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Yang H, Zhou JN, Zhang XM, Ling DD, Sun YB, Li CY, Zhou QQ, Shi GN, Wang SH, Lin XS, Fan T, Wang HY, Zeng Q, Jia YL, Xi JF, Jin YG, Pei XT, Yue W. Nanoengineered Red Blood Cells Loaded with TMPRSS2 and Cathepsin L Inhibitors Block SARS-CoV-2 Pseudovirus Entry into Lung ACE2 + Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310306. [PMID: 38194699 DOI: 10.1002/adma.202310306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/27/2023] [Indexed: 01/11/2024]
Abstract
The enzymatic activities of Furin, Transmembrane serine proteinase 2 (TMPRSS2), Cathepsin L (CTSL), and Angiotensin-converting enzyme 2 (ACE2) receptor binding are necessary for the entry of coronaviruses into host cells. Precise inhibition of these key proteases in ACE2+ lung cells during a viral infection cycle shall prevent viral Spike (S) protein activation and its fusion with a host cell membrane, consequently averting virus entry to the cells. In this study, dual-drug-combined (TMPRSS2 inhibitor Camostat and CTSL inhibitor E-64d) nanocarriers (NCs) are constructed conjugated with an anti-human ACE2 (hACE2) antibody and employ Red Blood Cell (RBC)-hitchhiking, termed "Nanoengineered RBCs," for targeting lung cells. The significant therapeutic efficacy of the dual-drug-loaded nanoengineered RBCs in pseudovirus-infected K18-hACE2 transgenic mice is reported. Notably, the modular nanoengineered RBCs (anti-receptor antibody+NCs+RBCs) precisely target key proteases of host cells in the lungs to block the entry of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), regardless of virus variations. These findings are anticipated to benefit the development of a series of novel and safe host-cell-protecting antiviral therapies.
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Affiliation(s)
- Hui Yang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jun-Nian Zhou
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xue-Mei Zhang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Dan-Dan Ling
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ying-Bao Sun
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chen-Yan Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Qian-Qian Zhou
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Gao-Na Shi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Si-Han Wang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiao-Song Lin
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Tao Fan
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hai-Yang Wang
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Quan Zeng
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Ya-Li Jia
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jia-Fei Xi
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yi-Guang Jin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xue-Tao Pei
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen Yue
- Stem Cell and Regenerative Medicine Lab, Beijing Institute of Radiation Medicine, Beijing, 100850, China
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2
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Zasedateleva OA, Surzhikov SA, Kuznetsova VE, Shershov VE, Barsky VE, Zasedatelev AS, Chudinov AV. Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency. Int J Mol Sci 2023; 24:13643. [PMID: 37686447 PMCID: PMC10487964 DOI: 10.3390/ijms241713643] [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: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
The approach based on molecular modeling was developed to study dNTP derivatives characterized by new polymerase-specific properties. For this purpose, the relative efficiency of PCR amplification with modified dUTPs was studied using Taq, Tth, Pfu, Vent, Deep Vent, Vent (exo-), and Deep Vent (exo-) DNA polymerases. The efficiency of PCR amplification with modified dUTPs was compared with the results of molecular modeling using the known 3D structures of KlenTaq polymerase-DNA-dNTP complexes. The dUTPs were C5-modified with bulky functional groups (the Cy5 dye analogs) or lighter aromatic groups. Comparing the experimental data and the results of molecular modeling revealed the decrease in PCR efficiency in the presence of modified dUTPs with an increase in the number of non-covalent bonds between the substituents and the DNA polymerase (about 15% decrease per one extra non-covalent bond). Generalization of the revealed patterns to all the studied polymerases of the A and B families is discussed herein. The number of non-covalent bonds between the substituents and polymerase amino acid residues is proposed to be a potentially variable parameter for regulating enzyme activity.
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Affiliation(s)
- Olga A. Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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3
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Fopase R, Panda C, Rajendran AP, Uludag H, Pandey LM. Potential of siRNA in COVID-19 therapy: Emphasis on in silico design and nanoparticles based delivery. Front Bioeng Biotechnol 2023; 11:1112755. [PMID: 36814718 PMCID: PMC9939533 DOI: 10.3389/fbioe.2023.1112755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Small interfering RNA (siRNA)-mediated mRNA degradation approach have imparted its eminence against several difficult-to-treat genetic disorders and other allied diseases. Viral outbreaks and resulting pandemics have repeatedly threatened public health and questioned human preparedness at the forefront of drug design and biomedical readiness. During the recent pandemic caused by the SARS-CoV-2, mRNA-based vaccination strategies have paved the way for a new era of RNA therapeutics. RNA Interference (RNAi) based approach using small interfering RNA may complement clinical management of the COVID-19. RNA Interference approach will primarily work by restricting the synthesis of the proteins required for viral replication, thereby hampering viral cellular entry and trafficking by targeting host as well as protein factors. Despite promising benefits, the stability of small interfering RNA in the physiological environment is of grave concern as well as site-directed targeted delivery and evasion of the immune system require immediate attention. In this regard, nanotechnology offers viable solutions for these challenges. The review highlights the potential of small interfering RNAs targeted toward specific regions of the viral genome and the features of nanoformulations necessary for the entrapment and delivery of small interfering RNAs. In silico design of small interfering RNA for different variants of SARS-CoV-2 has been discussed. Various nanoparticles as promising carriers of small interfering RNAs along with their salient properties, including surface functionalization, are summarized. This review will help tackle the real-world challenges encountered by the in vivo delivery of small interfering RNAs, ensuring a safe, stable, and readily available drug candidate for efficient management of SARS-CoV-2 in the future.
