1
|
Baskakova KO, Kuzmichev PK, Karbyshev MS. Advanced applications of Nanodiscs-based platforms for antibodies discovery. Biophys Chem 2024; 313:107290. [PMID: 39002246 DOI: 10.1016/j.bpc.2024.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Due to their fundamental biological importance, membrane proteins (MPs) are attractive targets for drug discovery, with cell surface receptors, transporters, ion channels, and membrane-bound enzymes being of particular interest. However, due to numerous challenges, these proteins present underutilized opportunities for discovering biotherapeutics. Antibodies hold the promise of exquisite specificity and adaptability, making them the ideal candidates for targeting complex membrane proteins. They can target specific conformations of a particular membrane protein and can be engineered into various formats. Generating specific and effective antibodies targeting these proteins is no easy task due to several factors. The antigen's design, antibody-generation strategies, lead optimization technologies, and antibody modalities can be modified to tackle these challenges. The rational employment of cutting-edge lipid nanoparticle systems for retrieving the membrane antigen has been successfully implemented to simplify the mechanism-based therapeutic antibody discovery approach. Despite the highlighted MP production challenges, this review unequivocally underscores the advantages of targeting complex membrane proteins with antibodies and designing membrane protein antigens. Selected examples of lipid nanoparticle success have been illustrated, emphasizing the potential of therapeutic antibody discovery in this regard. With further research and development, we can overcome these challenges and unlock the full potential of therapeutic antibodies directed to target complex MPs.
Collapse
Affiliation(s)
- Kristina O Baskakova
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Pavel K Kuzmichev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudniy, Russian Federation
| | - Mikhail S Karbyshev
- Laboratory of Molecular Therapy of Cancer, Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation; Department of Biochemistry and Molecular Biology, Pirogov Russian National Research Medical University, Moscow, Russian Federation.
| |
Collapse
|
2
|
Lomakin YA, Ovchinnikova LA, Terekhov SS, Dzhelad SS, Yaroshevich I, Mamedov I, Smirnova A, Grigoreva T, Eliseev IE, Filimonova IN, Mokrushina YA, Abrikosova V, Rubtsova MP, Kostin NN, Simonova MA, Bobik TV, Aleshenko NL, Alekhin AI, Boitsov VM, Zhang H, Smirnov IV, Rubtsov YP, Gabibov AG. Two-dimensional high-throughput on-cell screening of immunoglobulins against broad antigen repertoires. Commun Biol 2024; 7:842. [PMID: 38987383 PMCID: PMC11237129 DOI: 10.1038/s42003-024-06500-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Identifying high-affinity antibodies in human serum is challenging due to extremely low number of circulating B cells specific to the desired antigens. Delays caused by a lack of information on the immunogenic proteins of viral origin hamper the development of therapeutic antibodies. We propose an efficient approach allowing for enrichment of high-affinity antibodies against pathogen proteins with simultaneous epitope mapping, even in the absence of structural information about the pathogenic immunogens. To screen therapeutic antibodies from blood of recovered donors, only pathogen transcriptome is required to design an antigen polypeptide library, representing pathogen proteins, exposed on the bacteriophage surface. We developed a two-dimensional screening approach enriching lentiviral immunoglobulin libraries from the convalescent or vaccinated donors against bacteriophage library expressing the overlapping set of polypeptides covering the spike protein of SARS-CoV-2. This platform is suitable for pathogen-specific immunoglobulin enrichment and allows high-throughput selection of therapeutic human antibodies.
Collapse
Affiliation(s)
- Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia.
| | - Leyla A Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Stanislav S Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Samir S Dzhelad
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Igor Yaroshevich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Ilgar Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Anastasia Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Tatiana Grigoreva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Igor E Eliseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Ioanna N Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Yuliana A Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Victoria Abrikosova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Maria P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Nikita N Kostin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Maria A Simonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Tatiana V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Natalia L Aleshenko
- Federal State Budgetary Scientific Institution «Petrovsky National Research Centre of Surgery» (FSBSI «Petrovsky NRCS»), Moscow, Russia
| | - Alexander I Alekhin
- Federal State Budgetary Scientific Institution «Petrovsky National Research Centre of Surgery» (FSBSI «Petrovsky NRCS»), Moscow, Russia
| | - Vitali M Boitsov
- Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 194021, Saint Petersburg, Russia
| | - Hongkai Zhang
- College of Life Science, Nankai University, Tianjin, People's Republic of China
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Endocrinology Research Centre, Ministry of Health of Russia, 117036, Moscow, Russia
| | - Yuri P Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Blokhin National Medical Research Center of Oncology, Ministry of Health, Moscow, Russia
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia.
- Faculty of Biology and Biotechnology, HSE University, 101000, Moscow, Russia.
- Faculty of Medicine, Lomonosov Moscow State University, 119192, Moscow, Russia.
| |
Collapse
|
3
|
Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [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: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
Collapse
Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| |
Collapse
|
4
|
Omidfar K, Kashanian S. A mini review on recent progress of microfluidic systems for antibody development. J Diabetes Metab Disord 2024; 23:323-331. [PMID: 38932846 PMCID: PMC11196548 DOI: 10.1007/s40200-024-01386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/06/2024] [Indexed: 06/28/2024]
Abstract
Objectives Antibody is specific reagent that be utilized in various field of biomedical research. Monoclonal antibodies are mostly produced using two common techniques namely hybridoma and antibody engineering, which suffer from some limitations such as boring screening procedures, long production time, low efficacy and a degree of automation. To address these limitations, various microfluidics techniques have been developed for the antibody isolation and screening. Methods This study specifically investigates nearly recent reports published in peer-reviewed journals indexed in various databases including Web of Science, Scopus, PubMed, Google Scholar, and Science Direct. Results In this study, we identified a total of seventy papers from a pool of 130 articles. These papers focus on the application of three major groups of microfluidic platforms, namely valves, microwells, and droplets, in the development of antibodies using hybridoma method and phage display technology. We provide a summary of these applications and also discuss the key findings in this field. Additionally, we illustrate our discussion with several examples to enhance understanding. Conclusions Microfluidics has the potential to serve as a valuable tool in streamlining complex laboratory procedures involved in antibody discovery. However, it is important to note that microfluidics is limited to laboratory settings. Further enhancements are needed to address existing challenges and to make microfluidics a reliable, accurate, and cost-effective tool for antibody discovery.
