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Hannula L, Kuivanen S, Lasham J, Kant R, Kareinen L, Bogacheva M, Strandin T, Sironen T, Hepojoki J, Sharma V, Saviranta P, Kipar A, Vapalahti O, Huiskonen JT, Rissanen I. Nanobody engineering for SARS-CoV-2 neutralization and detection. Microbiol Spectr 2024; 12:e0419922. [PMID: 38363137 PMCID: PMC10986514 DOI: 10.1128/spectrum.04199-22] [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: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024] Open
Abstract
In response to the ongoing COVID-19 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., "nanobodies." Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants at high potency, with IC50 values as low as 50 pM. Despite simultaneous binding to distinct epitopes, Beta and Omicron variants were more resistant to neutralization by the multimodular nanobodies, which highlights the importance of accounting for antigenic drift in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present an assay based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious diseases. IMPORTANCE Nanobodies, small protein binders derived from the camelid antibody, are highly potent inhibitors of respiratory viruses that offer several advantages over conventional antibodies as candidates for specific therapies, including high stability and low production costs. In this work, we leverage the unique properties of nanobodies and apply them as building blocks for new therapeutic and diagnostic tools. We report ultra-potent SARS-CoV-2 inhibition by engineered nanobodies comprising multiple modules in structure-guided combinations and develop nanobodies that carry signal molecules, allowing rapid detection of the SARS-CoV-2 spike protein. Our results highlight the potential of engineered nanobodies in the development of effective countermeasures, both therapeutic and diagnostic, to manage outbreaks of emerging viruses.
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Affiliation(s)
- Liina Hannula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Suvi Kuivanen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland
| | - Lauri Kareinen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mariia Bogacheva
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tomas Strandin
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jussi Hepojoki
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Petri Saviranta
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Anja Kipar
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Olli Vapalahti
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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Jin X, Zhang M, Fu B, Li M, Yang J, Zhang Z, Li C, Zhang H, Wu H, Xue W, Liu Y. Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. J Chem Inf Model 2024; 64:1319-1330. [PMID: 38346323 DOI: 10.1021/acs.jcim.3c01327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is demand for discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and in vitro assays were utilized to determine the potential inhibitors from TCM compounds against SARS-CoV-2 Mpro, which is an important therapeutic target for SARS-CoV-2. The ensemble docking analysis of 18263 TCM compounds against 15 SARS-CoV-2 Mpro conformations identified 19 TCM compounds as promising candidates. Further in vitro testing validated three compounds as inhibitors of SARS-CoV-2 Mpro and showed IC50 values of 4.64 ± 0.11, 7.56 ± 0.78, and 11.16 ± 0.26 μM, with EC50 values of 12.25 ± 1.68, 15.58 ± 0.77, and 29.32 ± 1.25 μM, respectively. Molecular dynamics (MD) simulations indicated that the three complexes remained stable over the last 100 ns of production run. An analysis of the binding mode revealed that the active compounds occupy different subsites (S1, S2, S3, and S4) of the active site of SARS-CoV-2 Mpro via specific poses through noncovalent interactions with key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, this study provides evidence indicating that the three natural products obtained from TCM could be further used for anti-COVID-19 research, justifying the investigation of Chinese herbal medicinal ingredients as bioactive constituents for therapeutic targets.
