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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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2
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Wu M, Sun C, Shi Q, Luo Y, Wang Z, Wang J, Qin Y, Cui W, Yan C, Dai H, Wang Z, Zeng J, Zhou Y, Zhu M, Liu X. Dry eye disease caused by viral infection: Past, present and future. Virulence 2024; 15:2289779. [PMID: 38047740 PMCID: PMC10761022 DOI: 10.1080/21505594.2023.2289779] [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: 08/11/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Following viral infection, the innate immune system senses viral products, such as viral nucleic acids, to activate innate defence pathways, leading to inflammation and apoptosis, control of cell proliferation, and consequently, threat to the whole body. The ocular surface is exposed to the external environment and extremely vulnerable to viral infection. Several studies have revealed that viral infection can induce inflammation of the ocular surface and reduce tear secretion of the lacrimal gland (LG), consequently triggering ocular morphological and functional changes and resulting in dry eye disease (DED). Understanding the mechanisms of DED caused by viral infection and its potential therapeutic strategies are crucial for clinical interventional advances in DED. This review summarizes the roles of viral infection in the pathogenesis of DED, applicable diagnostic and therapeutic strategies, and potential regions of future studies.
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Affiliation(s)
- Min Wu
- Department of Pathogen Biology, Medical College, Nantong University, Nantong, Jiangsu, China
| | - Cuilian Sun
- Department of Pathogen Biology, Medical College, Nantong University, Nantong, Jiangsu, China
| | - Qin Shi
- Department of General Medicine, Gongli Hospital, Shanghai, China
| | - Yalu Luo
- Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Ziyu Wang
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Jianxiang Wang
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Yun Qin
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Weihang Cui
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Chufeng Yan
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Huangyi Dai
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Zhiyang Wang
- Medical College, Nantong University, Nantong, Jiangsu, China
| | - Jia Zeng
- Department of Pathogen Biology, Medical College, Nantong University, Nantong, Jiangsu, China
| | - Yamei Zhou
- Department of Microbiology Laboratory, Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, China
| | - Manhui Zhu
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaojuan Liu
- Department of Pathogen Biology, Medical College, Nantong University, Nantong, Jiangsu, China
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Kukułowicz J, Bajda M. In silico structural studies on the vesicular neutral amino acid transporter NTT4 (SLC6A17). Comput Struct Biotechnol J 2024; 23:3342-3347. [PMID: 39310277 PMCID: PMC11416165 DOI: 10.1016/j.csbj.2024.09.004] [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: 07/01/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
NTT4 is one of the neutral amino acid transporters that regulate neural concentration of precursors for glutamate biosynthesis. Here, we provide insight into the structure of NTT4 and rationalize substrate selectivity. Furthermore, we demonstrate how the mutations associated with mental disabilities imply malfunction of the transporter at the molecular level. We also compared the structures of NTT4 and B0AT2 (SLC6A15), which is a close homolog, sharing 66 % of the common amino acids. Our analyses may be useful in the search for compounds that inhibit substrate transport. Moreover, they allow a better understanding of the function of these transporters.
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Affiliation(s)
- Jędrzej Kukułowicz
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30–688, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Krakow 30–688, Poland
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Patel DR, Macpherson L, Bohm M, Upadhyaya H, Deveau C, Nirula A, Klekotka P, Williams M, Hufford MM. Efficacy and Safety of Low-Dose, Rapidly Infused Bamlanivimab and Etesevimab: Phase 3 BLAZE-1 Trial for Mild-to-Moderate COVID-19. Infect Dis Ther 2024; 13:2123-2134. [PMID: 39230829 PMCID: PMC11416433 DOI: 10.1007/s40121-024-01031-z] [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: 05/13/2024] [Accepted: 08/05/2024] [Indexed: 09/05/2024] Open
Abstract
INTRODUCTION The monoclonal antibody therapies bamlanivimab (BAM) + etesevimab (ETE) received emergency use authorization (EUA) from the US Food and Drug Administration (February 9, 2021) for treatment of mild-to-moderate COVID-19. The EUA of BAM + ETE was revoked (December 14, 2023) due to the high prevalence of BAM + ETE-resistant variants of SARS-CoV-2. Efficacy and safety of 700/1400 mg and 2800/2800 mg BAM + ETE are well established and published; however, efficacy and safety of 350/700 mg BAM + ETE have not been disclosed to date. METHODS This portion of phase 3, BLAZE-1 trial (J2X-MC-PYAB) enrolled patients (between June 17, 2020 and April 9, 2021) with mild-to-moderate COVID-19 within 3 days of laboratory diagnosis of SARS-CoV-2 infection. In total, 354 patients with at least one risk factor for severe COVID-19 were enrolled, randomized (2:3), and infused with placebo (N = 141) or 350/700 mg BAM + ETE (N = 213), over ~ 8 min. Primary endpoint was to assess proportion of patients with persistently high SARS-CoV-2 viral load (PHVL) (log viral load > 5.27) 7 days after infusion. RESULTS Patients were aged (mean) 53 years, 49.7% female, and 82.7% White. Seven days after drug infusion, 10.8% (95% confidence interval: 6.6, 15.0; p < 0.001) of BAM + ETE-treated patients and 34.8% (26.9, 42.6) of placebo-treated patients had PHVL, and the viral load change from baseline (least square mean [standard error]) was - 3.50 (0.15; p < 0.001) in BAM + ETE-treated patients versus - 2.51 (0.19) in placebo-treated patients. The majority of treatment-emergent adverse events were considered mild or moderate in severity (BAM + ETE: 6.6%; placebo: 14.2%). No deaths were reported. CONCLUSIONS Consistent with previous studies, patients treated with BAM + ETE (350/700 mg) had a significantly lower proportion of PHVL and greater reduction in viral load compared with placebo. The overall safety profile is consistent with higher doses of BAM + ETE. Infusions of over ~ 8 min did not result in meaningful increase in incidence of TEAEs compared to higher doses of BAM + ETE administered over 30-60 min. TRIAL REGISTRATION Clinical trial.gov identifier, NCT04427501.
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Affiliation(s)
- Dipak R Patel
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Lisa Macpherson
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Martin Bohm
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | | | - Carmen Deveau
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Ajay Nirula
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Paul Klekotka
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Mark Williams
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA
| | - Matthew M Hufford
- Eli Lilly and Company, 893 S Delaware St, Indianapolis, IN, 46220, USA.
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Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024; 278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [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: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.
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Affiliation(s)
- Aniruddh Jhanwar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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Sugiura K, Fujita H, Komine M, Yamanaka K, Akiyama M. The role of interleukin-36 in health and disease states. J Eur Acad Dermatol Venereol 2024; 38:1910-1925. [PMID: 38779986 DOI: 10.1111/jdv.19935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/29/2024] [Indexed: 05/25/2024]
Abstract
The interleukin (IL)-1 superfamily upregulates immune responses and maintains homeostasis between the innate and adaptive immune systems. Within the IL-1 superfamily, IL-36 plays a pivotal role in both innate and adaptive immune responses. Of the four IL-36 isoforms, three have agonist activity (IL-36α, IL-36β, IL-36γ) and the fourth has antagonist activity (IL-36 receptor antagonist [IL-36Ra]). All IL-36 isoforms bind to the IL-36 receptor (IL-36R). Binding of IL-36α/β/γ to the IL-36R recruits the IL-1 receptor accessory protein (IL-1RAcP) and activates downstream signalling pathways mediated by nuclear transcription factor kappa B and mitogen-activated protein kinase signalling pathways. Antagonist binding of IL-36Ra to IL-36R inhibits recruitment of IL-1RAcP, blocking downstream signalling pathways. Changes in the balance within the IL-36 cytokine family can lead to uncontrolled inflammatory responses throughout the body. As such, IL-36 has been implicated in numerous inflammatory diseases, notably a type of pustular psoriasis called generalized pustular psoriasis (GPP), a chronic, rare, potentially life-threatening, multisystemic skin disease characterised by recurrent fever and extensive sterile pustules. In GPP, IL-36 is central to disease pathogenesis, and the prevention of IL-36-mediated signalling can improve clinical outcomes. In this review, we summarize the literature describing the biological functions of the IL-36 pathway. We also consider the evidence for uncontrolled activation of the IL-36 pathway in a wide range of skin (e.g., plaque psoriasis, pustular psoriasis, hidradenitis suppurativa, acne, Netherton syndrome, atopic dermatitis and pyoderma gangrenosum), lung (e.g., idiopathic pulmonary fibrosis), gut (e.g., intestinal fibrosis, inflammatory bowel disease and Hirschsprung's disease), kidney (e.g., renal tubulointerstitial lesions) and infectious diseases caused by a variety of pathogens (e.g., COVID-19; Mycobacterium tuberculosis, Pseudomonas aeruginosa, Streptococcus pneumoniae infections), as well as in cancer. We also consider how targeting the IL-36 signalling pathway could be used in treating inflammatory disease states.
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Affiliation(s)
- Kazumitsu Sugiura
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hideki Fujita
- Department of Dermatology, Nihon University School of Medicine, Tokyo, Japan
| | - Mayumi Komine
- Department of Dermatology, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Keiichi Yamanaka
- Department of Dermatology, Graduate School of Medicine, Mie University, Tsu, Japan
| | - Masashi Akiyama
- Department of Dermatology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Zheng JR, Chang JL, Hu J, Lin ZJ, Lin KH, Lu BH, Chen XH, Liu ZG. Myelin oligodendrocyte glycoprotein-associated transverse myelitis after SARS-CoV-2 infection: A case report. World J Radiol 2024; 16:446-452. [DOI: 10.4329/wjr.v16.i9.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/23/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024] Open
Abstract
BACKGROUND Cases of myelin oligodendrocyte glycoprotein (MOG) antibody-related disease have a history of coronavirus disease 2019 infection or its vaccination before disease onset. Severe acute respiratory syndrome virus 2 (SARS-CoV-2) infection has been considered to be a trigger of central nervous system autoimmune diseases.
CASE SUMMARY Here we report a 20-year male with MOG-associated transverse myelitis after a SARS-CoV-2 infection. The patient received a near-complete recovery after standard immunological treatments.
CONCLUSION Attention should be paid to the evaluation of typical or atypical neurological symptoms that may be triggered by SARS-CoV-2 infection.