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Affiliation(s)
- Rushikesh Fopase
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Chinmaya Panda
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Amarnath P. Rajendran
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Hasan Uludag
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada,Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
| | - Lalit M. Pandey
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
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Alquraan L, Alzoubi KH, Rababa'h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. INFORMATICS IN MEDICINE UNLOCKED 2023; 39:101256. [PMID: 37131549 PMCID: PMC10127666 DOI: 10.1016/j.imu.2023.101256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
Numerous variations of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), including D614G, B.1.1.7 (United Kingdom), B.1.1.28 (Brazil P1, P2), CAL.20C (Southern California), B.1.351 (South Africa), B.1.617 (B.1.617.1 Kappa & Delta B.1.617.2) and B.1.1.529, have been reported worldwide. The receptor-binding domain (RBD) of the spike (S) protein is involved in virus-cell binding, where virus-neutralizing antibodies (NAbs) react. Novel variants in the S-protein could maximize viral affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor and increase virus transmission. Molecular detection with false-negative results may refer to mutations in the part of the virus's genome used for virus diagnosis. Furthermore, these changes in S-protein structure alter the neutralizing ability of NAbs, resulting in a reduction in vaccine efficiency. Further information is needed to evaluate how new mutations may affect vaccine efficacy.
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Affiliation(s)
- Laiali Alquraan
- Department of Biology, Faculty of Science, Yarmouk University, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Suzie Y Rababa'h
- Department of Medical Science, Irbid Faculty, Al-Balqa Applied University (BAU), Irbid, Jordan
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Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, Li Y. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern. Chemistry 2022; 28:e202200078. [PMID: 35084794 PMCID: PMC9015322 DOI: 10.1002/chem.202200078] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 12/15/2022]
Abstract
We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS‐CoV‐2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one‐round SELEX experiments using five different trimeric spike proteins from variants, followed by high‐throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed Kd values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS‐CoV‐2 with Kd values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well‐suited for molecular recognition of rapidly evolving targets such as those found in SARS‐CoV‐2.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Dawn White
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Carlos D. M. Filipe
- Department of Chemical Engineering McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Karen Mossman
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- McMaster Immunology Research Centre McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Department of Pathology and Molecular Medicine McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Payel Sen
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University 1280 Main Street West Hamilton, Ontario L8S 4K1 Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton, Ontario Canada L8S 4K1
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6
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Zhang W, He Y, Feng Z, Zhang J. Recent advances of functional nucleic acid-based sensors for point-of-care detection of SARS-CoV-2. Mikrochim Acta 2022; 189:128. [PMID: 35235065 PMCID: PMC8889384 DOI: 10.1007/s00604-022-05242-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/21/2022] [Indexed: 12/18/2022]
Abstract
This review focuses on critical scientific barriers that the field of point-of-care (POC) testing of SARS-CoV-2 is facing and possible solutions to overcome these barriers using functional nucleic acid (FNA)-based technology. Beyond the summary of recent advances in FNA-based sensors for COVID-19 diagnostics, our goal is to outline how FNA might serve to overcome the scientific barriers that currently available diagnostic approaches are suffering. The first introductory section on the operationalization of the COVID-19 pandemic in historical view and its clinical features contextualizes essential SARS-CoV-2-specific biomarkers. The second part highlights three major scientific barriers for POC COVID-19 diagnosis, that is, the lack of a general method for (1) designing receptors of SARS-CoV-2 variants; (2) improving sensitivity to overcome false negatives; and (3) signal readout in resource-limited settings. The subsequent part provides fundamental insights into FNA and technical tricks to successfully achieve effective COVID-19 diagnosis by using in vitro selection of FNA to overcome receptor design barriers, combining FNA with multiple DNA signal amplification strategies to improve sensitivity, and interfacing FNA with portable analyzers to overcome signal readout barriers. This review concludes with an overview of further opportunities and emerging applications for FNA-based sensors against COVID-19.
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Affiliation(s)
- Wenxian Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhe Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China.
