.78-3.60; P = 0.189), PNANC (HR 0.87; 95% CI 0.69-1.09; P = 0.220), length of stay (β - 0.82; 95% CI - 2.78 to 1.15; P = 0.414) and adverse event rate (3.21% vs. 4.41%, P = 0.538) between the two groups, although azvudine was slightly less effective than nirmatrelvir-ritonavir. Meanwhile, the azvudine group exhibited a significantly longer TFNANC (β 2.53; 95% CI 0.76-4.29; P = 0.005) than the nirmatrelvir-ritonavir group. Results were similar for propensity-score matching and multiple sensitivity analyses. CONCLUSION Azvudine probably possessed comparable efficacy and safety to nirmatrelvir-ritonavir, although it was less effective than nirmatrelvir-ritonavir for some outcomes.
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Affiliation(s)
- Qinqin Zhao
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Bei Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Bing Han
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Pinpin Feng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Zhongni Xia
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Hong Jiang
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Yin Ying
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Jun Zhu
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China
| | - Cheng Fei
- Department of Pharmacy, The 72nd Group Army Hospital of PLA, Huzhou, 313000, China
| | - Junlei Xiang
- Department of Pharmacy, Longquan People's Hospital, Longquan, 323700, China
| | - Lingli Shen
- Department of Pharmacy, Linping Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, 311100, China
| | - Qiliang Luo
- Department of Pharmacy, Zhaotong Mental Health Center, Zhaotong, 657000, China
| | - Yinhuan Wu
- Department of Pharmacy, Ruian Fifth People's Hospital, Ruian, 325200, China
| | - Ayiguzhali Wusiman
- Department of Pharmacy, Fourth People's Hospital of Aksu Region, Aksu, 843000, China
| | - Chuanwei Xin
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China.
| | - Meiling Zhang
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China.
| | - Gonghua Li
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, No. 234 Gucui Road, Xihu District, Hangzhou, 310012, Zhejiang Province, China.
| | - Xiang Li
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, No. 8 Yikang Street, Lin'an District, Hangzhou, 311399, Zhejiang Province, China.
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22
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Lindahl AL, Ahava MJ, Haukipää M, Kreivi HR, Lipponen A, Kortela E. Successful treatment of persisting SARS-CoV-2 infection in an immunocompromised patient with repeated nirmatrelvir/ritonavir courses: a case report. Infect Dis (Lond) 2023; 55:585-589. [PMID: 37334428 DOI: 10.1080/23744235.2023.2223274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND In immunocompromised patients, persistent SARS-CoV-2 viral shedding and relapsing COVID-19 pneumonia have been described. Currently, little is known about the management of persisting COVID-19, and immunocompromised patients are recommended to be treated using antivirals and immunomodulatory therapies at similar doses and durations as the general population. Previous case reports have described treatment with repeated and prolonged courses of remdesivir and some evidence is emerging in the use of nirmatrelvir/ritonavir combination (NMV/r). METHODS We describe a patient with recent chemotherapy including rituximab for follicular lymphoma with persisting SARS-CoV-2 infection. Polymerase chain reaction tests (PCR), cycle threshold values and blood SARS-CoV-2 antigen levels were evaluated. RESULTS The patient presented with persisting SARS-CoV-2 with relapsing COVID-19 pneumonia. The patient was treated successfully with repeated courses of NMV/r without any observed adverse effects. After the third, prolonged course, the patient remained afebrile and PCR negative, and no relapses have been observed four months after the third NMV/r course. CONCLUSIONS Nirmatrelvir-ritonavir could offer a more accessible alternative to remdesivir. Further research and guidelines for persisting SARS-CoV-2 infection in immunocompromised patients are urgently needed.