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Affiliation(s)
- Jian-Rong Zheng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
- Department of Neurology, Shenzhen Xinhua Hospital, Shenzhen 518000, Guangdong Province, China
| | - Jun-Lei Chang
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, Guangdong Province, China
| | - Jun Hu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
| | - Zhi-Jian Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
| | - Kai-Hua Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
| | - Bi-Hua Lu
- Department of Neurology, The Sixth People’s Hospital of Foshan Nanhai District, Foshan 528000, Guangdong Province, China
| | - Xu-Hui Chen
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, China
| | - Zhi-Gang Liu
- Laboratory of Functional Chemistry and Nutrition of Food, Northwest A&F University, Yangling 712100, Shaanxi Province, China
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Attiq A, Afzal S, Wahab HA, Ahmad W, Kandeel M, Almofti YA, Alameen AO, Wu YS. Cytokine Storm-Induced Thyroid Dysfunction in COVID-19: Insights into Pathogenesis and Therapeutic Approaches. Drug Des Devel Ther 2024; 18:4215-4240. [PMID: 39319193 PMCID: PMC11421457 DOI: 10.2147/dddt.s475005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Angiotensin-converting enzyme 2 receptors (ACE2R) are requisite to enter the host cells for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). ACE2R is constitutive and functions as a type I transmembrane metallo-carboxypeptidase in the renin-angiotensin system (RAS). On thyroid follicular cells, ACE2R allows SARS-CoV-2 to invade the thyroid gland, impose cytopathic effects and produce endocrine abnormalities, including stiff back, neck pain, muscle ache, lethargy, and enlarged, inflamed thyroid gland in COVID-19 patients. Further damage is perpetuated by the sudden bursts of pro-inflammatory cytokines, which is suggestive of a life-threatening syndrome known as a "cytokine storm". IL-1β, IL-6, IFN-γ, and TNF-α are identified as the key orchestrators of the cytokine storm. These inflammatory mediators upregulate transcriptional turnover of nuclear factor-kappa B (NF-κB), Janus kinase/signal transducer and activator of transcription (JAK/STAT), and mitogen-activated protein kinase (MAPK), paving the pathway for cytokine storm-induced thyroid dysfunctions including euthyroid sick syndrome, autoimmune thyroid diseases, and thyrotoxicosis in COVID-19 patients. Targeted therapies with corticosteroids (dexamethasone), JAK inhibitor (baricitinib), nucleotide analogue (remdesivir) and N-acetyl-cysteine have demonstrated effectiveness in terms of attenuating the severity and frequency of cytokine storm-induced thyroid dysfunctions, morbidity and mortality in severe COVID-19 patients. Here, we review the pathogenesis of cytokine storms and the mechanisms and pathways that establish the connection between thyroid disorder and COVID-19. Moreover, cross-talk interactions of signalling pathways and therapeutic strategies to address COVID-19-associated thyroid diseases are also discussed herein.
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Affiliation(s)
- Ali Attiq
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang, 11800, Malaysia
| | - Sheryar Afzal
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al Ahsa, 31982, Saudi Arabia
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang, 11800, Malaysia
| | - Waqas Ahmad
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang, 11800, Malaysia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al Ahsa, 31982, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrel Sheikh, 6860404, Egypt
| | - Yassir A Almofti
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al Ahsa, 31982, Saudi Arabia
- Department of Biochemistry, Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, 12217, Sudan
| | - Ahmed O Alameen
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al Ahsa, 31982, Saudi Arabia
- Department of Physiology, Faculty of Veterinary Medicine, University of Khartoum, Shambat, 13314, Sudan
| | - Yuan Seng Wu
- Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, Subang Jaya, Selangor, 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya, Selangor, 47500, Malaysia
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Deng W, Hu X, Tian X, Zhang Y, Shang W, Zhang L, Shang L. Peptidomimetic Analogues Act as Effective Inhibitors against SARS-CoV-2 by Blocking the Function of Cathepsin L. J Med Chem 2024. [PMID: 39292661 DOI: 10.1021/acs.jmedchem.4c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Cathepsin L (CatL) is a promising antiviral drug target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an important protease for cleaving the SARS-CoV-2 spike protein and enhancing viral entry to cells. We identified a tripeptide aldehyde candidate, D1-1, which exhibited inhibitory effects against SARS-CoV-2 in Vero E6 cells. The protease screening analysis and protein pull-down assays demonstrated the direct binding of D1-1 to CatL. Guided by molecular docking, we synthesized 72 analogues. Upon analyzing the structure-activity relationships of these inhibitors, the D6 series was developed. Among them, D6-3 functioned as the most potent CatL inhibitor (IC50 = 0.27 nM, EC50 = 0.26 μM). D6-3 effectively blocked the CatL function and substantially hindered the entry of the SARS-CoV-2 pseudovirus to cells. Our work presented novel compounds for targeting and inhibiting CatL, offering valuable insights into the development of SARS-CoV-2 antivirals.
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Affiliation(s)
- Weilong Deng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Xiao Hu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Xiaoman Tian
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Yuanyuan Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
| | - Weijuan Shang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Leike Zhang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Luqing Shang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, Nankai University, Tianjin 300353, People's Republic of China
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Skeeters S, Bagale K, Stepanyuk G, Thieker D, Aguhob A, Chan KK, Dutzar B, Shalygin S, Shajahan A, Yang X, DaRosa PA, Frazier E, Sauer MM, Bogatzki L, Byrnes-Blake KA, Song Y, Azadi P, Tarcha E, Zhang L, Procko E. Modulation of the pharmacokinetics of soluble ACE2 decoy receptors through glycosylation. Mol Ther Methods Clin Dev 2024; 32:101301. [PMID: 39185275 PMCID: PMC11342882 DOI: 10.1016/j.omtm.2024.101301] [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: 10/13/2023] [Accepted: 07/16/2024] [Indexed: 08/27/2024]
Abstract
The Spike of SARS-CoV-2 recognizes a transmembrane protease, angiotensin-converting enzyme 2 (ACE2), on host cells to initiate infection. Soluble derivatives of ACE2, in which Spike affinity is enhanced and the protein is fused to Fc of an immunoglobulin, are potent decoy receptors that reduce disease in animal models of COVID-19. Mutations were introduced into an ACE2 decoy receptor, including adding custom N-glycosylation sites and a cavity-filling substitution together with Fc modifications, which increased the decoy's catalytic activity and provided small to moderate enhancements of pharmacokinetics following intravenous and subcutaneous administration in humanized FcRn mice. Most prominently, sialylation of native glycans increases exposures by orders of magnitude, and the optimized decoy is therapeutically efficacious in a mouse COVID-19 model. Ultimately, an engineered and highly sialylated decoy receptor produced using methods suitable for manufacture of representative drug substance has high exposure with a 5- to 9-day half-life. Finally, peptide epitopes at mutated sites in the decoys generally have low binding to common HLA class II alleles and the predicted immunogenicity risk is low. Overall, glycosylation is a critical molecular attribute of ACE2 decoy receptors and modifications that combine tighter blocking of Spike with enhanced pharmacokinetics elevate this class of molecules as viable drug candidates.
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Affiliation(s)
| | - Kamal Bagale
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | | | | | | | | | - Sergei Shalygin
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Asif Shajahan
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Xu Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | | | | | | | | | | | - Yifan Song
- Cyrus Biotechnology, Seattle, WA 98121, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | | | - Lianghui Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erik Procko
- Cyrus Biotechnology, Seattle, WA 98121, USA
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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Cone AS, Zhou Y, McNamara RP, Eason AB, Arias GF, Landis JT, Shifflett KW, Chambers MG, Yuan R, Willcox S, Griffith JD, Dittmer DP. CD81 fusion alters SARS-CoV-2 Spike trafficking. mBio 2024; 15:e0192224. [PMID: 39140770 PMCID: PMC11389398 DOI: 10.1128/mbio.01922-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic caused the biggest public health crises in recent history. Many expect future coronavirus introductions into the human population. Hence, it is essential to understand the basic biology of these viruses. In natural infection, the SARS-CoV-2 Spike (S) glycoprotein is co-expressed with all other viral proteins, which modify cellular compartments to maximize virion assembly. By comparison, most of S is degraded when the protein is expressed in isolation, as in current molecular vaccines. To probe the maturation pathway of S, we redirected its maturation by fusing S to the tetraspanin protein CD81. CD81 is a defining constituent of extracellular vesicles (EVs) or exosomes. EVs are generated in large numbers by all cells, extruded into blood and lymph, and transfer cargo between cells and systemically (estimated 1012 EVs per mL plasma). EVs, like platelets, can be transfused between unrelated donors. When fusing the proline-stabilized form of strain Delta S into the flexible, large extracellular loop of CD81 rather than being degraded in the lysosome, S was extruded into EVs. CD81-S fusion containing EVs were produced in large numbers and could be isolated to high purity. Purified CD81::S EVs bound ACE2, and S displayed on individual EV was observed by cryogenic electron microscopy (EM). The CD81::S-fusion EVs were non-toxic and elicited an anti-S trimer and anti-RBD antibody response in mice. This report shows a design path to maximize viral glycoprotein assembly and release without relying on the co-expression of potentially pathogenic nonstructural viral proteins. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 pandemic caused the biggest public health crises in recent history. To understand the maturation pathway of S, we fused S to the tetraspanin protein CD81. The resulting molecule is secreted in extracellular vesicles and induces antibodies in mice. This may be a general design path for viral glycoprotein vaccines.
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Affiliation(s)
- Allaura S Cone
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yijun Zhou
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ryan P McNamara
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Anthony B Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gabriel F Arias
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin T Landis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle W Shifflett
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith G Chambers
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runjie Yuan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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12
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Tuttolomondo M, Pham STD, Terp MG, Cendán Castillo V, Kalisi N, Vogel S, Langkjær N, Hansen UM, Thisgaard H, Schrøder HD, Palarasah Y, Ditzel HJ. A novel multitargeted self-assembling peptide-siRNA complex for simultaneous inhibition of SARS-CoV-2-host cell interaction and replication. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102227. [PMID: 38939051 PMCID: PMC11203390 DOI: 10.1016/j.omtn.2024.102227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/22/2024] [Indexed: 06/29/2024]
Abstract
Effective therapeutics are necessary for managing severe COVID-19 disease despite the availability of vaccines. Small interfering RNA (siRNA) can silence viral genes and restrict SARS-CoV-2 replication. Cell-penetrating peptides is a robust method for siRNA delivery, enhancing siRNA stability and targeting specific receptors. We developed a peptide HE25 that blocks SARS-CoV-2 replication by various mechanisms, including the binding of multiple receptors involved in the virus's internalization, such as ACE2, integrins and NRP1. HE25 not only acts as a vehicle to deliver the SARS-CoV-2 RNA-dependent RNA polymerase siRNA into cells but also facilitates their internalization through endocytosis. Once inside endosomes, the siRNA is released into the cytoplasm through the Histidine-proton sponge effect and the selective cleavage of HE25 by cathepsin B. These mechanisms effectively inhibited the replication of the ancestral SARS-CoV-2 and the Omicron variant BA.5 in vitro. When HE25 was administered in vivo, either by intravenous injection or inhalation, it accumulated in lungs, veins and arteries, endothelium, or bronchial structure depending on the route. Furthermore, the siRNA/HE25 complex caused gene silencing in lung cells in vitro. The SARS-CoV-2 siRNA/HE25 complex is a promising therapeutic for COVID-19, and a similar strategy can be employed to combat future emerging viral diseases.
