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Dutta M, Su Y, Plescia CB, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. J Biol Chem 2024:107456. [PMID: 38866325 DOI: 10.1016/j.jbc.2024.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 06/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Caroline B Plescia
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA.
| | - Robert V Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Dutta M, Su Y, Voth GA, Stahelin RV. The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557899. [PMID: 37745364 PMCID: PMC10516002 DOI: 10.1101/2023.09.15.557899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we find the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, lipid binding is shown to occur in the N protein C-terminal domain, which is supported by extensive in silico analysis. Anionic lipid binding occurs for both the free and N oligomeric forms suggesting N can associate with membranes in the nucleocapsid form. Herein we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to M assembly sites in the lifecycle of SARS-CoV-2.
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Affiliation(s)
- Mandira Dutta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Yuan Su
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Frank Institute, The University of Chicago, Chicago, IL, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
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Khayat MT, Ghazawi KF, Samman WA, Alhaddad AA, Mohamed GA, Ibrahim SRM. Recent advances on natural depsidones: sources, biosynthesis, structure-activity relationship, and bioactivities. PeerJ 2023; 11:e15394. [PMID: 37197584 PMCID: PMC10184659 DOI: 10.7717/peerj.15394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
Depsidones are a class of polyphenolic polyketides that have been proposed to be biosynthesized from oxidative coupling of esters of two polyketidic benzoic acid derivatives. They are principally encountered in fungi and lichens. In addition to their diversified structural features, they revealed varied bioactivities such as antimicrobial, antimalarial, cytotoxic, anti-inflammatory, anti-Helicobacter pylori, antimycobacterial, antihypertensive, anti-diarrheal, antidiabetic, phytotoxic, anti-HIV, anti-osteoclastogenic, and butyrylcholinesterase, tyrosinase, hyaluronidase, and acetylcholinesterase inhibition. The current work was targeted to provide an overview on the naturally reported depsidones from various sources in the period from 2018 to the end of 2022 including their structures, biosynthesis, sources, and bioactivities, as well as the reported structure-activity relationship and semisynthetic derivatives. A total of 172 metabolites with 87 references were reviewed. The reported findings unambiguously demonstrated that these derivatives could be promising leads for therapeutic agents. However, further in-vivo evaluation of their potential biological properties and mechanistic investigations are needed.
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Affiliation(s)
- Maan T. Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kholoud F. Ghazawi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Waad A. Samman
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Aisha A. Alhaddad
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sabrin RM Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
- Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
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Do TH, Duong TH, Nguyen Minh An T, Vo TPG, Do VM, Nguyen NH, Sichaem J. Two New α-Glucosidase Inhibitory Depsidones from the Lichen Parmotrema cristiferum (Taylor) Hale. Chem Biodivers 2023; 20:e202201213. [PMID: 36775801 DOI: 10.1002/cbdv.202201213] [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: 12/20/2022] [Revised: 01/17/2023] [Accepted: 02/10/2023] [Indexed: 02/14/2023]
Abstract
A bioactivity-guided investigation of the lichen Parmotrema cristiferum (Taylor) Hale (Parmeliaceae) led to the isolation of two new depsidones, cristifones A and B (1 and 2). The structures of the isolated compounds were identified by spectroscopic methods and comparison with the literature data. Compound 1 showed the initial combined structures of depsidone and depside cores. The two isolated compounds were then evaluated for α-glucosidase inhibition. Compounds 1 and 2 were confirmed as potent, with IC50 values of 21.5 and 18.4 μM, respectively. Compound 2 was a non-competitive inhibitor against α-glucosidase, as indicated by the intersect in the second quadrant of each respective plot.
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Affiliation(s)
- Thanh-Hung Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, 754000, Vietnam
| | - Thuc-Huy Duong
- Department of Chemistry, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, District 5, Ho Chi Minh City, 700000, Vietnam
| | - Tran Nguyen Minh An
- Faculty of Chemical Engineering, Industrial University of Ho Chi Minh City, Ho Chi Minh City, 727000, Vietnam
| | - Thi-Phi-Giao Vo
- Faculty of Biology, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Van-Mai Do
- Nam Can Tho University, Nam Can Tho University, , Can Tho City, 900000, Vietnam
| | - Ngoc-Hong Nguyen
- CirTech Institute, HUTECH University, 475 A Dien Bien Phu Street, Binh Thanh District, Ho Chi Minh City, 717000, Vietnam
| | - Jirapast Sichaem
- Research Unit in Natural Products Chemistry and Bioactivities, Faculty of Science and Technology, Thammasat University Lampang Campus, Lampang, 52190, Thailand
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Secondary Metabolites of the Lichen Parmotrema cristiferum. Chem Nat Compd 2022. [DOI: 10.1007/s10600-022-03817-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Nguyen HH, Duong TH, Nguyen TVA, Do TH, Pham DD, Nguyen NH, Nguyen HT. α-Glucosidase inhibitory derivatives of protocetraric acid. Nat Prod Res 2022; 37:1935-1946. [DOI: 10.1080/14786419.2022.2110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Huu-Hung Nguyen
- Faculty of Applied Technology, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Thuc-Huy Duong
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Viet Nam
| | | | - Thanh-Hung Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Duc-Dung Pham
- Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Viet Nam
| | | | - Huy Truong Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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Promgool T, Kanokmedhakul K, Leewijit T, Song J, Soytong K, Yahuafai J, Kudera T, Kokoska L, Kanokmedhakul S. Cytotoxic and antibacterial depsidones from the endophytic fungus Chaetomium brasiliense isolated from Thai rice. Nat Prod Res 2021; 36:4605-4613. [PMID: 34736358 DOI: 10.1080/14786419.2021.1999947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Four new depsidones, mollicellins V-Y (1-4), together with eight known depsidones (5-12) were isolated from the endophytic fungus, Chaetomium brasiliense, detached from stems of Thai rice. Their structures were determined by extensive spectroscopic methods. Mollicellins X, H, and F (3, 8 and 10) showed potent cytotoxicity against the human oral epidermoid carcinoma (KB) cell line, and mollicellin F (10) also showed a potent cytotoxicity against the human hepatocellular carcinoma (HepG2) cell line. Besides, mollicellin B (11) exhibited cytotoxicity against the colorectal adenocarcinoma (HT-29) cell line. Moreover, most of the isolated depsidones displayed potent antibacterial activity against Gram-positive bacteria, Bacillus cereus and Bacillus subtilis, and several of them showed moderate activity against Methicillin-resistant Staphylococcus aureus (MRSA) and clinical isolates of S. aureus. In addition, a few of them also showed moderate activity against a Gram-negative bacteria Pseudomonas aeruginosa.
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Affiliation(s)
- Trinop Promgool
- Faculty of Science, Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Khon Kaen University, Khon Kaen, Thailand
| | - Kwanjai Kanokmedhakul
- Faculty of Science, Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Khon Kaen University, Khon Kaen, Thailand
| | - Thianrat Leewijit
- Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Jiaojiao Song
- Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Kasem Soytong
- Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Jantana Yahuafai
- Natural Products Research Section, Research Division, National Cancer Institute, Bangkok, Thailand
| | - Tomas Kudera
- Department of Crop Sciences and Agroforestry, Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Ladislav Kokoska
- Department of Crop Sciences and Agroforestry, Faculty of Tropical Agrisciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Somdej Kanokmedhakul
- Faculty of Science, Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Khon Kaen University, Khon Kaen, Thailand
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