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Affiliation(s)
- Anna L Lindahl
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Maarit J Ahava
- Diagnostic Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Mia Haukipää
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Hanna-Riikka Kreivi
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Anne Lipponen
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Elisa Kortela
- Inflammation Center, Helsinki University Hospital and University of Helsinki, Finland
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23
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Navitha Reddy G, Jogvanshi A, Naikwadi S, Sonti R. Nirmatrelvir and ritonavir combination: an antiviral therapy for COVID-19. Expert Rev Anti Infect Ther 2023; 21:943-955. [PMID: 37525997 DOI: 10.1080/14787210.2023.2241638] [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: 03/15/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
INTRODUCTION The emergence of the Omicron SARS-CoV-2 variant of concern in late November 2021 presaged yet another stage of the COVID-19 pandemic. Paxlovid, a co-packaged dosage form of two antiviral drugs (nirmatrelvir and ritonavir) developed by Pfizer, received its first FDA Emergency Use Authorization (EUA) and conditional marketing by European Medical Agency in patients at high risk of developing severe COVID-19. AREAS COVERED We reviewed the timeline of the drug nirmatrelvir from its discovery to authorization by FDA. After 1 year of its authorization, numerous studies and reports on paxlovid's use and post-use consequences are available. This review summarizes the complete journey of paxlovid from its development, preclinical studies, clinical trials, regulatory approvals, ongoing clinical trials, and safety measures, followed by discussions on recent updates on drug-drug interactions, adverse effects, and relapse of COVID-19. EXPERT OPINION Paxlovid, a new oral antiviral therapy for COVID-19, has shown promising results in clinical trials and has the potential to be effective against the pandemic, particularly for individuals at high risk of severe illness. Comorbidity usage and pharmacovigilance will play a significant stake in the future of paxlovid development. Second-generation Mpro inhibitors play an important role in the upcoming problems associated with COVID-19.
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Affiliation(s)
- Gangireddy Navitha Reddy
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Akanksha Jogvanshi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Sana Naikwadi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Rajesh Sonti
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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24
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Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [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: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
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Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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25
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Farkaš B, Minneci M, Misevicius M, Rozas I. A Tale of Two Proteases: M Pro and TMPRSS2 as Targets for COVID-19 Therapies. Pharmaceuticals (Basel) 2023; 16:834. [PMID: 37375781 DOI: 10.3390/ph16060834] [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: 04/27/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (MPro) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral MPro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel MPro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Barbara Farkaš
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Marco Minneci
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Matas Misevicius
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
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26
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Tsai YW, Wu JY, Liu TH, Chuang MH, Hsu WH, Huang PY, Lai CC, Tsai KT, Shiue YL. Clinical effectiveness of oral antiviral agents in older patients with COVID-19 based on real-world data. J Med Virol 2023; 95:e28869. [PMID: 37322616 DOI: 10.1002/jmv.28869] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Several randomized controlled trials and real-world cohort studies have demonstrated the efficacies of nirmatrelvir plus ritonavir (NMV-r) and molnupiravir (MOV) in at-risk patients with COVID-19; however, the effectiveness of antisevere acute respiratory syndrome-coronavirus 2 treatments on older patients (≥65 years) remains unclear. This retrospective cohort study aimed to assess the clinical effectiveness of the oral antiviral agents, MOV and NMV-r, in older patients (≥65 years) infected with severe acute respiratory syndrome-coronavirus 2. Nonhospitalized older patients with COVID-19 between January 1, 2022, and December 31, 2022, were recruited from the TriNetX Research Network. Propensity score matching (PSM) was used to match patients who received either NMV-r or MOV treatment with those who did not receive any oral antiviral agents. Hazard ratios (HRs) for composite all-cause hospitalization or death during the 30-day follow-up period were calculated. PSM revealed two cohorts with 28 824 patients each having balanced baseline characteristics. The antiviral group was associated with significantly lower risk of the primary composite outcome of all-cause hospitalization or death than the control group (241 vs. 801; HR, 0.307; 95% confidence interval (CI), 0.27-0.36) during the follow-up period. For the secondary outcome, the antiviral group had a significantly lower risk of all-cause hospitalization (288 vs. 725; HR, 0.322; 95% CI, 0.28-0.37) and mortality (16 vs. 94; HR, 0.176; 95% CI, 0.10-0.30) than the control group. Moreover, the reduced risk of all-cause hospitalization or death remained consistent in patients receiving NMV-r (HR, 0.279; 95% CI, 0.24-0.33) and MOV (HR, 0.279; 95% CI, 0.21-0.38). Our results revealed that NMV-r and MOV decreased the all-cause hospitalization and death rates among older patients with COVID-19, supporting the use of antivirals in this vulnerable population.