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Affiliation(s)
- Martina Tuttolomondo
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Stephanie Thuy Duong Pham
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Mikkel Green Terp
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Virginia Cendán Castillo
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Nazmie Kalisi
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5000 Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5000 Odense, Denmark
| | - Niels Langkjær
- Department of Nuclear Medicine, Odense University Hospital, 5000 Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ulla Melchior Hansen
- Department of Molecular Medicine, Imaging Core Facility, DaMBIC, University of Southern Denmark, 5000 Odense, Denmark
| | - Helge Thisgaard
- Department of Nuclear Medicine, Odense University Hospital, 5000 Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Henrik Daa Schrøder
- Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
- Department of Pathology, Odense University Hospital, 5000 Odense, Denmark
| | - Yaseelan Palarasah
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Henrik Jørn Ditzel
- Department of Molecular Medicine, Unit of Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark
- Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
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13
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V. J. A, P. J. A, T. M. A, Akhigbe RE. SARS-CoV-2 impairs male fertility by targeting semen quality and testosterone level: A systematic review and meta-analysis. PLoS One 2024; 19:e0307396. [PMID: 39250513 PMCID: PMC11383251 DOI: 10.1371/journal.pone.0307396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/04/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Since the discovery of COVID-19 in December 2019, the novel virus has spread globally causing significant medical and socio-economic burden. Although the pandemic has been curtailed, the virus and its attendant complication live on. A major global concern is its adverse impact on male fertility. AIM This study was aimed to give an up to date and robust data regarding the effect of COVID-19 on semen variables and male reproductive hormones. MATERIALS AND METHODS Literature search was performed according to the recommendations of PRISMA. Out of the 852 studies collected, only 40 were eligible for inclusion in assessing the effect SARS-CoV-2 exerts on semen quality and androgens. More so, a SWOT analysis was conducted. RESULTS The present study demonstrated that SARS-CoV-2 significantly reduced ejaculate volume, sperm count, concentration, viability, normal morphology, and total and progressive motility. Furthermore, SARS-CoV-2 led to a reduction in circulating testosterone level, but a rise in oestrogen, prolactin, and luteinizing hormone levels. These findings were associated with a decline in testosterone/luteinizing hormone ratio. CONCLUSIONS The current study provides compelling evidence that SARS-CoV-2 may lower male fertility by reducing semen quality through a hormone-dependent mechanism; reduction in testosterone level and increase in oestrogen and prolactin levels.
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Affiliation(s)
- Ashonibare V. J.
- Medical Faculty, Department of Cardiovascular Surgery and Research Group for Experimental Surgery, Cardiovascular Regenerative Medicine and Tissue Engineering 3D Lab, Heinrich Heine University, Düsseldorf, Germany
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
| | - Ashonibare P. J.
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | - Akhigbe T. M.
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Agronomy, Breeding and Genetic Unit, Osun State University, Osun State, Nigeria
| | - R. E. Akhigbe
- Reproductive Biology and Toxicology Research Laboratory, Oasis of Grace Hospital, Osogbo, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
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14
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Puray-Chavez M, Eschbach JE, Xia M, LaPak KM, Zhou Q, Jasuja R, Pan J, Xu J, Zhou Z, Mohammed S, Wang Q, Lawson DQ, Djokic S, Hou G, Ding S, Brody SL, Major MB, Goldfarb D, Kutluay SB. A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574522. [PMID: 38260460 PMCID: PMC10802478 DOI: 10.1101/2024.01.07.574522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. Here we report that SARS-CoV-2 replication is restricted at a post-entry step in a number of ACE2-positive airway-derived cell lines due to tonic activation of the cGAS-STING pathway mediated by mitochondrial DNA leakage and naturally occurring cGAS and STING variants. Genetic and pharmacological inhibition of the cGAS-STING and type I/III IFN pathways as well as ACE2 overexpression overcome these blocks. SARS-CoV-2 replication in STING knockout cell lines and primary airway cultures induces ISG expression but only in uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway in productively infected cells. Pharmacological inhibition of STING in primary airway cells enhances SARS-CoV-2 replication and reduces virus-induced innate immune activation. Together, our study highlights that tonic activation of the cGAS-STING and IFN pathways can impact SARS-CoV-2 cellular tropism in a manner dependent on ACE2 expression levels.
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15
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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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16
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Coppola F, Jafari R, McReynolds KD, Král P. Sulfoglycodendron Antivirals with Scalable Architectures and Activities. J Chem Inf Model 2024. [PMID: 39230262 DOI: 10.1021/acs.jcim.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Many viruses initiate their cell-entry by binding their multisubunit receptors to human heparan sulfate proteoglycans (HSPG) and other molecular components present on cellular membranes. These viral interactions could be blocked and the whole viruses could be eliminated by suitable HSPG-mimetics providing multivalent binding to viral protein receptors. Here, large sulfoglycodendron HSPG-mimetics of different topologies, structures, and sizes were designed to this purpose. Atomistic molecular dynamics simulations were used to examine the ability of these broad-spectrum antivirals to block multiprotein HSPG-receptors in HIV, SARS-CoV-2, HPV, and dengue viruses. To characterize the inhibitory potential of these mimetics, their binding to individual and multiple protein receptors was examined. In particular, vectorial distributions of binding energies between the mimetics and viral protein receptors were introduced and calculated along the simulated trajectories. Space-dependent residual analysis of the mimetic-receptor binding was also performed. This analysis revealed the detailed nature of binding between these antivirals and viral protein receptors and provided evidence that large inhibitors with multivalent binding might act like a molecular glue initiating the self-assembly of protein receptors in enveloped viruses.
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Affiliation(s)
- Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Katherine D McReynolds
- Departments of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, California 95819-6057, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Departments of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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17
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Yang H, Guo H, Wang A, Cao L, Fan Q, Jiang J, Wang M, Lin L, Ge X, Wang H, Zhang R, Liao M, Yan R, Ju B, Zhang Z. Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants. Nat Commun 2024; 15:7715. [PMID: 39231977 PMCID: PMC11374805 DOI: 10.1038/s41467-024-51973-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
The Omicron subvariants of SARS-CoV-2, especially for BA.2.86 and JN.1, have rapidly spread across multiple countries, posing a significant threat in the ongoing COVID-19 pandemic. Distinguished by 34 additional mutations on the Spike (S) protein compared to its BA.2 predecessor, the implications of BA.2.86 and its evolved descendant, JN.1 with additional L455S mutation in receptor-binding domains (RBDs), are of paramount concern. In this work, we systematically examine the neutralization susceptibilities of SARS-CoV-2 Omicron subvariants and reveal the enhanced antibody evasion of BA.2.86 and JN.1. We also determine the cryo-EM structures of the trimeric S proteins from BA.2.86 and JN.1 in complex with the host receptor ACE2, respectively. The mutations within the RBDs of BA.2.86 and JN.1 induce a remodeling of the interaction network between the RBD and ACE2. The L455S mutation of JN.1 further induces a notable shift of the RBD-ACE2 interface, suggesting the notably reduced binding affinity of JN.1 than BA.2.86. An analysis of the broadly neutralizing antibodies possessing core neutralizing epitopes reveals the antibody evasion mechanism underlying the evolution of Omicron BA.2.86 subvariant. In general, we construct a landscape of evolution in virus-receptor of the circulating Omicron subvariants.
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MESH Headings
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Humans
- Immune Evasion
- COVID-19/immunology
- COVID-19/virology
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/immunology
- Angiotensin-Converting Enzyme 2/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/chemistry
- Cryoelectron Microscopy
- Antibodies, Viral/immunology
- Antibodies, Viral/chemistry
- Mutation
- Evolution, Molecular
- Protein Binding
- Models, Molecular
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Affiliation(s)
- Haonan Yang
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Huimin Guo
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Aojie Wang
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Liwei Cao
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Qing Fan
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jie Jiang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Miao Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Lin Lin
- Sustech Core Research Facilities, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Runze Zhang
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Ming Liao
- College of Animal Science & Technology, Zhong Kai University of Agriculture and Engineering, Guangzhou, Guangdong Province, China.
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China.
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment, Chinese Academy of Medical Sciences, Shenzhen, Guangdong Province, China.
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18
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Babbitt GA, Rajendran M, Lynch ML, Asare-Bediako R, Mouli LT, Ryan CJ, Srivastava H, Rynkiewicz P, Phadke K, Reed ML, Moore N, Ferran MC, Fokoue EP. ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison. Biophys J 2024; 123:2705-2715. [PMID: 38515299 PMCID: PMC11393699 DOI: 10.1016/j.bpj.2024.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution. In addition, comparisons of different (i.e., nonhomologous) sites within MD simulations could be employed to identify functional shifts in local time-coordinated dynamics indicative of logic gating within proteins. However, comparative MD analysis is challenged by the large fraction of protein motion caused by random thermal noise in the surrounding solvent. Therefore, properly denoised MD comparisons could reveal functional sites involving these machine-like dynamics with good accuracy. Here, we introduce ATOMDANCE, a user-interfaced suite of comparative machine learning-based denoising tools designed for identifying functional sites and the patterns of coordinated motion they can create within MD simulations. ATOMDANCE-maxDemon4.0 employs Gaussian kernel functions to compute site-wise maximum mean discrepancy between learned features of motion, thereby assessing denoised differences in the nonrandom motions between functional or evolutionary states (e.g., ligand bound versus unbound, wild-type versus mutant). ATOMDANCE-maxDemon4.0 also employs maximum mean discrepancy to analyze potential random amino acid replacements allowing for a site-wise test of neutral versus nonneutral evolution on the divergence of dynamic function in protein homologs. Finally, ATOMDANCE-Choreograph2.0 employs mixed-model analysis of variance and graph network to detect regions where time-synchronized shifts in dynamics occur. Here, we demonstrate ATOMDANCE's utility for identifying key sites involved in dynamic responses during functional binding interactions involving DNA, small-molecule drugs, and virus-host recognition, as well as understanding shifts in global and local site coordination occurring during allosteric activation of a pathogenic protease.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York.
| | - Madhusudan Rajendran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Miranda L Lynch
- Hauptmann Woodward Medical Research Institute, Buffalo, New York
| | - Richmond Asare-Bediako
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Leora T Mouli
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Cameron J Ryan
- McQuaid Jesuit High School Computer Club, Rochester, New York
| | | | - Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Kavya Phadke
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Makayla L Reed
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Nadia Moore
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Maureen C Ferran
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York
| | - Ernest P Fokoue
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York.
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19
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Hung HC, Tan BF, Lin WS, Wu SC. Glycan masking of NTD loops with a chimeric RBD of the spike protein as a vaccine design strategy against emerging SARS-CoV-2 Omicron variants. J Med Virol 2024; 96:e29893. [PMID: 39192804 DOI: 10.1002/jmv.29893] [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: 01/17/2024] [Revised: 07/12/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
The N-terminal domain (NTD) of the SARS-CoV-2 S protein comprises five exposed protruding loops. Deletions, insertions, and substitutions within these NTD loops play a significant role in viral evolution and contribute to immune evasion. We reported previously that introducing the glycan masking mutation R158N/Y160T in the NTD loop led to increased titers of neutralizing antibodies against the SARS-CoV-2 Wuhan-Hu-01 strain, as well as the Alpha, Beta, and Delta variants. In this study, we conducted further investigations on 10 additional glycan-masking sites in the NTD loops. Our findings indicate that the introduction of glycan masking mutations, specifically N87/G89T, H146N/N148T, N185/K187T, and V213N/D215T significantly enhanced neutralizing antibody titers against the Delta variant. The combination of dual glycan-masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N results in a shift toward the Omicron BA.1. Furthermore, the introduction of the Omicron receptor binding domain (RBD) alongside these two dual glycan masking mutations of Wuhan-Hu-1 and XBB.1 NTD sequences resulted in a noticeable shift in antigenic distances, aligning with the Omicron BA.4/5, BA.2.75.2, BQ.1.1, and XBB.1 subvariants on the antigenic map. This strategic combination, which involves the dual glycan masking mutations R158N/Y160T+V213N/D215T and R158N/Y160T+G219N in the NTD loops, along with the domain swap incorporating the Omicron RBD, emerges as a promising vaccine design strategy for the continuous development of next-generation SARS-CoV-2 vaccines.