Collapse
Affiliation(s)
- Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular–Cellular Sciences Institute, Tehran University of Medical Sciences, P.O. Box 14395/1179, Tehran, IR Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sohiela Kashanian
- Faculty of Chemistry, Razi University, Kermanshah, 6714414971 Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah, 6714414971 Iran
| |
Collapse
|
5
|
Li Y, Li XM, Yang KD, Tong WH. Advancements in ovarian cancer immunodiagnostics and therapeutics via phage display technology. Front Immunol 2024; 15:1402862. [PMID: 38863706 PMCID: PMC11165035 DOI: 10.3389/fimmu.2024.1402862] [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: 03/18/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Ovarian cancer, ranking as the seventh most prevalent malignancy among women globally, faces significant challenges in diagnosis and therapeutic intervention. The difficulties in early detection are amplified by the limitations and inefficacies inherent in current screening methodologies, highlighting a pressing need for more efficacious diagnostic and treatment strategies. Phage display technology emerges as a pivotal innovation in this context, utilizing extensive phage-peptide libraries to identify ligands with specificity for cancer cell markers, thus enabling precision-targeted therapeutic strategies. This technology promises a paradigm shift in ovarian cancer management, concentrating on targeted drug delivery systems to improve treatment accuracy and efficacy while minimizing adverse effects. Through a meticulous review, this paper evaluates the revolutionary potential of phage display in enhancing ovarian cancer therapy, representing a significant advancement in combating this challenging disease. Phage display technology is heralded as an essential instrument for developing effective immunodiagnostic and therapeutic approaches in ovarian cancer, facilitating early detection, precision-targeted medication, and the implementation of customized treatment plans.
Collapse
Affiliation(s)
- Yang Li
- Obstetrics and Gynecology Center, First Hospital of Jilin University, Changchun, Jilin, China
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Xiao-meng Li
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Kai-di Yang
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Wei-hua Tong
- Obstetrics and Gynecology Center, First Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
6
|
Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
Collapse
Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| |
Collapse
|
7
|
Caballero-Ávila M, Lleixà C, Pascual-Goñi E, Martín-Aguilar L, Vidal-Fernandez N, Tejada-Illa C, Collet-Vidiella R, Rojas-Garcia R, Cortés-Vicente E, Turon-Sans J, Gallardo E, Olivé M, Vesperinas A, Carbayo Á, Llansó L, Martinez-Martinez L, Shock A, Christodoulou L, Dizier B, Freeth J, Soden J, Dawson S, Querol L. Membrane Proteome-Wide Screening of Autoantibodies in CIDP Using Human Cell Microarray Technology. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200216. [PMID: 38484217 PMCID: PMC11078148 DOI: 10.1212/nxi.0000000000200216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/19/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND AND OBJECTIVES Autoantibody discovery in complex autoimmune diseases is challenging. Diverse successful antigen identification strategies are available, but, so far, have often been unsuccessful, especially in the discovery of protein antigens in which conformational and post-translational modification are critical. Our study assesses the utility of a human membrane and secreted protein microarray technology to detect autoantibodies in chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). METHODS A cell microarray consisting of human embryonic kidney-293 cells expressing >5,000 human proteins was used. First, a validation step was performed with 4 serum samples from patients with autoimmune nodopathy (AN) to assess the ability of this technology to detect circulating known autoantibodies. The ability of the cell microarray technology to discover novel IgG autoantibodies was assessed incubating the array with 8 CIDP serum samples. Identified autoantibodies were subsequently validated using cell-based assays (CBAs), ELISA, and/or tissue immunohistochemistry and analyzed in a cohort of CIDP and AN (n = 96) and control (n = 100) samples. RESULTS Serum anti-contactin-1 and anti-neurofascin-155 were detected by the human cell microarray technology. Nine potentially relevant antigens were found in patients with CIDP without other detectable antibodies; confirmation was possible in six of them: ephrin type-A receptor 7 (EPHA7); potassium-transporting ATPase alpha chain 1 and subunit beta (ATP4A/4B); leukemia-inhibitory factor (LIF); and interferon lambda 1, 2, and 3 (IFNL1, IFNL2, IFNL3). Anti-ATP4A/4B and anti-EPHA7 antibodies were detected in patients and controls and considered unrelated to CIDP. Both anti-LIF and anti-IFNL antibodies were found in the same 2 patients and were not detected in any control. Both patients showed the same staining pattern against myelinating fibers of peripheral nerve tissue and of myelinating neuron-Schwann cell cocultures. Clinically relevant correlations could not be established for anti-LIF and anti-IFNL3 antibodies. DISCUSSION Our work demonstrates the utility of human cell microarray technology to detect known and discover unknown autoantibodies in human serum samples. Despite potential CIDP-associated autoantibodies (anti-LIF and anti-IFNL3) being identified, their clinical and pathogenic relevance needs to be elucidated in bigger cohorts.