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Affiliation(s)
- Ya-Wen Tsai
- Center for Integrative Medicine, Chi Mei Medical Center, Tainan City, Taiwan
- Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Jheng-Yan Wu
- Department of Nutrition, Chi Mei Medical Center, Tainan, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ting-Hui Liu
- Department of Psychiatry, Chi Mei Medical Center, Tainan, Taiwan
| | - Min-Hsiang Chuang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Wan-Hsuan Hsu
- Department of General Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Po-Yu Huang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Kang-Ting Tsai
- Division of Geriatrics and Gerontology, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
- Department of Senior Welfare and Services, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
- Institute of Precision Medicine, National Sun-Yat-Sen University, Kaohsiung, Taiwan
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27
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Globenko AA, Kuzin GV, Rydlovskaya AV, Isaeva EI, Vetrova EN, Pritchina TN, Baranova A, Nebolsin VE. Curtailing virus-induced inflammation in respiratory infections: emerging strategies for therapeutic interventions. Front Pharmacol 2023; 14:1087850. [PMID: 37214455 PMCID: PMC10196389 DOI: 10.3389/fphar.2023.1087850] [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: 11/02/2022] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Acute respiratory viral infections (ARVI) are the most common illnesses worldwide. In some instances, mild cases of ARVI progress to hyperinflammatory responses, which are damaging to pulmonary tissue and requiring intensive care. Here we summarize available information on preclinical and clinical effects of XC221GI (1-[2-(1-methyl imidazole-4-yl)-ethyl]perhydroazin-2,6-dione), an oral drug with a favorable safety profile that has been tested in animal models of influenza, respiratory syncytial virus, highly pathogenic coronavirus strains and other acute viral upper respiratory infections. XC221GI is capable of controlling IFN-gamma-driven inflammation as it is evident from the suppression of the production of soluble cytokines and chemokines, including IL-6, IL-8, CXCL10, CXCL9 and CXCL11 as well as a decrease in migration of neutrophils into the pulmonary tissue. An excellent safety profile of XC221GI, which is not metabolized by the liver, and its significant anti-inflammatory effects indicate utility of this compound in abating conversion of ambulatory cases of respiratory infections into the cases with aggravated presentation that require hospitalization. This drug is especially useful when rapid molecular assays determining viral species are impractical, or when direct antiviral drugs are not available. Moreover, XC221GI may be combined with direct antiviral drugs to enhance their therapeutic effects.