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Affiliation(s)
- Hao-Chan Hung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Boon-Fatt Tan
- Department of Pediatrics, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wei-Shuo Lin
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Adimmune Corporation, Taichung, Taiwan
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20
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Guo ZY, Tang YQ, Zhang ZB, Liu J, Zhuang YX, Li T. COVID-19: from immune response to clinical intervention. PRECISION CLINICAL MEDICINE 2024; 7:pbae015. [PMID: 39139990 PMCID: PMC11319938 DOI: 10.1093/pcmedi/pbae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 08/15/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has highlighted the pivotal role of the immune response in determining the progression and severity of viral infections. In this paper, we review the most recent studies on the complicated dynamics between SARS-CoV-2 and the host immune system, highlight the importance of understanding these dynamics in developing effective treatments and formulate potent management strategies for COVID-19. We describe the activation of the host's innate immunity and the subsequent adaptive immune response following infection with SARS-CoV-2. In addition, the review emphasizes the immune evasion strategies of the SARS-CoV-2, including inhibition of interferon production and induction of cytokine storms, along with the resulting clinical outcomes. Finally, we assess the efficacy of current treatment strategies, including antiviral drugs, monoclonal antibodies, and anti-inflammatory treatments, and discuss their role in providing immunity and preventing severe disease.
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Affiliation(s)
- Zheng-yang Guo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Yan-qing Tang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Zi-bo Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Yu-xin Zhuang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Ting Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
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21
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Khare S, Villalba MI, Canul-Tec JC, Cajiao AB, Kumar A, Backovic M, Rey FA, Pardon E, Steyaert J, Perez C, Reyes N. Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins. Nat Struct Mol Biol 2024; 31:1368-1376. [PMID: 38671230 DOI: 10.1038/s41594-024-01295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Human syncytin-1 and suppressyn are cellular proteins of retroviral origin involved in cell-cell fusion events to establish the maternal-fetal interface in the placenta. In cell culture, they restrict infections from members of the largest interference group of vertebrate retroviruses, and are regarded as host immunity factors expressed during development. At the core of the syncytin-1 and suppressyn functions are poorly understood mechanisms to recognize a common cellular receptor, the membrane transporter ASCT2. Here, we present cryo-electron microscopy structures of human ASCT2 in complexes with the receptor-binding domains of syncytin-1 and suppressyn. Despite their evolutionary divergence, the two placental proteins occupy similar positions in ASCT2, and are stabilized by the formation of a hybrid β-sheet or 'clamp' with the receptor. Structural predictions of the receptor-binding domains of extant retroviruses indicate overlapping binding interfaces and clamping sites with ASCT2, revealing a competition mechanism between the placental proteins and the retroviruses. Our work uncovers a common ASCT2 recognition mechanism by a large group of endogenous and disease-causing retroviruses, and provides high-resolution views on how placental human proteins exert morphological and immunological functions.
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Affiliation(s)
- Shashank Khare
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Miryam I Villalba
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Juan C Canul-Tec
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | | | - Anand Kumar
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Felix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Nicolas Reyes
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France.
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22
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Wilson JD, Dworsky-Fried M, Ismail N. Neurodevelopmental implications of COVID-19-induced gut microbiome dysbiosis in pregnant women. J Reprod Immunol 2024; 165:104300. [PMID: 39004033 DOI: 10.1016/j.jri.2024.104300] [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: 04/04/2024] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
The global public health emergency of COVID-19 in January 2020 prompted a surge in research focusing on the pathogenesis and clinical manifestations of the virus. While numerous reports have been published on the acute effects of COVID-19 infection, the review explores the multifaceted long-term implications of COVID-19, with a particular focus on severe maternal COVID-19 infection, gut microbiome dysbiosis, and neurodevelopmental disorders in offspring. Severe COVID-19 infection has been associated with heightened immune system activation and gastrointestinal symptoms. Severe COVID-19 may also result in gut microbiome dysbiosis and a compromised intestinal mucosal barrier, often referred to as 'leaky gut'. Increased gut permeability facilitates the passage of inflammatory cytokines, originating from the inflamed intestinal mucosa and gut, into the bloodstream, thereby influencing fetal development during pregnancy and potentially elevating the risk of neurodevelopmental disorders such as autism and schizophrenia. The current review discusses the role of cytokine signaling molecules, microglia, and synaptic pruning, highlighting their potential involvement in the pathogenesis of neurodevelopmental disorders following maternal COVID-19 infection. Additionally, this review addresses the potential of probiotic interventions to mitigate gut dysbiosis and inflammatory responses associated with COVID-19, offering avenues for future research in optimizing maternal and fetal health outcomes.
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Affiliation(s)
- Jacob D Wilson
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada
| | - Michaela Dworsky-Fried
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada
| | - Nafissa Ismail
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada; LIFE Research Institute, Ottawa, Ontario K1N 6N5, Canada; University of Ottawa Brain and Mind Research Institute, Ottawa, Ontario K1H 8M5, Canada.
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23
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Park U, Lee JH, Kim U, Jeon K, Kim Y, Kim H, Kang JI, Park MY, Park SH, Cha JS, Yoon GY, Jeong DE, Kim T, Oh S, Yoon SH, Jin L, Ahn Y, Lim MY, Han SR, Kim HY, Kim MH, Zhang YH, Kang JG, Lee MS, Jeon YK, Cho HS, Lee HW, Cho NH. A humanized ACE2 mouse model recapitulating age- and sex-dependent immunopathogenesis of COVID-19. J Med Virol 2024; 96:e29915. [PMID: 39279412 DOI: 10.1002/jmv.29915] [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: 04/15/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/18/2024]
Abstract
In the ongoing battle against coronavirus disease 2019 (COVID-19), understanding its pathogenesis and developing effective treatments remain critical challenges. The creation of animal models that closely replicate human infection stands as a critical step forward in this research. Here, we present a genetically engineered mouse model with specifically-humanized knock-in ACE2 (hiACE2) receptors. This model, featuring nine specific amino acid substitutions for enhanced interaction with the viral spike protein, enables efficient severe acute respiratory syndrome coronavirus 2 replication in respiratory organs without detectable infection in the central nervous system. Moreover, it mirrors the age- and sex-specific patterns of morbidity and mortality, as well as the immunopathological features observed in human COVID-19 cases. Our findings further demonstrate that the depletion of eosinophils significantly reduces morbidity and mortality, depending on the infecting viral dose and the sex of the host. This reduction is potentially achieved by decreasing the pathogenic contribution of eosinophil-mediated inflammation, which is strongly correlated with neutrophil activity in human patients. This underscores the model's utility in studying the immunopathological aspects of COVID-19 and represents a significant advancement in COVID-19 modeling. It offers a valuable tool for testing vaccines and therapeutics, enhancing our understanding of the disease mechanisms and potentially guiding more targeted and effective treatments.
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Affiliation(s)
- Uni Park
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, South Korea
| | - Jae Hoon Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- GEMCRO Inc., Seoul, South Korea
| | - Uijin Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Kyeongseok Jeon
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, South Korea
| | - Hyeran Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Ju-Il Kang
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, South Korea
| | | | | | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Ga-Yeon Yoon
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Da-Eun Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeollabuk-do, South Korea
| | - Taehun Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Songhyeok Oh
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sang Ho Yoon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Physiology & Biomedical Sciences, Ischemic/hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Liyuan Jin
- Department of Physiology & Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoojin Ahn
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea
| | - Min Yeong Lim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea
| | - Seung Ro Han
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Hye Young Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea
| | - Myoung-Hwan Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Department of Physiology & Biomedical Sciences, Ischemic/hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
- Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, South Korea
| | - Yin Hua Zhang
- Department of Physiology & Biomedical Sciences, Ischemic/hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Physiology & Biomedical Sciences, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jun-Gu Kang
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeollabuk-do, South Korea
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Han-Woong Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- GEMCRO Inc., Seoul, South Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, South Korea
- Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, South Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
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24
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Ansari AW, Ahmad F, Alam MA, Raheed T, Zaqout A, Al-Maslamani M, Ahmad A, Buddenkotte J, Al-Khal A, Steinhoff M. Virus-Induced Host Chemokine CCL2 in COVID-19 Pathogenesis: Potential Prognostic Marker and Target of Anti-Inflammatory Strategy. Rev Med Virol 2024; 34:e2578. [PMID: 39192485 DOI: 10.1002/rmv.2578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/28/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
A wide variety of inflammatory mediators, mainly cytokines and chemokines, are induced during SARS CoV-2 infection. Among these proinflammatory mediators, chemokines tend to play a pivotal role in virus-mediated immunopathology. The C-C chemokine ligand 2 (CCL2), also known as monocyte chemoattractant protein-1 (MCP-1) is a potent proinflammatory cytokine and strong chemoattractant of monocytes, macrophages and CD4+ T cells bearing C-C chemokine receptor type-2 (CCR2). Besides controlling immune cell trafficking, CCL2 is also involved in multiple pathophysiological processes including systemic hyperinflammation associated cytokine release syndrome (CRS), organ fibrosis and blood coagulation. These pathological features are commonly manifested in severe and fatal cases of COVID-19. Given the crucial role of CCL2 in COVID-19 pathogenesis, the CCL2:CCR2 axis may constitute a potential therapeutic target to control virus-induced hyperinflammation and multi-organ dysfunction. Herein we describe recent advances on elucidating the role of CCL2 in COVID-19 pathogenesis, prognosis, and a potential target of anti-inflammatory interventions.