Collapse
Affiliation(s)
- Marta Caballero-Ávila
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Cinta Lleixà
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Elba Pascual-Goñi
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Lorena Martín-Aguilar
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Núria Vidal-Fernandez
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Clara Tejada-Illa
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Roger Collet-Vidiella
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Ricardo Rojas-Garcia
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Elena Cortés-Vicente
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Janina Turon-Sans
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Eduard Gallardo
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Montse Olivé
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Ana Vesperinas
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Álvaro Carbayo
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Laura Llansó
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Laura Martinez-Martinez
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Anthony Shock
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Louis Christodoulou
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Benjamin Dizier
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Jim Freeth
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Jo Soden
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Sarah Dawson
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| | - Luis Querol
- From the Neuromuscular Diseases Unit (M.C.-Á., C.L., E.P.-G., L.M.-A., N.V.-F., C.T.-I., R.C.-V., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., A.V., Á.C., L.L., L.Q.), Department of Neurology, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona; Neuromuscular Diseases (C.L., R.R.-G., E.C.-V., J.T.-S., E.G., M.O., L.Q.), Centro para la Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid; Department of Immunology (L.M.-M.), Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Universitat Autònoma de Barcelona, Spain; UCB Pharma (A.S., L.C., B.D.), Slough; and Retrogenix (Charles River's company) (J.F., J.S., S.D.), United Kingdom
| |
Collapse
|
8
|
Chance R, Kang AS. Eukaryotic ribosome display for antibody discovery: A review. Hum Antibodies 2024:HAB240001. [PMID: 38788063 DOI: 10.3233/hab-240001] [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: 05/26/2024]
Abstract
Monoclonal antibody biologics have significantly transformed the therapeutic landscape within the biopharmaceutical industry, partly due to the utilisation of discovery technologies such as the hybridoma method and phage display. While these established platforms have streamlined the development process to date, their reliance on cell transformation for antibody identification faces limitations related to library diversification and the constraints of host cell physiology. Cell-free systems like ribosome display offer a complementary approach, enabling antibody selection in a completely in vitro setting while harnessing enriched cellular molecular machinery. This review aims to provide an overview of the fundamental principles underlying the ribosome display method and its potential for advancing antibody discovery and development.
Collapse
|
9
|
Machado Marinho AC, Chapeaurouge A, Dutra BM, Quintela BCSF, Pereira SS, Fernandes CFC. The role of venom proteomics and single-domain antibodies for antivenoms: Progress in snake envenoming treatment. Drug Discov Today 2024; 29:103967. [PMID: 38555033 DOI: 10.1016/j.drudis.2024.103967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Single-domain antibodies (sdAbs) hold promise for developing new biopharmaceuticals to treat neglected tropical diseases (NTDs), including snakebites, which are severe and occur frequently. In addition, limitations of conventional snakebite treatments, especially in terms of local action, and the global antivenom crisis incentivize the use of this biotechnological tool to design next-generation snakebite antivenoms. Conventional antivenoms for snakebite treatment are usually composed of immunoglobulin G or F(ab')2 fragments derived from the plasma of immunized animals. sdAbs, the smallest antigen-binding fragments, are derived from the variable domains of camelid heavy-chain antibodies. sdAbs may have some advantages over conventional antivenoms for local toxicity, such as better penetration into tissues due to their small size, and high solubility and affinity for venom antigens due to their unique antigen-binding loops and ability to access cryptic epitopes. We present an overview of current antivenom therapy in the context of sdAb development for toxin neutralization. Furthermore, strategies are presented for identifying snake venom's major toxins as well as for developing antisnake toxin sdAbs by employing proteomic tools for toxin neutralization.
Collapse
Affiliation(s)
- Anna Carolina Machado Marinho
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, UFC, Fortaleza, Brazil
| | - Alexander Chapeaurouge
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Brunheld Maia Dutra
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Barbara Cibelle S F Quintela
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil
| | - Soraya S Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz Rondônia, FIOCRUZ RO, Porto Velho-RO, Brazil
| | - Carla Freire C Fernandes
- Laboratório Multiusuário de Pesquisa e Desenvolvimento, Fundação Oswaldo Cruz Ceará, FIOCRUZ CE, Eusébio-CE, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Ceará, UFC, Fortaleza, Brazil
| |
Collapse
|
10
|
Li J, Zhou B, Wang S, Ouyang J, Jiang X, Wang C, Zhou T, Zheng KW, Wang J, Wang J. Development of a Human B7-H3-Specific Antibody with Activity against Colorectal Cancer Cells through a Synthetic Nanobody Library. Bioengineering (Basel) 2024; 11:381. [PMID: 38671802 PMCID: PMC11047927 DOI: 10.3390/bioengineering11040381] [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: 03/28/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies have emerged as promising tools in biomedicine due to their single-chain structure and inherent stability. They generally have convex paratopes, which potentially prefer different epitope sites in an antigen compared to traditional antibodies. In this study, a synthetic phage display nanobody library was constructed and used to identify nanobodies targeting a tumor-associated antigen, the human B7-H3 protein. Combining next-generation sequencing and single-clone validation, two nanobodies were identified to specifically bind B7-H3 with medium nanomolar affinities. Further characterization revealed that these two clones targeted a different epitope compared to known B7-H3-specific antibodies, which have been explored in clinical trials. Furthermore, one of the clones, dubbed as A6, exhibited potent antibody-dependent cell-mediated cytotoxicity (ADCC) against a colorectal cancer cell line with an EC50 of 0.67 nM, upon conversion to an Fc-enhanced IgG format. These findings underscore a cost-effective strategy that bypasses the lengthy immunization process, offering potential rapid access to nanobodies targeting unexplored antigenic sites.