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Affiliation(s)
- Xiaojie Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Min Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Mi Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Jingyi Yang
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Zhiming Zhang
- Gansu Provincial Hospital of TCM, Lanzhou 730000, China
| | - Chenghao Li
- Medical College, Yangzhou University, Yangzhou 225000, China
| | - Huijuan Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Yongqi Liu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
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Rodriguez-Nuñez M, Cepeda MDV, Bello C, Lopez MA, Sulbaran Y, Loureiro CL, Liprandi F, Jaspe RC, Pujol FH, Rangel HR. Neutralization of Different Variants of SARS-CoV-2 by a F(ab')2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain. Antibodies (Basel) 2023; 12:80. [PMID: 38131802 PMCID: PMC10740526 DOI: 10.3390/antib12040080] [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: 09/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively mutations in its genome, particularly in the RBD region, many of them associated with immune evasion of the host neutralizing antibodies. Some of the viral lineages derived from this evolution have been classified as Variant of Interest (VOI) or Concern (VOC). The neutralizing capacity of a F(ab')2 preparation from sera of horses immunized with viral RBD was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A F(ab')2 preparation of a hyperimmune serum after nine immunizations with RBD exhibited a high titer of neutralizing antibodies against the ancestral-like strain (1/18,528). A reduction in the titer of the F(ab')2 preparation was observed against the different variants tested compared to the neutralizing activity against the ancestral-like strain. The highest reduction in the neutralization titer was observed for the Omicron VOC (4.7-fold), followed by the Mu VOI (2.6), Delta VOC (1.8-fold), and Gamma VOC (1.5). Even if a progressive reduction in the neutralizing antibodies titer against the different variants evaluated was observed, the serum still exhibited a neutralizing titer against the Mu VOI and the Omicron VOC (1/7113 and 1/3918, respectively), the evaluated strains most resistant to neutralization. Therefore, the preparation retained neutralizing activity against all the strains tested.
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Affiliation(s)
- Mariajosé Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Mariana del Valle Cepeda
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Carlos Bello
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Miguel Angel Lopez
- Biotecfar S.A., Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1050, Venezuela; (M.d.V.C.); (C.B.); (M.A.L.)
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Carmen Luisa Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela;
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas 1020, Venezuela; (M.R.-N.); (Y.S.); (C.L.L.); (R.C.J.)
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Kong X, Gao P, Jiang Y, Lu L, Zhao M, Liu Y, Deng G, Zhu H, Cao Y, Ma L. Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis. Virol J 2023; 20:192. [PMID: 37626353 PMCID: PMC10463914 DOI: 10.1186/s12985-023-02137-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron strain has multiple immune-escape mutations in the spike protein receptor-binding domain (RBD). Rapid detection of these mutations to identify Omicron and its lineages is essential for guiding public health strategies and patient treatments. We developed a two-tube, four-color assay employing asymmetric polymerase chain reaction (PCR)-based melting curve analysis to detect Omicron mutations and discriminate the BA.1, BA.2, BA.4/5, and BA.2.75 lineages. METHODS The presented technique involves combinatory analysis of the detection of six fluorescent probes targeting the immune-escape mutations L452R, N460K, E484A, F486V, Q493R, Q498R, and Y505H within one amplicon in the spike RBD and probes targeting the ORF1ab and N genes. After protocol optimization, the analytical performance of the technique was evaluated using plasmid templates. Sensitivity was assessed based on the limit of detection (LOD), and reliability was assessed by calculating the intra- and inter-run precision of melting temperatures (Tms). Specificity was assessed using pseudotyped lentivirus of common human respiratory pathogens and human genomic DNA. The assay was used to analyze 40 SARS-CoV-2-positive clinical samples (including 36 BA.2 and 4 BA.4/5 samples) and pseudotyped lentiviruses of wild-type and BA.1 viral RNA control materials, as well as 20 SARS-CoV-2-negative clinical samples, and its accuracy was evaluated by comparing the results with those of sequencing. RESULTS All genotypes were sensitively identified using the developed method with a LOD of 39.1 copies per reaction. The intra- and inter-run coefficients of variation for the Tms were ≤ 0.69% and ≤ 0.84%, with standard deviations ≤ 0.38 °C and ≤ 0.41 °C, respectively. Validation of the assay using known SARS-CoV-2-positive samples demonstrated its ability to correctly identify the targeted mutations and preliminarily characterize the Omicron lineages. CONCLUSION The developed assay can provide accurate, reliable, rapid, simple and low-cost detection of the immune-escape mutations located in the spike RBD to detect the Omicron variant and discriminate its lineages, and its use can be easily generalized in clinical laboratories with a fluorescent PCR platform.
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Affiliation(s)
- Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Lixia Lu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Haoyan Zhu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
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