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Affiliation(s)
- Abdul Wahid Ansari
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Fareed Ahmad
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Majid Ali Alam
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Thesni Raheed
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ahmed Zaqout
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | - Muna Al-Maslamani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | - Aamir Ahmad
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Joerg Buddenkotte
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar
| | - Abdullatif Al-Khal
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- Communicable Diseases Centre, Hamad Medical Corporation, Doha, Qatar
| | - Martin Steinhoff
- Dermatology Institute, Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Department of Dermatology and Venereology, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Dermatology, Weill Cornell University, New York, New York, USA
- College of Medicine, Qatar University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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25
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Hadni H, Fitri A, Touimi Benjelloun A, Benzakour M, Mcharfi M, Benbrahim M. Identification of terpenoids as potential inhibitors of SARS-CoV-2 (main protease) and spike (RBD) via computer-aided drug design. J Biomol Struct Dyn 2024; 42:8145-8158. [PMID: 37548619 DOI: 10.1080/07391102.2023.2245051] [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: 04/02/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
The scientific community has been faced with a major challenge in the fight against the SARS-CoV-2 virus responsible for the COVID-19 pandemic, due to the lack of targeted antiviral drugs. To address this issue, we used an in silico approach to screen 23 natural compounds from the terpenoid class for their ability to target key SARS-CoV-2 therapeutic proteins. The results revealed that several compounds showed promising interactions with SARS-CoV-2 proteins, specifically the main protease and the spike receptor binding domain. The molecular docking analysis revealed the importance of certain residues, such as GLY143, SER144, CYS145 and GLU166, in the main protease of the SARS-CoV-2 protein, which play a crucial role in interactions with the ligand. In addition, our study highlighted the importance of interactions with residues GLY496, ARG403, SER494 and ARG393 of the spike receptor-binding domain within the SARS-CoV-2 protein. ADMET and drug similarity analyses were also performed, followed by molecular dynamics and MM-GBSA calculations, to identify potential drugs could be repurposed to combat COVID-19. Indeed, the results suggest that certain terpenoid compounds of plant origin have promising potential as therapeutic targets for SARS-CoV-2. However, additional experimental studies are required to confirm their efficacy as drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Asmae Fitri
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Adil Touimi Benjelloun
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Benzakour
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Mcharfi
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Benbrahim
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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26
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Yang W, Bai X, Jia X, Li H, Min J, Li H, Zhang H, Zhou J, Zhao Y, Liu W, Xin H, Sun L. The binding of extracellular cyclophilin A to ACE2 and CD147 triggers psoriasis-like inflammation. J Autoimmun 2024; 148:103293. [PMID: 39096717 DOI: 10.1016/j.jaut.2024.103293] [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: 02/19/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
Psoriasis is a chronic, proliferative, and inflammatory skin disease closely associated with inflammatory cytokine production. Cyclophilin A (CypA) is an important proinflammatory factor; however, its role in psoriasis remains unclear. The present data indicate that CypA levels are increased in the lesion skin and serum of patients with psoriasis, which is positively correlated with the psoriasis area severity index. Furthermore, extracellular CypA (eCypA) triggered psoriasis-like inflammatory responses in keratinocytes. Moreover, anti-CypA mAb significantly reduced pathological injury, keratinocyte proliferation, cytokine expression in imiquimod-induced mice. Notably, the therapeutic effect of anti-CypA mAb was better than that of the clinically used anti-IL-17A mAb and methotrexate. Mechanistically, eCypA binds to ACE2 and CD147 and is blocked by anti-CypA mAb. eCypA not only induces the dimerization and phosphorylation of ACE2 to trigger the JAK1/STAT3 signaling pathway for cytokine expression but also interacts with CD147 to promote PI3K/AKT/mTOR signaling-mediated keratinocyte proliferation. These findings demonstrate that the binding of eCypA to ACE2 and CD147 cooperatively triggers psoriasis-like inflammation and anti-CypA mAb is a promising candidate for the treatment of psoriasis.
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Affiliation(s)
- Wenxian Yang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518107, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, 100730, China
| | - Xiaoyuan Bai
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518107, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoxiao Jia
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huizi Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Min
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heqiao Li
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518107, China
| | - Haoran Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianjing Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuna Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjun Liu
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518107, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiming Xin
- Center of Burns, Plastic Cosmetic and Dermatology, The 924th Hospital of the Joint Logistics Support Force of Chinese PLA, Guilin, Guangxi, 541002, China.
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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27
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Istifli ES, Okumus N, Sarikurkcu C, Kuhn ER, Netz PA, Tepe AS. Comparative docking and molecular dynamics studies of molnupiravir (EIDD-2801): implications for novel mechanisms of action on influenza and SARS-CoV-2 protein targets. J Biomol Struct Dyn 2024; 42:8202-8214. [PMID: 37811782 DOI: 10.1080/07391102.2023.2267696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023]
Abstract
Molnupiravir (EIDD-2801) (MLN) is an oral antiviral drug for COVID-19 treatment, being integrated into viral RNA through RNA-dependent RNA polymerase (RdRp). Upon ingestion, MLN is transformed into two active metabolites: β-d-N4-hydroxycytidine (NHC) (EIDD-1931) in the host plasma, and EIDD-1931-triphosphate (MTP) within the host cells. However, recent studies provide increasing evidence of MLN's interactions with off-target proteins beyond the viral genome, suggesting that the complete mechanisms of action of MLN remain unclear. The aim of this study was therefore to investigate the molecular interactions of MLN in the form of NHC and MTP with the non-RNA structural components of avian influenza (hemagglutinin, neuraminidase) and SARS-CoV-2 (spike glycoprotein, Mpro, and RdRp) viruses and to elucidate whether these two metabolites possess the ability to form stable complexes with these major viral components. Molecular docking of NHC and MTP was performed using AutoDock 4.2.6 and the obtained protein-drug complexes were submitted to 200-ns molecular dynamics simulations in triplicate with subsequent free energy calculations using GROMACS. Docking scores, molecular dynamics and MM/GBSA results showed that MTP was tightly bound within the active site of SARS-CoV-2 RdRp and remained highly stable throughout the 200-ns simulations. Besides, it was also shown that NHC and MTP formed moderately-to-highly stable molecular complexes with off-target receptors hemagglutinin, neuraminidase and Mpro, but rather weak interactions with spike glycoprotein. Our computational findings suggest that NHC and MTP may directly inhibit these receptors, and propose that additional studies on the off-target effects of MLN, i.e. real-time protein binding assays, should be performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Erman Salih Istifli
- Faculty of Science and Literature, Department of Biology, Cukurova University, Adana, Turkey
| | - Nurullah Okumus
- Faculty of Medicine, Department of Pediatrics, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Cengiz Sarikurkcu
- Faculty of Pharmacy, Department of Analytical Chemistry, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Eduardo Ramires Kuhn
- Theoretical Chemistry Group, Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo A Netz
- Theoretical Chemistry Group, Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arzuhan Sihoglu Tepe
- Department of Pharmacy Services, Kilis 7 Aralik University, Vocational High School of Health Services, Kilis, Turkey
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Kolesnichenko AV, Pleshakova TO. Fundamentals of protein chemistry at the Institute of Biomedical Chemistry. BIOMEDITSINSKAIA KHIMIIA 2024; 70:263-272. [PMID: 39324192 DOI: 10.18097/pbmc20247005263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Eighty years ago, the Institute of Biomedical Chemistry (IBMC) initially known as the Institute of Biological and Medical Chemistry of the Academy of Sciences of the USSR was founded. During the first decades significant studies were performed; they not only contributed to a deeper understanding of biochemical processes in the living organisms, but also laid the foundation for further development of these fields. The main directions of IBMC were focused on studies of structures of enzymes (primarily various proteases), their substrates and inhibitors, the role of enzymes of carbohydrate metabolism in the development of pathologies, study of the mechanisms of hydrolytic and oxidative-hydrolytic transformation of organic compounds, studies of connective tissue proteins, including collagens, study of amino acid metabolism. It is difficult to find papers from that period in current online literature databases, so this review will help to understand the value of studies performed at IBMC during the first 40 years after its organization, as well as their impact on modern research.
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Park YJ, Liu C, Lee J, Brown JT, Ma CB, Liu P, Xiong Q, Stewart C, Addetia A, Craig CJ, Tortorici MA, Alshukari A, Starr T, Yan H, Veesler D. Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.608351. [PMID: 39253417 PMCID: PMC11383307 DOI: 10.1101/2024.08.28.608351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
DPP4 was considered a canonical receptor for merbecoviruses until the recent discovery of African bat-borne MERS-related coronaviruses using ACE2. The extent and diversity with which merbecoviruses engage ACE2 and their receptor species tropism remain unknown. Here, we reveal that HKU5 enters host cells utilizing Pipistrellus abramus (P.abr) and several non-bat mammalian ACE2s through a binding mode distinct from that of any other known ACE2-using coronaviruses. These results show that several merbecovirus clades independently evolved ACE2 utilization, which appears to be a broadly shared property among these pathogens, through an extraordinary diversity of ACE2 recognition modes. We show that MERS-CoV and HKU5 have markedly distinct antigenicity, due to extensive genetic divergence, and identified several HKU5 inhibitors, including two clinical compounds. Our findings profoundly alter our understanding of coronavirus evolution and pave the way for developing countermeasures against viruses poised for human emergence.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
| | - Chen Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Jimin Lee
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Jack T Brown
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Chen-Bao Ma
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Peng Liu
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - Cameron Stewart
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
| | - Caroline J Craig
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Abeer Alshukari
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Tyler Starr
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Huan Yan
- State Key Laboratory of Virology, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University; Wuhan, Hubei, 430072, China
| | - David Veesler
- Department of Biochemistry, University of Washington; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington; Seattle, WA 98195, USA
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Wang H, Xiao D, Zhou H, Chen S, Xiao G, Hu J, Quan H, Luo M, Zhang S. Visceral Adiposity and Neutralizing Antibody Expression: An Adult-Based Cross-Sectional Study. J Inflamm Res 2024; 17:5633-5643. [PMID: 39219813 PMCID: PMC11363935 DOI: 10.2147/jir.s477526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose Visceral adiposity is a significant risk factor for severe COVID-19. However, the impact of the Chinese visceral adiposity index (CVAI) on the efficacy of SARS-CoV-2 vaccines remains poorly understood. This study aims to explore the impact of CVAI on the production of neutralizing antibodies (NAb) in inactivated SARS-CoV-2 vaccines and the potential mechanism, thereby optimizing vaccination guidance. Methods In this cross-sectional study, 206 health workers (completed two SARS-CoV-2 vaccination on February 8th and March 10th, 2021, respectively) were recruited. All baseline anthropometric parameters of the participants were collected, and venous blood samples were obtained 6 weeks later to measure peripheral innate immune cells, inflammatory cytokines, and NAb titers against SARS-CoV-2. CVAI were calculated according to the formula and divided participants into two groups depending on CVAI median. Results The median NAb titer among healthcare workers was 12.94 AU/mL, with an efficacy of 87.86% for the SARS-CoV-2 vaccine. NAb titers were lower in the CVAI dysfunction group than in the CVAI reference group (median: 11.40 AU/mL vs 15.57 AU/mL), the hsCRP levels (median: 0.50 mg/L vs 0.30 mg/L) and peripheral monocyte count (mean: 0.47 × 109/L vs 0.42 × 109/L) in the CVAI dysfunction group were higher than in the CVAI reference group. Additionally, CVAI showed positive correlations with hsCRP, monocytes, lymphocytes, and B-lymphocytes, and a negative correlation with NAb titers. Conclusion CVAI may inhibit SARS-CoV-2 neutralizing antibody expression through inducing immune dysfunction and chronic inflammation. Thus, more attention should be paid to the vaccination for high CVAI population to improve the effectiveness of vaccination, which could provide more robust support for COVID-19 epidemic prevention and control.