Collapse
Affiliation(s)
- Jingxian Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Bingjie Zhou
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Shiting Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Jiayi Ouyang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Xinyi Jiang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd., Shenzhen 518107, China;
| | - Teng Zhou
- School of Cyberspace Security, Hainan University, Haikou 570228, China;
| | - Ke-wei Zheng
- School of Biomedical Sciences, Hunan University, Changsha 410082, China;
| | - Junqing Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| | - Jiaqi Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (J.L.); (B.Z.); (S.W.); (J.O.); (X.J.); (J.W.)
| |
Collapse
|
11
|
Mustafa MI, Mohammed A. Developing recombinant antibodies by phage display technology to neutralize viral infectious diseases. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100140. [PMID: 38182043 DOI: 10.1016/j.slasd.2024.01.001] [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: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
The use of recombinant antibodies developed through phage display technology offers a promising approach for combating viral infectious diseases. By specifically targeting antigens on viral surfaces, these antibodies have the potential to reduce the severity of infections or even prevent them altogether. With the emergence of new and more virulent strains of viruses, it is crucial to develop innovative methods to counteract them. Phage display technology has proven successful in generating recombinant antibodies capable of targeting specific viral antigens, thereby providing a powerful tool to fight viral infections. In this mini-review article, we examine the development of these antibodies using phage display technology, and discuss the associated challenges and opportunities in developing novel treatments for viral infectious diseases. Furthermore, we provide an overview of phage display technology. As these methods continue to evolve and improve, novel and sophisticated tools based on phage display and peptide display systems are constantly emerging, offering exciting prospects for solving scientific, medical, and technological problems related to viral infectious diseases in the near future.
Collapse
Affiliation(s)
- Mujahed I Mustafa
- Department of Biotechnology, College of Applied and Industrial Sciences, University of Bahri, Khartoum, Sudan.
| | - Ahmed Mohammed
- Department of Biotechnology, School of Life Sciences and Technology, Omdurman Islamic university, Omdurman, Sudan
| |
Collapse
|
12
|
Rivera‐de‐Torre E, Lampadariou S, Møiniche M, Bohn MF, Kazemi SM, Laustsen AH. Discovery of broadly-neutralizing antibodies against brown recluse spider and Gadim scorpion sphingomyelinases using consensus toxins as antigens. Protein Sci 2024; 33:e4901. [PMID: 38358130 PMCID: PMC10868436 DOI: 10.1002/pro.4901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/16/2024]
Abstract
Broadly-neutralizing monoclonal antibodies are becoming increasingly important tools for treating infectious diseases and animal envenomings. However, designing and developing broadly-neutralizing antibodies can be cumbersome using traditional low-throughput iterative protein engineering methods. Here, we present a new high-throughput approach for the standardized discovery of broadly-neutralizing monoclonal antibodies relying on phage display technology and consensus antigens representing average sequences of related proteins. We showcase the utility of this approach by applying it to toxic sphingomyelinases from the venoms of species from very distant orders of the animal kingdom, the recluse spider and Gadim scorpion. First, we designed a consensus sphingomyelinase and performed three rounds of phage display selection, followed by DELFIA-based screening and ranking, and benchmarked this to a similar campaign involving cross-panning against recombinant versions of the native toxins. Second, we identified two scFvs that not only bind the consensus toxins, but which can also neutralize sphingomyelinase activity of native whole venom in vitro. Finally, we conclude that the phage display campaign involving the use of the consensus toxin was more successful in yielding cross-neutralizing scFvs than the phage display campaign involving cross-panning.
Collapse
Affiliation(s)
| | - Stefanos Lampadariou
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Mark Møiniche
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Markus F. Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | | | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| |
Collapse
|
13
|
Roman J, Ge S, Bouaraphan S, Fink M, Trausch JJ, Verch T. Use of a Microfluidic Platform To Evaluate and Predict Reagent Performance in Microtiter Plate-Based Immunoassays. Anal Chem 2024; 96:3489-3497. [PMID: 38349730 DOI: 10.1021/acs.analchem.3c05278] [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: 02/28/2024]
Abstract
Selection and characterization of antibodies are critically important in establishing robust immunoassays to support the development efforts of vaccines. Plate-based ELISA can be time- and resource-intensive to select initial antibody clones or characterize downstream resupply lots while providing limited information regarding the binding characteristics of the antibodies beyond concentration-response curves. This work applied the microfluidic Gyrolab to holistically evaluate immunoassay reagents through analyses of concentration-response curves as well as antibody-antigen interactions visualized in column images and affinity estimates. We exploited the automation capability of the Gyrolab to reduce the resources (time, reagents, and scientists) required for screening and evaluating antibody reagents. Using a flexible semi-universal assay format, we compared antibody clones for selection and resupply lots of sera and monoclonal antibodies in a simple "plug-and-play" manner without antibody modifications. We found that the performance of antibodies in the Gyrolab correlated well with the trends observed in traditional ELISAs, while the Gyrolab provided additional advantages over plate-based assays such as column images of antibody binding and affinity measurements.
Collapse
Affiliation(s)
- Jeanette Roman
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shencheng Ge
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Malorie Fink
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Thorsten Verch
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| |
Collapse
|
14
|
Li Q, Liu K, Cai G, Yang X, Ngo JCK. Developing Lipase Inhibitor as a Novel Approach to Address the Rice Bran Rancidity Issue─A Critical Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3277-3290. [PMID: 38329044 DOI: 10.1021/acs.jafc.3c07492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Rice bran is a valuable byproduct from the food processing industry, which contains abundant protein, essential unsaturated fatty acids, and numerous bioactive compounds. However, its susceptibility to rancidity greatly restricts its wide utilization. Many strategies have been proposed to delay the rancidity of rice bran, but most of them have their respective limitations. Here, we proposed that developing rice ban lipase peptide inhibitors represents an alternative and promising prescription for impeding the rancidity of rice bran, in contrast to the conventional stabilization approaches for rice bran. For this reason, the rancidity mechanisms of rice bran and the research progress of rice bran lipases were discussed. In addition, the feasibility of utilizing in silico screening and phage display, two state-of-the-art technologies, in the design of the related peptide inhibitors was also highlighted. This knowledge is expected to provide a theoretical basis for opening a new avenue for stabilizing rice bran.
