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Sultana A, Geethakumari AM, Islam Z, Kolatkar PR, Biswas KH. BRET-based biosensors for SARS-CoV-2 oligonucleotide detection. Front Bioeng Biotechnol 2024; 12:1353479. [PMID: 38887615 PMCID: PMC11181354 DOI: 10.3389/fbioe.2024.1353479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The need for the early detection of emerging pathogenic viruses and their newer variants has driven the urgent demand for developing point-of-care diagnostic tools. Although nucleic acid-based methods such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and loop-mediated isothermal amplification (LAMP) have been developed, a more facile and robust platform is still required. To address this need, as a proof-of-principle study, we engineered a prototype-the versatile, sensitive, rapid, and cost-effective bioluminescence resonance energy transfer (BRET)-based biosensor for oligonucleotide detection (BioOD). Specifically, we designed BioODs against the SARS-CoV-2 parental (Wuhan strain) and B.1.617.2 Delta variant through the conjugation of specific, fluorescently modified molecular beacons (sensor module) through a complementary oligonucleotide handle DNA functionalized with the NanoLuc (NLuc) luciferase protein such that the dissolution of the molecular beacon loop upon the binding of the viral oligonucleotide will result in a decrease in BRET efficiency and, thus, a change in the bioluminescence spectra. Following the assembly of the BioODs, we determined their kinetics response, affinity for variant-specific oligonucleotides, and specificity, and found them to be rapid and highly specific. Furthermore, the decrease in BRET efficiency of the BioODs in the presence of viral oligonucleotides can be detected as a change in color in cell phone camera images. We envisage that the BioODs developed here will find application in detecting viral infections with variant specificity in a point-of-care-testing format, thus aiding in large-scale viral infection surveillance.
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Affiliation(s)
- Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Prasanna R. Kolatkar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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Ahmed WS, Geethakumari AM, Sultana A, Fatima A, Philip AM, Uddin SMN, Biswas KH. A slow but steady nanoLuc: R162A mutation results in a decreased, but stable, nanoLuc activity. Int J Biol Macromol 2024; 269:131864. [PMID: 38692549 DOI: 10.1016/j.ijbiomac.2024.131864] [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: 11/04/2023] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
NanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays, including gene expression analysis, protein-protein interaction, and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remain elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in living cells and in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in live cell and in vitro assays performed using lysates prepared from cells expressing the proteins and with the furimazine substrate. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity. SIGNIFICANCE: Bioluminescence has been extensively utilized in developing a variety of biological and biomedical assays. In this regard, engineering of brighter bioluminescent proteins, i.e. luciferases, has played a significant role. This is acutely exemplified by the engineering of the NLuc luciferase, which is small in size and displays much enhanced bioluminescence and thermal stability compared to previously available luciferases. While enhanced bioluminescent activity is desirable in a multitude of biological and biomedical assays, it would also be useful to develop variants of the protein that display a prolonged bioluminescence activity. This is specifically relevant in designing assays that require bioluminescence for extended periods, such as in the case of biosensors designed for monitoring slow enzymatic or cellular signaling reactions, without necessitating multiple rounds of luciferase substrate addition or any specialized reagents that result in increased assay costs. In the current manuscript, we report a mutant NLuc that possesses a stable and prolonged bioluminescence activity, albeit lower than the wild-type NLuc, and envisage a wider application of the mutant NLuc in designing biosensors for monitoring slower biological and biomedical events.
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Affiliation(s)
- Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Angelin M Philip
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - S M Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar.