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Affiliation(s)
- Huanhuan Wang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, People’s Republic of China
| | - Dan Xiao
- Department of Laboratory Medicine, the Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, Sichuan, People’s Republic of China
| | - Hua Zhou
- Department of Laboratory Medicine, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Shu Chen
- Department of Laboratory Medicine, Suining Central Hospital, Suining, Sichuan, People’s Republic of China
| | - Guangjun Xiao
- Department of Laboratory Medicine, Suining Central Hospital, Suining, Sichuan, People’s Republic of China
| | - Juan Hu
- Department of Laboratory Medicine, Suining Central Hospital, Suining, Sichuan, People’s Republic of China
| | - Hui Quan
- Department of Laboratory Medicine, the Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, Sichuan, People’s Republic of China
| | - Miao Luo
- Department of Laboratory Medicine, the People’s Hospital of Yubei District of Chongqing, Chongqing, People’s Republic of China
| | - Shaocheng Zhang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Chengdu Medical College (Nuclear Industry 416 Hospital), Chengdu, Sichuan, People’s Republic of China
- School of Clinical Medicine, Chengdu Medical College, Chengdu, Sichuan, People’s Republic of China
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Ma H, Wang Y, Li YX, Xie BK, Hu ZL, Yu RJ, Long YT, Ying YL. Label-Free Mapping of Multivalent Binding Pathways with Ligand-Receptor-Anchored Nanopores. J Am Chem Soc 2024. [PMID: 39180483 DOI: 10.1021/jacs.4c04934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Understanding single-molecule multivalent ligand-receptor interactions is crucial for comprehending molecular recognition at biological interfaces. However, label-free identifications of these transient interactions during multistep binding processes remains challenging. Herein, we introduce a ligand-receptor-anchored nanopore that allows the protein to maintain structural flexibility and favorable orientations in native states, mapping dynamic multivalent interactions. Using a four-state Markov chain model, we clarify two concentration-dependent binding pathways for the Omicron spike protein (Omicron S) and soluble angiotensin-converting enzyme 2 (sACE2): sequential and concurrent. Real-time kinetic analysis at the single-monomeric subunit level reveals that three S1 monomers of Omicron S exhibit a consistent and robust binding affinity toward sACE2 (-13.1 ± 0.2 kcal/mol). These results highlight the enhanced infectivity of Omicron S compared to other homologous spike proteins (WT S and Delta S). Notably, the preceding binding of sACE2 to Omicron S facilitates the subsequent binding steps, which was previously obscured in bulk measurements. Our single-molecule studies resolve the controversy over the disparity between the measured spike protein binding affinity with sACE2 and the viral infectivity, offering valuable insights for drug design and therapies.
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Affiliation(s)
- Hui Ma
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yongyong Wang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Ya-Xue Li
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Bao-Kang Xie
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Zheng-Li Hu
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Ru-Jia Yu
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
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32
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Haoyu W, Meiqin L, Jiaoyang S, Guangliang H, Haofeng L, Pan C, Xiongzhi Q, Kaixin W, Mingli H, Xuejie Y, Lämmermann I, Grillari J, Zhengli S, Jiekai C, Guangming W. Premature aging effects on COVID-19 pathogenesis: new insights from mouse models. Sci Rep 2024; 14:19703. [PMID: 39181932 PMCID: PMC11344828 DOI: 10.1038/s41598-024-70612-2] [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: 04/24/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
Aging is identified as a significant risk factor for severe coronavirus disease-2019 (COVID-19), often resulting in profound lung damage and mortality. Yet, the biological relationship between aging, aging-related comorbidities, and COVID-19 remains incompletely understood. This study aimed to elucidate the age-related COVID19 pathogenesis using an Hutchinson-Gilford progeria syndrome (HGPS) mouse model, a premature aging disease model, with humanized ACE2 receptors. Pathological features were compared between young, aged, and HGPS hACE2 mice following SARS-CoV-2 challenge. We demonstrated that young mice display robust interferon response and antiviral activity, whereas this response is attenuated in aged mice. Viral infection in aged mice results in severe respiratory tract hemorrhage, likely contributing a higher mortality rate. In contrast, HGPS hACE2 mice exhibit milder disease manifestations characterized by minor immune cell infiltration and dysregulation of multiple metabolic processes. Comprehensive transcriptome analysis revealed both shared and unique gene expression dynamics among different mouse groups. Collectively, our studies evaluated the impact of SARS-CoV-2 infection on progeroid syndromes using a HGPS hACE2 mouse model, which holds promise as a useful tool for investigating COVID-19 pathogenesis in individuals with premature aging.
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Affiliation(s)
- Wu Haoyu
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Liu Meiqin
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory Clinical Base, Guangzhou Medical University, Guangzhou, China
| | - Sun Jiaoyang
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Hong Guangliang
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Lin Haofeng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Pan
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Quan Xiongzhi
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Wu Kaixin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou, China
| | - Hu Mingli
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yang Xuejie
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | | | - Johannes Grillari
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
- Institute of Molecular Biotechnology, BOKU University, Vienna, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, 1200, Vienna, Austria
| | - Shi Zhengli
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Chen Jiekai
- Center for Cell Lineage Atlas, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Kowloon, 999077, Hong Kong SAR, China.
| | - Wu Guangming
- Division of Basic Research, Guangzhou National Laboratory, Guangzhou, 510005, China.
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Xu J, Hu Z, Dai L, Yadav A, Jiang Y, Bröer A, Gardiner MG, McLeod M, Yan R, Bröer S. Molecular basis of inhibition of the amino acid transporter B 0AT1 (SLC6A19). Nat Commun 2024; 15:7224. [PMID: 39174516 PMCID: PMC11341722 DOI: 10.1038/s41467-024-51748-1] [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: 01/09/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
The epithelial neutral amino acid transporter B0AT1 (SLC6A19) is the major transporter for the absorption of neutral amino acids in the intestine and their reabsorption in the kidney. Mouse models have demonstrated that lack of B0AT1 can normalize elevated plasma amino acids in rare disorders of amino acid metabolism such as phenylketonuria and urea-cycle disorders, implying a pharmacological approach for their treatment. Here we employ a medicinal chemistry approach to generate B0AT1 inhibitors with IC50-values of 31-90 nM. High-resolution cryo-EM structures of B0AT1 in the presence of two compounds from this series identified an allosteric binding site in the vestibule of the transporter. Mechanistically, binding of these inhibitors prevents a movement of TM1 and TM6 that is required for the transporter to make a conformational change from an outward open state to the occluded state.
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Affiliation(s)
- Junyang Xu
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Ziwei Hu
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Dai
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Aditya Yadav
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Yashan Jiang
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Angelika Bröer
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Michael G Gardiner
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Malcolm McLeod
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Stefan Bröer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Coppola F, Jafari R, McReynolds KD, Král P. Sulfoglycodendron Antivirals with Scalable Architectures and Activities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.606251. [PMID: 39131386 PMCID: PMC11312539 DOI: 10.1101/2024.08.01.606251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Many viruses initiate their cell-entry by binding their multi-protein receptors to human heparan sulfate proteoglycans (HSPG) and other molecular components present on cellular membranes. These viral interactions could be blocked and the whole viruses could be eliminated by suitable HSPG-mimetics providing multivalent binding to viral protein receptors. Here, large sulfoglycodendron HSPG-mimetics of different topologies, structures, and sizes were designed to this purpose. Atomistic molecular dynamics simulations were used to examine the ability of these broad-spectrum antivirals to block multi-protein HSPG-receptors in HIV, SARS-CoV-2, HPV, and dengue viruses. To characterize the inhibitory potential of these mimetics, their binding to individual and multiple protein receptors was examined. In particular, vectorial distributions of binding energies between the mimetics and viral protein receptors were introduced and calculated along the simulated trajectories. Space-dependent residual analysis of the mimetic-receptor binding was also performed. This analysis revealed detail nature of binding between these antivirals and viral protein receptors, and provided evidence that large inhibitors with multivalent binding might act like a molecular glue initiating the self-assembly of protein receptors in enveloped viruses.
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Affiliation(s)
- Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Katherine D. McReynolds
- Departments of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819–6057, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Departments of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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35
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Bröer A, Hu Z, Kukułowicz J, Yadav A, Zhang T, Dai L, Bajda M, Yan R, Bröer S. Cryo-EM structure of ACE2-SIT1 in complex with tiagabine. J Biol Chem 2024; 300:107687. [PMID: 39159813 DOI: 10.1016/j.jbc.2024.107687] [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: 02/01/2024] [Revised: 08/03/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
The pharmacology of amino acid transporters in the SLC6 family is poorly developed compared to that of the neurotransmitter transporters. To identify new inhibitors of the proline transporter SIT1 (SLC6A20), its expression in Xenopus laevis oocytes was optimized. Trafficking of SIT1 was augmented by co-expression of angiotensin-converting enzyme 2 (ACE2) in oocytes but there was no strict requirement for co-expression of ACE2. A pharmacophore-guided screen identified tiagabine as a potent non-competitive inhibitor of SIT1. To understand its binding mode, we determined the cryo-electron microscopy (cryo-EM) structure of ACE2-SIT1 bound with tiagabine. The inhibitor binds close to the orthosteric proline binding site, but due to its size extends into the cytosolic vestibule. This causes the transporter to adopt an inward-open conformation, in which the intracellular gate is blocked. This study provides the first structural insight into inhibition of SIT1 and generates tools for a better understanding of the ACE2-SIT1 complex. These findings may have significance for SARS-CoV-2 binding to its receptor ACE2 in human lung alveolar cells where SIT1 and ACE2 are functionally expressed.
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Affiliation(s)
- Angelika Bröer
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ziwei Hu
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jędrzej Kukułowicz
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Cracow, Poland
| | - Aditya Yadav
- Research School of Biology, Australian National University, Canberra, Australia
| | - Ting Zhang
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Dai
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Cracow, Poland
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Stefan Bröer
- Research School of Biology, Australian National University, Canberra, Australia.
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Grunst MW, Qin Z, Dodero-Rojas E, Ding S, Prévost J, Chen Y, Hu Y, Pazgier M, Wu S, Xie X, Finzi A, Onuchic JN, Whitford PC, Mothes W, Li W. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science 2024; 385:757-765. [PMID: 39146425 DOI: 10.1126/science.adn5658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/15/2024] [Indexed: 08/17/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds the receptor angiotensin converting enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its S2 domain. Whereas the S1 domain contains high sequence variability, the S2 domain is conserved and is a promising pan-betacoronavirus vaccine target. We applied cryo-electron tomography to capture intermediates of S2 refolding and understand inhibition by antibodies to the S2 stem-helix. Subtomogram averaging revealed ACE2 dimers cross-linking spikes before transitioning into S2 intermediates, which were captured at various stages of refolding. Pan-betacoronavirus neutralizing antibodies targeting the S2 stem-helix bound to and inhibited refolding of spike prehairpin intermediates. Combined with molecular dynamics simulations, these structures elucidate the process of SARS-CoV-2 entry and reveal how pan-betacoronavirus S2-targeting antibodies neutralize infectivity by arresting prehairpin intermediates.