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Affiliation(s)
| | | | | | - Elena I. Isaeva
- N F Gamaleya Federal Research Center for Epidemiology & Microbiology, Moscow, Russia
| | - Elizaveta N. Vetrova
- N F Gamaleya Federal Research Center for Epidemiology & Microbiology, Moscow, Russia
| | - Tat’yana N. Pritchina
- N F Gamaleya Federal Research Center for Epidemiology & Microbiology, Moscow, Russia
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
- Research Centre for Medical Genetics, Moscow, Russia
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28
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Petrakis V, Rafailidis P, Trypsianis G, Papazoglou D, Panagopoulos P. The Antiviral Effect of Nirmatrelvir/Ritonavir during COVID-19 Pandemic Real-World Data. Viruses 2023; 15:v15040976. [PMID: 37112956 PMCID: PMC10144059 DOI: 10.3390/v15040976] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
INTRODUCTION Vaccination against SARS-CoV-2 and the prevalence of Omicron variants have reduced the risk of the severe clinical progress of COVID-19. However, the risk of breakthrough infections has increased, and early administration of an effective antiviral treatment is significant in order to prevent the severe progression of COVID-19 in vulnerable patients with comorbidities. PATIENTS AND METHODS Adults with confirmed SARS-CoV-2 infection were included in a matched-pair retrospective study based on age, gender, comorbidities and vaccination status. They were divided into two groups: group A (n = 200) consisted of outpatients at increased risk of severe clinical progress who were treated with nirmatrelvir/ritonavir and group B (n = 200) consisted of non-hospitalized patients who did not receive antiviral treatment. Demographic data, clinical outcome (death, intubation), days of hospitalization, time for recovery, adverse events and treatment compliance were reported. RESULTS The median age (75.24 ± 13.12 years in the study group and 76.91 ± 14.02 years in the comparison group) and the proportion of males (59% vs. 60.5%, respectively) were similar between the two groups. A total of 6.5% of patients in group A and 10.5% in group B were unvaccinated against SARS-CoV-2. Three patients from group A (1.5%) and one hundred eleven (55.5%) from group B required hospitalization. The duration of hospitalization (3 days vs. 10 days in group B, p < 0.001) and the total time needed for recovery (5 days vs. 9 days, p < 0.001) was shorter in the study group. A rebound of SARS-CoV-2 infection within 8-12 days after diagnosis was documented in 6.5% of patients in group A and 8% of patients in group B. CONCLUSION Oral treatment with nirmatrelvir/ritonavir in high-risk non-hospitalized patients was safe and effective in preventing the severe clinical progress of COVID-19 pneumonia. Early administration of antiviral agents in vulnerable outpatients combined with a full vaccination scheme is significant in order to avoid hospitalization and severe clinical outcomes.
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Affiliation(s)
- Vasilios Petrakis
- Department of Infectious Diseases, 2nd University Department of Internal Medicine, University General Hospital Alexandroupolis, Democritus University Thrace, 68132 Alexandroupolis, Greece
| | - Petros Rafailidis
- Department of Infectious Diseases, 2nd University Department of Internal Medicine, University General Hospital Alexandroupolis, Democritus University Thrace, 68132 Alexandroupolis, Greece
| | - Grigorios Trypsianis
- Department of Medical Statistics, Medical School, Democritus University of Thrace, 69100 Komotini, Greece
| | - Dimitrios Papazoglou
- Department of Infectious Diseases, 2nd University Department of Internal Medicine, University General Hospital Alexandroupolis, Democritus University Thrace, 68132 Alexandroupolis, Greece
| | - Periklis Panagopoulos
- Department of Infectious Diseases, 2nd University Department of Internal Medicine, University General Hospital Alexandroupolis, Democritus University Thrace, 68132 Alexandroupolis, Greece
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29
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Zabidi NZ, Liew HL, Farouk IA, Puniyamurti A, Yip AJW, Wijesinghe VN, Low ZY, Tang JW, Chow VTK, Lal SK. Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies. Viruses 2023; 15:v15040944. [PMID: 37112923 PMCID: PMC10145020 DOI: 10.3390/v15040944] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.