Collapse
Affiliation(s)
- Qingyun Li
- College of Food Science and Engineering and School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Kunlun Liu
- College of Food Science and Engineering and School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Gongli Cai
- School of Life Sciences and Hong Kong Branch of National Engineering Research Center of Genetic Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, SAR 999077, China
| | - Xi Yang
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jacky Chi Ki Ngo
- School of Life Sciences and Hong Kong Branch of National Engineering Research Center of Genetic Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, SAR 999077, China
| |
Collapse
|
15
|
Sørensen CV, Hofmann N, Rawat P, Sørensen FV, Ljungars A, Greiff V, Laustsen AH, Jenkins TP. ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns. BIOINFORMATICS ADVANCES 2024; 4:vbae020. [PMID: 38425781 PMCID: PMC10902677 DOI: 10.1093/bioadv/vbae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Summary High-throughput sequencing (HTS) offers a modern, fast, and explorative solution to unveil the full potential of display techniques, like antibody phage display, in molecular biology. However, a significant challenge lies in the processing and analysis of such data. Furthermore, there is a notable absence of open-access user-friendly software tools that can be utilized by scientists lacking programming expertise. Here, we present ExpoSeq as an easy-to-use tool to explore, process, and visualize HTS data from antibody discovery campaigns like an expert while only requiring a beginner's knowledge. Availability and implementation The pipeline is distributed via GitHub and PyPI, and it can either be installed as a package with pip or the user can choose to clone the repository.
Collapse
Affiliation(s)
- Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Nils Hofmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, NO-0316 Oslo, Norway
| | | | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, NO-0316 Oslo, Norway
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| |
Collapse
|
16
|
Notin P, Rollins N, Gal Y, Sander C, Marks D. Machine learning for functional protein design. Nat Biotechnol 2024; 42:216-228. [PMID: 38361074 DOI: 10.1038/s41587-024-02127-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.
Collapse
Affiliation(s)
- Pascal Notin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Computer Science, University of Oxford, Oxford, UK.
| | | | - Yarin Gal
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
17
|
Li XT, Peng SY, Feng SM, Bao TY, Li SZ, Li SY. Recent Progress in Phage-Based Nanoplatforms for Tumor Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307111. [PMID: 37806755 DOI: 10.1002/smll.202307111] [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: 08/18/2023] [Revised: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Nanodrug delivery systems have demonstrated a great potential for tumor therapy with the development of nanotechnology. Nonetheless, traditional drug delivery systems are faced with issues such as complex synthetic procedures, low reproducibility, nonspecific distribution, impenetrability of biological barrier, systemic toxicity, etc. In recent years, phage-based nanoplatforms have attracted increasing attention in tumor treatment for their regular structure, fantastic carrying property, high transduction efficiency and biosafety. Notably, therapeutic or targeting peptides can be expressed on the surface of the phages through phage display technology, enabling the phage vectors to possess multifunctions. As a result, the drug delivery efficiency on tumor will be vastly improved, thereby enhancing the therapeutic efficacy while reducing the side effects on normal tissues. Moreover, phages can overcome the hindrance of biofilm barrier to elicit antitumor effects, which exhibit great advantages compared with traditional synthetic drug delivery systems. Herein, this review not only summarizes the structure and biology of the phages, but also presents their potential as prominent nanoplatforms against tumor in different pathways to inspire the development of effective nanomedicine.
Collapse
Affiliation(s)
- Xiao-Tong Li
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shu-Yi Peng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shao-Mei Feng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Ting-Yu Bao
- Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Sheng-Zhang Li
- Department of Clinical Medicine, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shi-Ying Li
- Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, P. R. China
| |
Collapse
|
18
|
Kelbauskas L, Legutki JB, Woodbury NW. Highly heterogenous humoral immune response in Lyme disease patients revealed by broad machine learning-assisted antibody binding profiling with random peptide arrays. Front Immunol 2024; 15:1335446. [PMID: 38318184 PMCID: PMC10838964 DOI: 10.3389/fimmu.2024.1335446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Lyme disease (LD), a rapidly growing public health problem in the US, represents a formidable challenge due to the lack of detailed understanding about how the human immune system responds to its pathogen, the Borrelia burgdorferi bacterium. Despite significant advances in gaining deeper insight into mechanisms the pathogen uses to evade immune response, substantial gaps remain. As a result, molecular tools for the disease diagnosis are lacking with the currently available tests showing poor performance. High interpersonal variability in immune response combined with the ability of the pathogen to use a number of immune evasive tactics have been implicated as underlying factors for the limited test performance. Methods This study was designed to perform a broad profiling of the entire repertoire of circulating antibodies in human sera at the single-individual level using planar arrays of short linear peptides with random sequences. The peptides sample sparsely, but uniformly the entire combinatorial sequence space of the same length peptides for profiling the humoral immune response to a B.burg. infection and compare them with other diseases with etiology similar to LD and healthy controls. Results The study revealed substantial variability in antibody binding profiles between individual LD patients even to the same antigen (VlsE protein) and strong similarity between individuals diagnosed with Lyme disease and healthy controls from the areas endemic to LD suggesting a high prevalence of seropositivity in endemic healthy control. Discussion This work demonstrates the utility of the approach as a valuable analytical tool for agnostic profiling of humoral immune response to a pathogen.