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Affiliation(s)
- Michael W Grunst
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | - Zhuan Qin
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | | | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Yanping Hu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Shenping Wu
- Department of Pharmacology, Yale University, West Haven, CT 06516, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University, New Haven, CT, USA
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37
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Bosch A, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 PMCID: PMC11323246 DOI: 10.1021/acs.jcim.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
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Affiliation(s)
- Antonio
M. Bosch
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V. Guzman
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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38
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Yu W, Yi SZ, Jiang CY, Guan JW, Xue R, Zhang XX, Zeng T, Tang H, Chen W, Han B. Biosensor-based active ingredient recognition system for screening potential small molecular Severe acute respiratory syndrome coronavirus 2 entry blockers targeting the spike protein from Rugosa rose. Biomed Chromatogr 2024:e5987. [PMID: 39126351 DOI: 10.1002/bmc.5987] [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: 06/20/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
The traditional formulation Hanchuan zupa granules (HCZPs) have been widely used for controlling coronavirus disease 2019 (COVID-19). However, its active components remain unknown. Here, HCZP components targeting the spike receptor-binding domain (S-RBD) of SARS-CoV-2 were investigated using a surface plasmon resonance (SPR) biosensor-based active ingredient recognition system (SPR-AIRS). Recombinant S-RBD proteins were immobilized on the SPR chip by amine coupling for the prescreening of nine HCZP medicinal herbs. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified gallic acid (GA) and methyl gallate (MG) from Rosa rugosa as S-RBD ligands, with KD values of 2.69 and 0.95 μM, respectively, as shown by SPR. Molecular dynamics indicated that GA formed hydrogen bonds with G496, N501, and Y505 of S-RBD, and MG with G496 and Y505, inhibiting S-RBD binding to angiotensin-converting enzyme 2 (ACE2). SPR-based competition analysis verified that both compounds blocked S-RBD and ACE2 binding, and SPR demonstrated that GA and MG bound to ACE2 (KD = 5.10 and 4.05 μM, respectively), suggesting that they blocked the receptor and neutralized SARS-CoV-2. Infection with SARS-CoV-2 pseudovirus showed that GA and MG suppressed viral entry into 293T-ACE2 cells. These S-RBD inhibitors have potential for drug design, while the findings provide a reference on HCZP composition and its use for treating COVID-19.
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Affiliation(s)
- Wei Yu
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Sheng-Zhe Yi
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Cheng-Yu Jiang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Jia-Wei Guan
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Rui Xue
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Xu-Xuan Zhang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Tao Zeng
- Corps Center for Food and Drug Evaluation and Verification, Xinjiang Production and Construction Corps Market Supervision Administration, Urumqi, China
| | - Hui Tang
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Wen Chen
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
| | - Bo Han
- School of Pharmacy/Key Laboratory of Xinjiang Phytomedicine Resource and Utilization/School of Medical, Shihezi University, Shihezi, China
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39
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Fujimoto A, Kawai H, Kawamura R, Kitamura A. Interaction of Receptor-Binding Domain of the SARS-CoV-2 Omicron Variant with hACE2 and Actin. Cells 2024; 13:1318. [PMID: 39195208 DOI: 10.3390/cells13161318] [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: 07/03/2024] [Revised: 08/01/2024] [Accepted: 08/04/2024] [Indexed: 08/29/2024] Open
Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in 2021 as a variant with heavy amino acid mutations in the spike protein, which is targeted by most vaccines, compared to previous variants. Amino acid substitutions in the spike proteins may alter their affinity for host viral receptors and the host interactome. Here, we found that the receptor-binding domain (RBD) of the omicron variant of SARS-CoV-2 exhibited an increased affinity for human angiotensin-converting enzyme 2, a viral cell receptor, compared to the prototype RBD. Moreover, we identified β- and γ-actin as omicron-specific binding partners of RBD. Protein complex predictions revealed that many omicron-specific amino acid substitutions affected the affinity between RBD of the omicron variant and actin. Our findings indicate that proteins localized to different cellular compartments exhibit strong binding to the omicron RBD.
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Affiliation(s)
- Ai Fujimoto
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Haruki Kawai
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Rintaro Kawamura
- Laboratory of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
| | - Akira Kitamura
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo 001-0021, Hokkaido, Japan
- PRIME, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004, Japan
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40
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Daniels A, Padariya M, Fletcher S, Ball K, Singh A, Carragher N, Hupp T, Tait-Burkard C, Kalathiya U. Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2. Antiviral Res 2024; 228:105949. [PMID: 38942150 DOI: 10.1016/j.antiviral.2024.105949] [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: 02/20/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
The SARS-CoV-2 Spike glycoprotein (S) utilizes a unique trimeric conformation to interact with the ACE2 receptor on host cells, making it a prime target for inhibitors that block viral entry. We have previously identified a novel proteinaceous cavity within the Spike protein homotrimer that could serve as a binding site for small molecules. However, it is not known whether these molecules would inhibit, stimulate, or have no effect on viral replication. To address this, we employed structural-based screening to identify small molecules that dock into the trimer cavity and assessed their impact on viral replication. Our findings show that a cohort of identified small molecules binding to the Spike trimer cavity effectively reduces the replication of various SARS-CoV-2 variants. These molecules exhibited inhibitory effects on B.1 (European original, D614G, EDB2) and B.1.617.2 (δ) variants, while showing moderate activity against the B.1.1.7 (α) variant. We further categorized these molecules into distinct groups based on their structural similarities. Our experiments demonstrated a dose-dependent viral replication inhibitory activity of these compounds, with some, like BCC0040453 exhibiting no adverse effects on cell viability even at high concentrations. Further investigation revealed that pre-incubating virions with compounds like BCC0031216 at different temperatures significantly inhibited viral replication, suggesting their specificity towards the S protein. Overall, our study highlights the inhibitory impact of a diverse set of chemical molecules on the biological activity of the Spike protein. These findings provide valuable insights into the role of the trimer cavity in the viral replication cycle and aid drug discovery programs aimed at targeting the coronavirus family.
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Affiliation(s)
- Alison Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland
| | - Sarah Fletcher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Kathryn Ball
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ashita Singh
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Neil Carragher
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland.
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41
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Margaret MS, Melrose J. Impaired instructive and protective barrier functions of the endothelial cell glycocalyx pericellular matrix is impacted in COVID-19 disease. J Cell Mol Med 2024; 28:e70033. [PMID: 39180511 PMCID: PMC11344469 DOI: 10.1111/jcmm.70033] [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: 02/02/2024] [Revised: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 08/26/2024] Open
Abstract
The aim of this study was to review the roles of endothelial cells in normal tissue function and to show how COVID-19 disease impacts on endothelial cell properties that lead to much of its associated symptomatology. This places the endothelial cell as a prominent cell type to target therapeutically in the treatment of this disorder. Advances in glycosaminoglycan analytical techniques and functional glycomics have improved glycosaminoglycan mimetics development, providing agents that can more appropriately target various aspects of the behaviour of the endothelial cell in-situ and have also provided polymers with potential to prevent viral infection. Thus, promising approaches are being developed to combat COVID-19 disease and the plethora of symptoms this disease produces. Glycosaminoglycan mimetics that improve endothelial glycocalyx boundary functions have promising properties in the prevention of viral infection, improve endothelial cell function and have disease-modifying potential. Endothelial cell integrity, forming tight junctions in cerebral cell populations in the blood-brain barrier, prevents the exposure of the central nervous system to circulating toxins and harmful chemicals, which may contribute to the troublesome brain fogging phenomena reported in cognitive processing in long COVID disease.
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Affiliation(s)
- M. Smith Margaret
- Raymond Purves Bone and Joint Research LaboratoryKolling Institute, Northern Sydney Local Health DistrictSt. LeonardsNew South WalesAustralia
- Arthropharm Australia Pharmaceuticals Pty LtdBondi JunctionSydneyNew South WalesAustralia
| | - James Melrose
- Raymond Purves Bone and Joint Research LaboratoryKolling Institute, Northern Sydney Local Health DistrictSt. LeonardsNew South WalesAustralia
- Graduate School of Biomedical EngineeringUniversity of New South WalesSydneyNew South WalesAustralia
- Sydney Medical SchoolNorthern, The University of SydneySydneyNew South WalesAustralia
- Faculty of Medicine and HealthThe University of Sydney, Royal North Shore HospitalSt. LeonardsNew South WalesAustralia
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42
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Chen J, Sun J, Xu Z, Li L, Kang X, Luo C, Wang Q, Guo X, Li Y, Liu K, Wu Y. The binding and structural basis of fox ACE2 to RBDs from different sarbecoviruses. Virol Sin 2024; 39:609-618. [PMID: 38866203 PMCID: PMC11401476 DOI: 10.1016/j.virs.2024.06.004] [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: 03/19/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Foxes are susceptible to SARS-CoV-2 in laboratory settings, and there have also been reports of natural infections of both SARS-CoV and SARS-CoV-2 in foxes. In this study, we assessed the binding capacities of fox ACE2 to important sarbecoviruses, including SARS-CoV, SARS-CoV-2, and animal-origin SARS-CoV-2 related viruses. Our findings demonstrated that fox ACE2 exhibits broad binding capabilities to receptor-binding domains (RBDs) of sarbecoviruses. We further determined the cryo-EM structures of fox ACE2 complexed with RBDs of SARS-CoV, SARS-CoV-2 prototype (PT), and Omicron BF.7. Through structural analysis, we identified that the K417 mutation can weaken the ability of SARS-CoV-2 sub-variants to bind to fox ACE2, thereby reducing the susceptibility of foxes to SARS-CoV-2 sub-variants. In addition, the Y498 residue in the SARS-CoV RBD plays a crucial role in forming a vital cation-π interaction with K353 in the fox ACE2 receptor. This interaction is the primary determinant for the higher affinity of the SARS-CoV RBD compared to that of the SARS-CoV-2 PT RBD. These results indicate that foxes serve as potential hosts for numerous sarbecoviruses, highlighting the critical importance of surveillance efforts.
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Affiliation(s)
- Junsen Chen
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Junqing Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Beijing Life Science Academy, Beijing, 102209, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinrui Kang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Xueyang Guo
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Yan Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kefang Liu
- Beijing Life Science Academy, Beijing, 102209, China.
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China.
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43
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Banerjee T, Gosai A, Yousefi N, Garibay OO, Seal S, Balasubramanian G. Examining sialic acid derivatives as potential inhibitors of SARS-CoV-2 spike protein receptor binding domain. J Biomol Struct Dyn 2024; 42:6342-6358. [PMID: 37424217 DOI: 10.1080/07391102.2023.2234044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanumoy Banerjee
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | | | - Niloofar Yousefi
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Ozlem Ozmen Garibay
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Sudipta Seal
- College of Medicine, Bionix Cluster, University of Central Florida, Orlando, FL, USA
- Advanced Materials Processing and Analysis Center, Dept. of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Ganesh Balasubramanian
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
- Institute of Functional Materials & Devices and College of Health, Lehigh University, Bethlehem, PA, USA
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44
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Dou WT, Tong PH, Xing M, Liu JJ, Hu XL, James TD, Zhou DM, He XP. Fluorogenic Peptide Sensor Array Derived from Angiotensin-Converting Enzyme 2 Classifies Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern. J Am Chem Soc 2024; 146:21017-21024. [PMID: 39029108 PMCID: PMC11295173 DOI: 10.1021/jacs.4c06172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/21/2024]
Abstract
The devastating COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made society acutely aware of the urgency in developing effective techniques to timely monitor the outbreak of previously unknown viral species as well as their mutants, which could be even more lethal and/or contagious. Here, we report a fluorogenic sensor array consisting of peptides truncated from the binding domain of human angiotensin-converting enzyme 2 (hACE2) for SARS-CoV-2. A set of five fluorescently tagged peptides were used to construct the senor array in the presence of different low-dimensional quenching materials. When orthogonally incubated with the wild-type SARS-CoV-2 and its variants of concern (VOCs), the fluorescence of each peptide probe was specifically recovered, and the different recovery rates provide a "fingerprint" characteristic of each viral strain. This, in turn, allows them to be differentiated from each other using principal component analysis. Interestingly, the classification result from our sensor array agrees well with the evolutionary relationship similarity of the VOCs. This study offers insight into the development of effective sensing tools for highly contagious viruses and their mutants based on rationally truncating peptide ligands from human receptors.