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Jan Z, Ahmed WS, Biswas KH, Jithesh PV. Identification of a potential DNA methyltransferase (DNMT) inhibitor. J Biomol Struct Dyn 2024; 42:4730-4744. [PMID: 37424222 DOI: 10.1080/07391102.2023.2233637] [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: 01/13/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]
Abstract
DNA methyltransferases (DNMTs) play an important role in the epigenetic regulation of gene expression through the methylation of DNA. Since hypermethylation and consequent suppression of tumor suppressor genes are associated with cancer development and progression, DNA hypomethylating agents (HMAs) such as DNMT inhibitors have been proposed for cancer therapy. Two nucleoside analogues approved for the treatment of hematological cancers, decitabine and azacytidine, have poor pharmacokinetic properties, and hence there is a critical need for identifying novel HMAs. Virtual screening of a library of ∼40,000 compounds from the ZINC database, followed by molecular docking of 4,000 compounds having potential druggable properties with DNMT1, DNMT3A and DNMT3B were performed. One unique inhibitor (ZINC167686681) was identified that successfully passed through the Lipinski Rule of 5, geometry constraints as well as ADME/Tox filters and having strong binding energy for DNMTs. Further, molecular dynamics simulations of the docked complexes showed detailed structural features critical for its binding with the DNMTs and the stability of their interaction. Our study identified a compound with potential druggable properties and predicted to bind and inhibit DNMTs. Further investigations involving cellular and animal models of ZINC167686681 will help in potentially taking it into clinical trials for the treatment of cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zainab Jan
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Puthen Veettil Jithesh
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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Yu J, Zhao K, Zhang Z, Zhang Y, Zhang X, Ren H. Development of a bioluminescence resonance energy transfer Quenchbody sensor for the detection of organophosphorus pesticides in water bodies. WATER RESEARCH 2024; 250:121051. [PMID: 38157605 DOI: 10.1016/j.watres.2023.121051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Rapid and precise quantification of organophosphorus pesticides (OPPs) in environmental water bodies is crucial for evaluating ecological risks and safeguarding human health. Traditional instrumental methods are complex, time-consuming, and expensive, while enzyme-based biosensors suffer from instability and require a constant supply of substrates. Hence, there is an urgent need for a fast, simple, and sensitive biosensor for OPPs. In this study, we developed a novel non-enzymatic biosensor for the detection of methyl parathion (MP) by employing the bioluminescence resonance energy transfer (BRET) Q-body strategy. Optimizing the spacer arm and screening fluorescent dyes identified the R6G BRET MP Q-body sensor with the best performance. Key parameters affecting the sensor's detection performance were optimized by using single-factor experiments. Under optimal conditions, the detection exhibited a detection limit of 5.09 ng·mL-1 and a linear range of 16.21-848.81 ng·mL-1. The sensor's accuracy was validated using standard recovery experiments, yielding a recovery rate of 84.47 %-102.08 % with a standard deviation of 1.93 %-9.25 %. The detection results of actual water samples demonstrate that this fast, simple, and highly sensitive BRET Q-body sensor holds great promise for practical water quality monitoring.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Kanglin Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhanao Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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Mohammed I, Selvaraj S, Ahmed WS, Al-Barazenji T, Hammad AS, Dauleh H, Saraiva LR, Al-Shafai M, Hussain K. Functional Characterization of Novel MC4R Variants Identified in Two Unrelated Patients with Morbid Obesity in Qatar. Int J Mol Sci 2023; 24:16361. [PMID: 38003551 PMCID: PMC10671262 DOI: 10.3390/ijms242216361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The leptin-melanocortin pathway is pivotal in appetite and energy homeostasis. Pathogenic variants in genes involved in this pathway lead to severe early-onset monogenic obesity (MO). The MC4R gene plays a central role in leptin-melanocortin signaling, and heterozygous variants in this gene are the most common cause of MO. A targeted gene panel consisting of 52 obesity-related genes was used to screen for variants associated with obesity. Variants were analyzed and filtered to identify potential disease-causing activity and validated using Sanger sequencing. We identified two novel heterozygous variants, c.253A>G p.Ser85Gly and c.802T>C p.Tyr268His, in the MC4R gene in two unrelated patients with morbid obesity and evaluated the functional impact of these variants. The impact of the variants on the MC4R gene was assessed using in silico prediction tools and molecular dynamics simulation. To further study the pathogenicity of the identified variants, GT1-7 cells were transfected with plasmid DNA encoding either wild-type or mutant MC4R variants. The effects of allelic variations in the MC4R gene on cAMP synthesis, MC4R protein level, and activation of PKA, ERB, and CREB signaling pathways in both stimulated and unstimulated ɑ-MSH paradigms were determined for their functional implications. In silico analysis suggested that the variants destabilized the MC4R structure and affected the overall dynamics of the MC4R protein, possibly leading to intracellular receptor retention. In vitro analysis of the functional impact of these variants showed a significant reduction in cell surface receptor expression and impaired extracellular ligand binding activity, leading to reduced cAMP production. Our analysis shows that the variants do not affect total protein expression; however, they are predicted to affect the post-translational localization of the MC4R protein to the cell surface and impair downstream signaling cascades such as PKA, ERK, and CREB signaling pathways. This finding might help our patients to benefit from the novel therapeutic advances for monogenic forms of obesity.
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Affiliation(s)
- Idris Mohammed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Senthil Selvaraj
- Department of Disease Modeling and Therapeutics, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Wesam S. Ahmed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
| | - Tara Al-Barazenji
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
| | - Ayat S Hammad
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hajar Dauleh
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Luis R. Saraiva
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
- Department of Disease Modeling and Therapeutics, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
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Jan Z, Geethakumari AM, Biswas KH, Jithesh PV. Protegrin-2, a potential inhibitor for targeting SARS-CoV-2 main protease M pro. Comput Struct Biotechnol J 2023; 21:3665-3671. [PMID: 37576748 PMCID: PMC10412832 DOI: 10.1016/j.csbj.2023.07.020] [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: 03/24/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Background SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (Mpro) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of Mpro. Methods We studied around 200 antimicrobial peptides using in silico methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based Mpro biosensor, which reports Mpro activity through a decrease in energy transfer. Results Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with Mpro allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to Mpro using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of Mpro. Conclusions Our in silico and experimental studies identified Protegrin-2 as a potent inhibitor of Mpro that could be pursued further towards drug development against COVID-19 infection.