Collapse
Affiliation(s)
- L Kelbauskas
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Biomorph Technologies, Chandler, AZ, United States
| | - J B Legutki
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Biomorph Technologies, Chandler, AZ, United States
| | - N W Woodbury
- Biodesign Institute, Arizona State University, Tempe, AZ, United States
| |
Collapse
|
19
|
Zhang C, Zhao Z, Jia YJ, Zhang PQ, Sun Y, Zhou YC, Wang GX, Zhu B. Rationally Designed Self-Assembling Nanovaccines Elicit Robust Mucosal and Systemic Immunity against Rhabdovirus. ACS APPLIED MATERIALS & INTERFACES 2024; 16:228-244. [PMID: 38055273 DOI: 10.1021/acsami.3c14305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Viral diseases have constantly caused great threats to global public health, resulting in an urgent need for effective vaccines. However, the current viral vaccines often show low immunogenicity. To counter this, we report a smart strategy of a well-designed modular nanoparticle (LSG-TDH) that recapitulates the dominant antigen SG, low-molecular-weight protamine, and tetralysine-modified H-chain apoferritin (TDH). The constructed LSG-TDH nanovaccine could self-assemble into a nanocage structure, which confers excellent mucus-penetrating, cellular affinity, and uptake ability. Studies demonstrate that the LSG-TDH nanovaccine could strongly activate both mucosal and systemic immune responses. Importantly, by immunizing wild-type and TLR2 knockout (TLR2-KO) zebrafish, we found that TLR2 could mediate LSG-TDH-induced adaptive mucosal and systemic immune responses by activating antigen-presenting cells. Collectively, our findings offer new insights into rational viral vaccine design and provide additional evidence of the vital role of TLR2 in regulating adaptive immunity.
Collapse
Affiliation(s)
- Chen Zhang
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Zhao Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Yi-Jun Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Peng-Qi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Yun Sun
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
| | - Yong-Can Zhou
- Collaborative Innovation Center of Marine Science and Technology, Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou 570228, P. R. China
| | - Gao-Xue Wang
- College of Animal Science and Technology, Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Bin Zhu
- College of Animal Science and Technology, Key Laboratory of Livestock Biology, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| |
Collapse
|
20
|
Wang H, Chen M, Zhang X, Xie S, Qin J, Li J. Peptide-based PROTACs: Current Challenges and Future Perspectives. Curr Med Chem 2024; 31:208-222. [PMID: 36718000 DOI: 10.2174/0929867330666230130121822] [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: 08/11/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are an attractive means to target previously undruggable or drug-resistant mutant proteins. While small molecule-based PROTACs are stable and can cross cell membranes, there is limited availability of suitable small molecule warheads capable of recruiting proteins to an E3 ubiquitin ligase for degradation. With advances in structural biology and in silico protein structure prediction, it is now becoming easier to define highly selective peptides suitable for PROTAC design. As a result, peptide-based PROTACs are becoming a feasible proposition for targeting previously "undruggable" proteins not amenable to small molecule inhibition. In this review, we summarize recent progress in the design and application of peptide-based PROTACs as well as several practical approaches for obtaining candidate peptides for PROTACs. We also discuss the major hurdles preventing the translation of peptide-based PROTACs from bench to bedside, such as their delivery and bioavailability, with the aim of stimulating discussion about how best to accelerate the clinical development of peptide- based PROTACs in the near future.
Collapse
Affiliation(s)
- Huidan Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Miao Chen
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Xiaoyuan Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Songbo Xie
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Jie Qin
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Jingrui Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| |
Collapse
|
21
|
Wang Y, Zhao J, Jiang Z, Ma Y, Zhang R. Single-Cell Proteomics by Barcoded Phage-Displayed Screening via an Integrated Microfluidic Chip. Methods Mol Biol 2024; 2793:101-112. [PMID: 38526726 DOI: 10.1007/978-1-0716-3798-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Recent advancements in the profiling of proteomes at the single-cell level necessitate the development of quantitative and versatile platforms, particularly for analyzing rare cells like circulating tumor cells (CTCs). In this chapter, we present an integrated microfluidic chip that utilizes magnetic nanoparticles to capture single tumor cells with exceptional efficiency. This chip enables on-chip incubation and facilitates in situ analysis of cell-surface protein expression. By combining phage-based barcoding with next-generation sequencing technology, we successfully monitored changes in the expression of multiple surface markers induced by CTC adherence. This innovative platform holds significant potential for comprehensive screening of multiple surface antigens simultaneously in rare cells, offering single-cell resolution. Consequently, it will contribute valuable insights into biological heterogeneity and human disease.
Collapse
Affiliation(s)
- Yujiao Wang
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, China
| | - Jing Zhao
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, China
- Department of Clinical Laboratory, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Zhenwei Jiang
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, China
| | - Yuan Ma
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, China.
| | - Rui Zhang
- Department of Clinical Laboratory, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
22
|
Song BPC, Ch'ng ACW, Lim TS. Review of phage display: A jack-of-all-trades and master of most biomolecule display. Int J Biol Macromol 2024; 256:128455. [PMID: 38013083 DOI: 10.1016/j.ijbiomac.2023.128455] [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: 09/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Phage display was first described by George P. Smith when it was shown that virus particles were capable of presenting foreign proteins on their surface. The technology has paved the way for the evolution of various biomolecules presentation and diverse selection strategies. This unique feature has been applied as a versatile platform for numerous applications in drug discovery, protein engineering, diagnostics, and vaccine development. Over the decades, the limits of biomolecules displayed on phage particles have expanded from peptides to proteomes and even alternative scaffolds. This has allowed phage display to be viewed as a versatile display platform to accommodate various biomolecules ranging from small peptides to larger proteomes which has significantly impacted advancements in the biomedical industry. This review will explore the vast array of biomolecules that have been successfully employed in phage display technology in biomedical research.