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Affiliation(s)
- Wei-Tao Dou
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, Frontiers Center for
Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular
Engineering, East China University of Science
and Technology, 130 Meilong Rd., Shanghai 200237, China
| | - Pei-Hong Tong
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, Frontiers Center for
Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular
Engineering, East China University of Science
and Technology, 130 Meilong Rd., Shanghai 200237, China
| | - Man Xing
- Department
of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jiao-Jiao Liu
- Department
of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xi-Le Hu
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, Frontiers Center for
Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular
Engineering, East China University of Science
and Technology, 130 Meilong Rd., Shanghai 200237, China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
- School of
Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, China
| | - Dong-Ming Zhou
- Vaccine
and Immunity Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Department
of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiao-Peng He
- Key
Laboratory for Advanced Materials and Joint International Research
Laboratory of Precision Chemistry and Molecular Engineering, Feringa
Nobel Prize Scientist Joint Research Center, Frontiers Center for
Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular
Engineering, East China University of Science
and Technology, 130 Meilong Rd., Shanghai 200237, China
- The
International Cooperation Laboratory on Signal Transduction, National
Center for Liver Cancer, Eastern Hepatobiliary
Surgery Hospital, Shanghai 200438, China
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45
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Hangyu W, Panpan L, Jie S, Hongyan W, Linmiao W, Kangning H, Yichen S, Shuai W, Cheng W. Advancements in Antiviral Drug Development: Comprehensive Insights into Design Strategies and Mechanisms Targeting Key Viral Proteins. J Microbiol Biotechnol 2024; 34:1376-1384. [PMID: 38934770 PMCID: PMC11294656 DOI: 10.4014/jmb.2403.03008] [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: 03/07/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 06/28/2024]
Abstract
Viral infectious diseases have always been a threat to human survival and quality of life, impeding the stability and progress of human society. As such, researchers have persistently focused on developing highly efficient, low-toxicity antiviral drugs, whether for acute or chronic infectious diseases. This article presents a comprehensive review of the design concepts behind virus-targeted drugs, examined through the lens of antiviral drug mechanisms. The intention is to provide a reference for the development of new, virus-targeted antiviral drugs and guide their clinical usage.
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Affiliation(s)
- Wang Hangyu
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Li Panpan
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Shen Jie
- School of Medical Laboratory, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wang Hongyan
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wei Linmiao
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Han Kangning
- Key Laboratory of Immune Microenvironment and Inflammatory Disease Research in Universities of Shandong Province, School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Shi Yichen
- School of Stomatology, Shandong Second Medical University, Weifang 261053, P.R. China
| | - Wang Shuai
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia 010050, P.R. China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, Inner Mongolia 010110, P.R. China
| | - Wang Cheng
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Inner Mongolia 010050, P.R. China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, Inner Mongolia 010110, P.R. China
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Xu Z, Zhang H, Tian J, Ku X, Wei R, Hou J, Zhang C, Yang F, Zou X, Li Y, Kaji H, Tao SC, Kuno A, Yan W, Da LT, Zhang Y. O-glycosylation of SARS-CoV-2 spike protein by host O-glycosyltransferase strengthens its trimeric structure. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1118-1129. [PMID: 39066577 PMCID: PMC11399440 DOI: 10.3724/abbs.2024127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024] Open
Abstract
Protein O-glycosylation, also known as mucin-type O-glycosylation, is one of the most abundant glycosylation in mammalian cells. It is initially catalyzed by a family of polypeptide GalNAc transferases (ppGalNAc-Ts). The trimeric spike protein (S) of SARS-CoV-2 is highly glycosylated and facilitates the virus's entry into host cells and membrane fusion of the virus. However, the functions and relationship between host ppGalNAc-Ts and O-glycosylation on the S protein remain unclear. Herein, we identify 15 O-glycosites and 10 distinct O-glycan structures on the S protein using an HCD-product-dependent triggered ETD mass spectrometric analysis. We observe that the isoenzyme T6 of ppGalNAc-Ts (ppGalNAc-T6) exhibits high O-glycosylation activity for the S protein, as demonstrated by an on-chip catalytic assay. Overexpression of ppGalNAc-T6 in HEK293 cells significantly enhances the O-glycosylation level of the S protein, not only by adding new O-glycosites but also by increasing O-glycan heterogeneity. Molecular dynamics simulations reveal that O-glycosylation on the protomer-interface regions, modified by ppGalNAc-T6, potentially stabilizes the trimeric S protein structure by establishing hydrogen bonds and non-polar interactions between adjacent protomers. Furthermore, mutation frequency analysis indicates that most O-glycosites of the S protein are conserved during the evolution of SARS-CoV-2 variants. Taken together, our finding demonstrate that host O-glycosyltransferases dynamically regulate the O-glycosylation of the S protein, which may influence the trimeric structural stability of the protein. This work provides structural insights into the functional role of specific host O-glycosyltransferases in regulating the O-glycosylation of viral envelope proteins.
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Affiliation(s)
- Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
| | - Han Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou 221000, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rumeng Wei
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingli Hou
- Intrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Can Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fang Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Kaji
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Atsushi Kuno
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8577, Japan
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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Caohuy H, Eidelman O, Chen T, Mungunsukh O, Yang Q, Walton NI, Pollard BS, Khanal S, Hentschel S, Florez C, Herbert AS, Pollard HB. Inflammation in the COVID-19 airway is due to inhibition of CFTR signaling by the SARS-CoV-2 spike protein. Sci Rep 2024; 14:16895. [PMID: 39043712 PMCID: PMC11266487 DOI: 10.1038/s41598-024-66473-4] [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: 12/15/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2-contributes to sickness and death in COVID-19 patients partly by inducing a hyper-proinflammatory immune response in the host airway. This hyper-proinflammatory state involves activation of signaling by NFκB, and unexpectedly, ENaC, the epithelial sodium channel. Post-infection inflammation may also contribute to "Long COVID"/PASC. Enhanced signaling by NFκB and ENaC also marks the airway of patients suffering from cystic fibrosis, a life-limiting proinflammatory genetic disease due to inactivating mutations in the CFTR gene. We therefore hypothesized that inflammation in the COVID-19 airway might similarly be due to inhibition of CFTR signaling by SARS-CoV-2 spike protein, and therefore activation of both NFκB and ENaC signaling. We used western blot and electrophysiological techniques, and an organoid model of normal airway epithelia, differentiated on an air-liquid-interface (ALI). We found that CFTR protein expression and CFTR cAMP-activated chloride channel activity were lost when the model epithelium was exposed to SARS-CoV-2 spike proteins. As hypothesized, the absence of CFTR led to activation of both TNFα/NFκB signaling and α and γ ENaC. We had previously shown that the cardiac glycoside drugs digoxin, digitoxin and ouabain blocked interaction of spike protein and ACE2. Consistently, addition of 30 nM concentrations of the cardiac glycoside drugs, prevented loss of both CFTR protein and CFTR channel activity. ACE2 and CFTR were found to co-immunoprecipitate in both basal cells and differentiated epithelia. Thus spike-dependent CFTR loss might involve ACE2 as a bridge between Spike and CFTR. In addition, spike exposure to the epithelia resulted in failure of endosomal recycling to return CFTR to the plasma membrane. Thus, failure of CFTR recovery from endosomal recycling might be a mechanism for spike-dependent loss of CFTR. Finally, we found that authentic SARS-CoV-2 virus infection induced loss of CFTR protein, which was rescued by the cardiac glycoside drugs digitoxin and ouabain. Based on experiments with this organoid model of small airway epithelia, and comparisons with 16HBE14o- and other cell types expressing normal CFTR, we predict that inflammation in the COVID-19 airway may be mediated by inhibition of CFTR signaling by the SARS-CoV-2 spike protein, thus inducing a cystic fibrosis-like clinical phenotype. To our knowledge this is the first time COVID-19 airway inflammation has been experimentally traced in normal subjects to a contribution from SARS-CoV-2 spike-dependent inhibition of CFTR signaling.
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Affiliation(s)
- Hung Caohuy
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Tinghua Chen
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ognoon Mungunsukh
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Qingfeng Yang
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for the Study of Traumatic Stress (CSTS), and Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Nathan I Walton
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | | | - Sara Khanal
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Shannon Hentschel
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- Cherokee Nation Assurance, Catoosa, OK, 74015, USA
| | - Catalina Florez
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Andrew S Herbert
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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Díaz-Salinas MA, Jain A, Durham ND, Munro JB. Single-molecule imaging reveals allosteric stimulation of SARS-CoV-2 spike receptor binding domain by host sialic acid. SCIENCE ADVANCES 2024; 10:eadk4920. [PMID: 39018397 PMCID: PMC466946 DOI: 10.1126/sciadv.adk4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/13/2024] [Indexed: 07/19/2024]
Abstract
Conformational dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S) mediate exposure of the binding site for the cellular receptor, angiotensin-converting enzyme 2 (ACE2). The N-terminal domain (NTD) of S binds terminal sialic acid (SA) moieties on the cell surface, but the functional role of this interaction in virus entry is unknown. Here, we report that NTD-SA interaction enhances both S-mediated virus attachment and ACE2 binding. Through single-molecule Förster resonance energy transfer imaging of individual S trimers, we demonstrate that SA binding to the NTD allosterically shifts the S conformational equilibrium, favoring enhanced exposure of the ACE2-binding site. Antibodies that target the NTD block SA binding, which contributes to their mechanism of neutralization. These findings inform on mechanisms of S activation at the cell surface.
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Affiliation(s)
- Marco A. Díaz-Salinas
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Natasha D. Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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50
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Datta G, Rezagholizadeh N, Hasler WA, Khan N, Chen X. SLC38A9 regulates SARS-CoV-2 viral entry. iScience 2024; 27:110387. [PMID: 39071889 PMCID: PMC11277692 DOI: 10.1016/j.isci.2024.110387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/13/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
SARS-CoV-2 viral entry into host cells depends on the cleavage of spike (S) protein into S1 and S2 proteins. Such proteolytic cleavage by furin results in the exposure of a multibasic motif on S1, which is critical for SARS-CoV-2 viral infection and transmission; however, how such a multibasic motif contributes to the infection of SARS-CoV-2 remains elusive. Here, we demonstrate that the multibasic motif on S1 is critical for its interaction with SLC38A9, an endolysosome-resident arginine sensor. SLC38A9 knockdown prevents S1-induced endolysosome de-acidification and blocks the S protein-mediated entry of pseudo-SARS-CoV-2 in Calu-3, U87MG, Caco-2, and A549 cells. Our findings provide a novel mechanism in regulating SARS-CoV-2 viral entry; S1 present in endolysosome lumen could interact with SLC38A9, which mediates S1-induced endolysosome de-acidification and dysfunction, facilitating the escape of SARS-CoV-2 from endolysosomes and enhancing viral entry.
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Affiliation(s)
- Gaurav Datta
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Neda Rezagholizadeh
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Wendie A. Hasler
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Nabab Khan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
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