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Affiliation(s)
- Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Hern Liang Liew
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Isra Ahmad Farouk
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | | | - Zheng Yao Low
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Julian W Tang
- Department of Respiratory Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Vincent T K Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Sunil K Lal
- School of Science, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor, Malaysia
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30
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Hus I, Szymczyk A, Mańko J, Drozd-Sokołowska J. COVID-19 in Adult Patients with Hematological Malignancies-Lessons Learned after Three Years of Pandemic. BIOLOGY 2023; 12:biology12040545. [PMID: 37106746 PMCID: PMC10136203 DOI: 10.3390/biology12040545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
The COVID-19 pandemic is undoubtedly the most difficult health challenge of the 21st century with more than 600 million laboratory-confirmed SARS-CoV-2 infections and over 6.5 million deaths worldwide. The coronavirus pandemic contributed to rapid development of mRNA vaccines, which, along with new antiviral drugs, have been the subject of extensive research for many decades. Nevertheless, elderly, multi-morbid and immunocompromised patients continue to face a more severe clinical course and a higher risk of death from COVID-19, even now that the risk of COVID-19 in the general population is significantly reduced due to the introduction of global vaccination strategies. In this paper, we present the mechanisms of increased susceptibility to infectious complications and the evolution of the clinical course of COVID-19 in patients with hematological malignancies, taking into account the mutation of the virus and the introduction of vaccines and new antiviral drugs. We also present current recommendations for prophylactic and therapeutic management in patients with hematological malignancies.
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Affiliation(s)
- Iwona Hus
- Department of Hematology, National Medical Institute of the Ministry of Interior and Administration, 137 Wołoska Str., 02-507 Warsaw, Poland
- Department of Clinical Transplantology, Medical University of Lublin, 7 Chodźki Str., 20-093 Lublin, Poland
| | - Agnieszka Szymczyk
- Department of Hematology, National Medical Institute of the Ministry of Interior and Administration, 137 Wołoska Str., 02-507 Warsaw, Poland
- Department of Clinical Transplantology, Medical University of Lublin, 7 Chodźki Str., 20-093 Lublin, Poland
| | - Joanna Mańko
- Department of Hematology, National Medical Institute of the Ministry of Interior and Administration, 137 Wołoska Str., 02-507 Warsaw, Poland
| | - Joanna Drozd-Sokołowska
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, 1a Banacha Str., 02-097 Warsaw, Poland
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Mori M, Quaglio D, Calcaterra A, Ghirga F, Sorrentino L, Cammarone S, Fracella M, D’Auria A, Frasca F, Criscuolo E, Clementi N, Mancini N, Botta B, Antonelli G, Pierangeli A, Scagnolari C. Natural Flavonoid Derivatives Have Pan-Coronavirus Antiviral Activity. Microorganisms 2023; 11:microorganisms11020314. [PMID: 36838279 PMCID: PMC9960971 DOI: 10.3390/microorganisms11020314] [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: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The SARS-CoV-2 protease (3CLpro) is one of the key targets for the development of efficacious drugs for COVID-19 treatment due to its essential role in the life cycle of the virus and exhibits high conservation among coronaviruses. Recent studies have shown that flavonoids, which are small natural molecules, have antiviral activity against coronaviruses (CoVs), including SARS-CoV-2. In this study, we identified the docking sites and binding affinity of several natural compounds, similar to flavonoids, and investigated their inhibitory activity towards 3CLpro enzymatic activity. The selected compounds were then tested in vitro for their cytotoxicity, for antiviral activity against SARS-CoV-2, and the replication of other coronaviruses in different cell lines. Our results showed that Baicalein (100 μg/mL) exerted strong 3CLpro activity inhibition (>90%), whereas Hispidulin and Morin displayed partial inhibition. Moreover, Baicalein, up to 25 μg/mL, hindered >50% of SARS-CoV-2 replication in Vero E6 cultures. Lastly, Baicalein displayed antiviral activity against alphacoronavirus (Feline-CoV) and betacoronavirus (Bovine-CoV and HCoV-OC43) in the cell lines. Our study confirmed the antiviral activity of Baicalein against SARS-CoV-2 and demonstrated clear evidence of its pan-coronaviral activity.
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Affiliation(s)
- Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Deborah Quaglio
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Andrea Calcaterra
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Ghirga
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Leonardo Sorrentino
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Cammarone
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Matteo Fracella
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandra D’Auria
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Federica Frasca
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Elena Criscuolo
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Bruno Botta
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, 00185 Rome, Italy
| | - Guido Antonelli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandra Pierangeli
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Carolina Scagnolari
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence:
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