Collapse
Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
23
|
Song BPC, Lai JY, Lim TS. Generation of a Naïve Human scFv Phage Display Library and Panning Selection. Methods Mol Biol 2024; 2793:21-40. [PMID: 38526721 DOI: 10.1007/978-1-0716-3798-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Phage display antibody libraries have been successfully used as the essential tool to produce monoclonal antibodies against a plethora of targets ranging from diseases to native biologically important proteins as well as small molecules. It is well documented that diverse antibody genes are the major genetic source for the construction of a high-quality antibody library and selection of high-affinity antibodies. Naïve antibody libraries are derived using the IgM repertoire of healthy donors obtained from B-cells isolated from human peripheral blood mononuclear cell (PBMC). Single-chain fragment variable (scFv) is a routinely used format due to its smaller size and preference for phage display. The process involves the use of a two-step cloning method for library construction. The protocol also covers the biopanning process for target positive clone selection.
Collapse
Affiliation(s)
- Brenda Pei Chui Song
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia.
| |
Collapse
|
24
|
Zhang P, Wang K, Hu T, Xu M, You X, Chen M, Tang X, Hu H, Jiang Y, Zhao W, Tan S. A novel fully human anti-NT-ANGPTL3 antibody from phage display library exhibits potent ApoB, TG, and LDL-C lowering activities in hyperlipidemia mice. FASEB J 2024; 38:e23399. [PMID: 38174870 DOI: 10.1096/fj.202301564rr] [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: 08/02/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Dyslipidemia is characterized by elevated plasma levels of low-density lipoprotein cholesterol (LDL-C), triglycerides (TG), and TG-rich lipoprotein (TGRLs) in circulation, and is closely associated with the incidence and development of cardiovascular disease. Angiopoietin-like protein 3 (ANGPTL3) deficiency has been identified as a cause of familial combined hypolipidemia in humans, which allows it to be an important therapeutic target for reducing plasma lipids. Here, we report the discovery and characterization of a novel fully human antibody F1519-D95aA against N-terminal ANGPTL3 (NT-ANGPTL3), which potently inhibits NT-ANGPTL3 with a KD as low as 9.21 nM. In hyperlipidemic mice, F1519-D95aA shows higher apolipoprotein B (ApoB) and TG-lowering, and similar LDL-C reducing activity as compared to positive control Evinacumab (56.50% vs 26.01% decrease in serum ApoB levels, 30.84% vs 25.28% decrease in serum TG levels, 23.32% vs 22.52% decrease in serum LDLC levels, relative to vehicle group). Molecular docking and binding energy calculations reveal that the F1519-D95aA-ANGPTL3 complex (10 hydrogen bonds, -65.51 kcal/mol) is more stable than the Evinacumab-ANGPTL3 complex (4 hydrogen bonds, -63.76 kcal/mol). Importantly, F1519-D95aA binds to ANGPTL3 with different residues in ANGPTL3 from Evinacumab, suggesting that F1519-D95aA may be useful for the treatment of patients resistant to Evinacumab. In conclusion, F1519-D95aA is a novel fully human anti-NT-ANGPTL3 antibody with potent plasma ApoB, TG, and LDL-C lowering activities, which can potentially serve as a therapeutic agent for hyperlipidemia and relevant cardiovascular diseases.
Collapse
Affiliation(s)
- Panpan Zhang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Ke Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Tuo Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xiangyan You
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Manman Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xuan Tang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Huajing Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Yiwei Jiang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| |
Collapse
|
25
|
Thumtecho S, Burlet NJ, Ljungars A, Laustsen AH. Towards better antivenoms: navigating the road to new types of snakebite envenoming therapies. J Venom Anim Toxins Incl Trop Dis 2023; 29:e20230057. [PMID: 38116472 PMCID: PMC10729942 DOI: 10.1590/1678-9199-jvatitd-2023-0057] [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: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Snakebite envenoming is a significant global health challenge, and for over a century, traditional plasma-derived antivenoms from hyperimmunized animals have been the primary treatment against this infliction. However, these antivenoms have several inherent limitations, including the risk of causing adverse reactions when administered to patients, batch-to-batch variation, and high production costs. To address these issues and improve treatment outcomes, the development of new types of antivenoms is crucial. During this development, key aspects such as improved clinical efficacy, enhanced safety profiles, and greater affordability should be in focus. To achieve these goals, modern biotechnological methods can be applied to the discovery and development of therapeutic agents that can neutralize medically important toxins from multiple snake species. This review highlights some of these agents, including monoclonal antibodies, nanobodies, and selected small molecules, that can achieve broad toxin neutralization, have favorable safety profiles, and can be produced on a large scale with standardized manufacturing processes. Considering the inherent strengths and limitations related to the pharmacokinetics of these different agents, a combination of them might be beneficial in the development of new types of antivenom products with improved therapeutic properties. While the implementation of new therapies requires time, it is foreseeable that the application of biotechnological advancements represents a promising trajectory toward the development of improved therapies for snakebite envenoming. As research and development continue to advance, these new products could emerge as the mainstay treatment in the future.
Collapse
Affiliation(s)
- Suthimon Thumtecho
- Division of Toxicology, Department of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nick J. Burlet
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
26
|
Ma X, Jiang J, An X, Zu W, Ma C, Zhang Z, Lu Y, Zhao L, Wang L. Advances in research based on antibody-cell conjugation. Front Immunol 2023; 14:1310130. [PMID: 38162639 PMCID: PMC10755917 DOI: 10.3389/fimmu.2023.1310130] [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: 10/09/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Antibody-cell conjugation (ACC) technology is a new research direction in medicine and biotechnology in recent years. The concept of ACC was proposed by Hsiao et al. and developed into a viable cell therapy technology, which refers to the cells with specific functions. Such as natural killer cells (NK cells), cytokine induced killer cells (CIK) and other immune cells and monoclonal antibodies through the linker together formed conjugate. ACC directly modifies specific antibodies on the cell surface through a simple and effective chemical coupling method to enable cells to have new functions. ACC has been developed for the treatment of various diseases, including cancers of the blood system and solid tumors. This paper reviews the current ACC construction methods, challenges and future development directions.