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Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg C, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, Li Y. High‐Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild‐Type and B.1.1.7 SARS‐CoV‐2 in Unprocessed Saliva. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Richa Pandey
- Department of Engineering Physics McMaster University Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dawn White
- Biointerfaces Institute McMaster University Canada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | | | - Alfredo Capretta
- Biointerfaces Institute McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
| | | | - Karen Mossman
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- Department of Medicine McMaster University Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine McMaster University Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- McMaster Immunology Research Centre McMaster University Canada
| | | | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- Department of Pathology and Molecular Medicine McMaster University Canada
| | - Leyla Soleymani
- Department of Engineering Physics McMaster University Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Biointerfaces Institute McMaster University Canada
- Michael G. DeGroote Institute of Infectious Disease Research McMaster University Canada
- School of Biomedical Engineering McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
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8
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Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg C, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, Li Y. High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva. Angew Chem Int Ed Engl 2021; 60:24266-24274. [PMID: 34464491 PMCID: PMC8596624 DOI: 10.1002/anie.202110819] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 01/05/2023]
Abstract
We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively. To develop a highly sensitive test, DSA1N5 was immobilized onto gold electrodes to produce an electrochemical impedance sensor, which was capable of detecting 1000 viral particles per mL in 1:1 diluted saliva in under 10 min without any further sample processing. Evaluation of 36 positive and 37 negative patient saliva samples produced a clinical sensitivity of 80.5 % and specificity of 100 % and the sensor could detect the wildtype virus as well as the Alpha and Delta variants in the patient samples, which is the first reported rapid test that can detect any emerging variant of SARS-CoV-2.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Richa Pandey
- Department of Engineering PhysicsMcMaster UniversityCanada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Dawn White
- Biointerfaces InstituteMcMaster UniversityCanada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Alfredo Capretta
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
| | | | - Karen Mossman
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of MedicineMcMaster UniversityCanada
| | - Cynthia Balion
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Leyla Soleymani
- Department of Engineering PhysicsMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
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Xeno-Nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. Viruses 2021; 13:v13101983. [PMID: 34696413 PMCID: PMC8539646 DOI: 10.3390/v13101983] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023] Open
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor-binding domain (RBD) on the viral S protein with angiotensin-converting enzyme 2 (ACE2) on the surface of human host cells. Systematic evolution of ligands by exponential enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2ʹ-fluoro-arabinonucleic acid (FANA). The best selected ~79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~10–20 nM, and binding half-life for the RBD, S1 domain, and full trimeric S protein of 53 ± 18, 76 ± 5, and 127 ± 7 min, respectively. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S1 protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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Kacherovsky N, Yang LF, Dang HV, Cheng EL, Cardle II, Walls AC, McCallum M, Sellers DL, DiMaio F, Salipante SJ, Corti D, Veesler D, Pun SH. Discovery and Characterization of Spike N‐Terminal Domain‐Binding Aptamers for Rapid SARS‐CoV‐2 Detection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Lucy F. Yang
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Ha V. Dang
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Emmeline L. Cheng
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Ian I. Cardle
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Alexandra C. Walls
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Matthew McCallum
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Drew L. Sellers
- Department of Bioengineering University of Washington Seattle WA 98105 USA
| | - Frank DiMaio
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology 6500 Bellinzona Switzerland
| | - David Veesler
- Department of Biochemistry University of Washington Seattle WA 98105 USA
| | - Suzie H. Pun
- Department of Bioengineering University of Washington Seattle WA 98105 USA
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11
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Kacherovsky N, Yang LF, Dang HV, Cheng EL, Cardle II, Walls AC, McCallum M, Sellers DL, DiMaio F, Salipante SJ, Corti D, Veesler D, Pun SH. Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection. Angew Chem Int Ed Engl 2021; 60:21211-21215. [PMID: 34328683 PMCID: PMC8426805 DOI: 10.1002/anie.202107730] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/13/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for distinct viral proteins are critical components for rapid diagnostics and targeted therapeutics. In this work, we demonstrate the selection of novel DNA aptamers that bind to the SARS‐CoV‐2 spike glycoprotein with high specificity and affinity (<80 nM). Through binding assays and high resolution cryo‐EM, we demonstrate that SNAP1 (SARS‐CoV‐2 spike protein N‐terminal domain‐binding aptamer 1) binds to the S N‐terminal domain. We applied SNAP1 in lateral flow assays (LFAs) and ELISAs to detect UV‐inactivated SARS‐CoV‐2 at concentrations as low as 5×105 copies mL−1. SNAP1 is therefore a promising molecular tool for SARS‐CoV‐2 diagnostics.
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Affiliation(s)
- Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Lucy F Yang
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Ha V Dang
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Drew L Sellers
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA
| | - Davide Corti
- Humabs BioMed SA, a subsidiary of, Vir Biotechnology, 6500, Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98105, USA
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
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12
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Ferreira-Bravo IA, DeStefano JJ. Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34282416 DOI: 10.1101/2021.07.13.452259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2'-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants ( K D,app ) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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