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Affiliation(s)
- Zainab Jan
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
| | - Puthen Veettil Jithesh
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha 34110, Qatar
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Basit SA, Qureshi R, Musleh S, Guler R, Rahman MS, Biswas KH, Alam T. COVID-19Base v3: Update of the knowledgebase for drugs and biomedical entities linked to COVID-19. Front Public Health 2023; 11:1125917. [PMID: 36950105 PMCID: PMC10025554 DOI: 10.3389/fpubh.2023.1125917] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
COVID-19 has taken a huge toll on our lives over the last 3 years. Global initiatives put forward by all stakeholders are still in place to combat this pandemic and help us learn lessons for future ones. While the vaccine rollout was not able to curb the spread of the disease for all strains, the research community is still trying to develop effective therapeutics for COVID-19. Although Paxlovid and remdesivir have been approved by the FDA against COVID-19, they are not free of side effects. Therefore, the search for a therapeutic solution with high efficacy continues in the research community. To support this effort, in this latest version (v3) of COVID-19Base, we have summarized the biomedical entities linked to COVID-19 that have been highlighted in the scientific literature after the vaccine rollout. Eight different topic-specific dictionaries, i.e., gene, miRNA, lncRNA, PDB entries, disease, alternative medicines registered under clinical trials, drugs, and the side effects of drugs, were used to build this knowledgebase. We have introduced a BLSTM-based deep-learning model to predict the drug-disease associations that outperforms the existing model for the same purpose proposed in the earlier version of COVID-19Base. For the very first time, we have incorporated disease-gene, disease-miRNA, disease-lncRNA, and drug-PDB associations covering the largest number of biomedical entities related to COVID-19. We have provided examples of and insights into different biomedical entities covered in COVID-19Base to support the research community by incorporating all of these entities under a single platform to provide evidence-based support from the literature. COVID-19Base v3 can be accessed from: https://covidbase-v3.vercel.app/. The GitHub repository for the source code and data dictionaries is available to the community from: https://github.com/91Abdullah/covidbasev3.0.
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Affiliation(s)
- Syed Abdullah Basit
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Saleh Musleh
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, University of Cape Town, Cape Town, South Africa
- Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - M. Sohel Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Kabir H. Biswas
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression. Proc Natl Acad Sci U S A 2023; 120:e2208525120. [PMID: 36574644 PMCID: PMC9910621 DOI: 10.1073/pnas.2208525120] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β2-microglobulin (β2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that down-regulate MHC-I expression to avoid CD8+ T cell recognition. Here, we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, down-regulate MHC-I expression using distinct mechanisms. First, ORF3a, a viroporin, reduces the global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a specific mechanism that allows immune evasion by SARS-CoV-2.
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Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease. Biomolecules 2022; 12:biom12121754. [PMID: 36551182 PMCID: PMC9775371 DOI: 10.3390/biom12121754] [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: 09/29/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022] Open
Abstract
The recent global health emergency caused by the coronavirus disease 2019 (COVID-19) pandemic has taken a heavy toll, both in terms of lives and economies. Vaccines against the disease have been developed, but the efficiency of vaccination campaigns worldwide has been variable due to challenges regarding production, logistics, distribution and vaccine hesitancy. Furthermore, vaccines are less effective against new variants of the SARS-CoV-2 virus and vaccination-induced immunity fades over time. These challenges and the vaccines' ineffectiveness for the infected population necessitate improved treatment options, including the inhibition of the SARS-CoV-2 main protease (Mpro). Drug repurposing to achieve inhibition could provide an immediate solution for disease management. Here, we used structure-based virtual screening (SBVS) to identify natural products (from NP-lib) and FDA-approved drugs (from e-Drug3D-lib and Drugs-lib) which bind to the Mpro active site with high-affinity and therefore could be designated as potential inhibitors. We prioritized nine candidate inhibitors (e-Drug3D-lib: Ciclesonide, Losartan and Telmisartan; Drugs-lib: Flezelastine, Hesperidin and Niceverine; NP-lib: three natural products) and predicted their half maximum inhibitory concentration using DeepPurpose, a deep learning tool for drug-target interactions. Finally, we experimentally validated Losartan and two of the natural products as in vitro Mpro inhibitors, using a bioluminescence resonance energy transfer (BRET)-based Mpro sensor. Our study suggests that existing drugs and natural products could be explored for the treatment of COVID-19.
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