Collapse
Affiliation(s)
- Xiaoxuan Ma
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Jian Jiang
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Xiaoye An
- Department of Pharmacy, Tacheng People's Hospital, Tacheng City, Xinjiang Uygur Autonomous Region, China
| | - Wanting Zu
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Chi Ma
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Zhuo Zhang
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Yaci Lu
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Lijing Zhao
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| | - Lisheng Wang
- Department of Rehabilitation, School of Nursing, Jilin University, Changchun, China
| |
Collapse
|
27
|
Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
Collapse
Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| |
Collapse
|
28
|
Tulika T, Pedersen RW, Rimbault C, Ahmadi S, Rivera‐de‐Torre E, Fernández‐Quintero ML, Loeffler JR, Bohn M, Ljungars A, Ledsgaard L, Voldborg BG, Ruso‐Julve F, Andersen JT, Laustsen AH. Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library. Protein Sci 2023; 32:e4821. [PMID: 37897425 PMCID: PMC10659949 DOI: 10.1002/pro.4821] [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: 05/10/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
Recycling IgG antibodies bind to their target antigen at physiological pH in the blood stream and release them upon endocytosis when pH levels drop, allowing the IgG antibodies to be recycled into circulation via FcRn-mediated cellular pathways, while the antigens undergo lysosomal degradation. This enables recycling antibodies to achieve comparable therapeutic effect at lower doses than their non-recycling counterparts. The development of such antibodies is typically achieved by histidine doping of their variable regions or by performing in vitro antibody selection campaigns utilizing histidine doped libraries. Both are strategies that may introduce sequence liabilities. Here, we present a methodology that employs a naïve antibody phage display library, consisting of natural variable domains, to discover antibodies that bind α-cobratoxin from the venom of Naja kaouthia in a pH-dependent manner. As a result, an antibody was discovered that exhibits a 7-fold higher off-rate at pH 5.5 than pH 7.4 in bio-layer interferometry experiments. Interestingly, no histidine residues were found in its variable domains, and in addition, the antibody showed pH-dependent binding to a histidine-devoid antigen mutant. As such, the results demonstrate that pH-dependent antigen-antibody binding may not always be driven by histidine residues. By employing molecular dynamics simulations, different protonation states of titratable residues were found, which potentially could be responsible for the observed pH-dependent antigen binding properties of the antibody. Finally, given the typically high diversity of naïve antibody libraries, the methodology presented here can likely be applied to discover recycling antibodies against different targets ab initio without the need for histidine doping.
Collapse
Affiliation(s)
- Tulika Tulika
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Rasmus W. Pedersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Charlotte Rimbault
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Shirin Ahmadi
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | - Monica L. Fernández‐Quintero
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck, Department of GeneralInorganic and Theoretical Chemistry, University of InnsbruckInnsbruckAustria
| | - Markus‐Frederik Bohn
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Anne Ljungars
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Line Ledsgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Bjørn G. Voldborg
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Fulgencio Ruso‐Julve
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Jan Terje Andersen
- Department of PharmacologyUniversity of OsloOsloNorway
- Department of ImmunologyOslo University Hospital RikshospitaletOsloNorway
- Precision Immunotherapy AllianceUniversity of OsloOsloNorway
| | - Andreas H. Laustsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| |
Collapse
|
29
|
De Plano LM, Oddo S, Guglielmino SPP, Caccamo A, Conoci S. Generation of a helper phage for the fluorescent detection of peptide-target interactions by dual-display phages. Sci Rep 2023; 13:18927. [PMID: 37919374 PMCID: PMC10622537 DOI: 10.1038/s41598-023-45087-2] [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: 07/27/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
Phage display is a molecular biology technique that allows the presentation of foreign peptides on the surface of bacteriophages. It is widely utilized for applications such as the discovery of biomarkers, the development of therapeutic antibodies, and the investigation of protein-protein interactions. When employing phages in diagnostic and therapeutic monitoring assays, it is essential to couple them with a detection system capable of revealing and quantifying the interaction between the peptide displayed on the phage capsid and the target of interest. This process is often technically challenging and costly. Here, we generated a fluorescent helper phage vector displaying sfGFP in-frame to the pIII of the capsid proteins. Further, we developed an exchangeable dual-display phage system by combining our newly developed fluorescent helper phage vector with a phagemid vector harboring the engineered pVIII with a peptide-probe. By doing so, the sfGFP and a peptide-probe are displayed on the same phage particle. Notably, our dual-display approach is highly flexible as it allows for easy exchange of the displayed peptide-probe on the pVIII to gain the desired selectivity, while maintaining the sfGFP gene, which allows easy visualization and quantification of the interaction peptide-probe. We anticipate that this system will reduce time and costs compared to the current phage-based detection systems.
Collapse
Affiliation(s)
- Laura Maria De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Salvatore Oddo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Salvatore P P Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
| | - Antonella Caccamo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy.
| | - Sabrina Conoci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, Messina, Italy
- Department of Chemistry G. Ciamician, University of Bologna, Via F. Selmi 2, Bologna, Italy
- LAB Sense Beyond Nano-DSFTM CNR, Viale F. Stagno d'Alcontres 31, Messina, Italy
- CNR Institute for Microelectronics and Microsystems, Strada VIII, 5, Catania, Italy
- STMicroelectronics, Stradale Primosole 50, 95121, Catania, Italy
| |
Collapse
|
30
|
Furuhashi T, Sakamoto K, Wada A. Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides. Int J Mol Sci 2023; 24:15661. [PMID: 37958644 PMCID: PMC10650079 DOI: 10.3390/ijms242115661] [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: 09/03/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research.
Collapse
Affiliation(s)
- Takuto Furuhashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
- Department of Drug Target Protein Research, School of Medicine, Shinshu University, 3-1-1 Asahi, Matsumoto 390-8621, Nagano, Japan
| | - Akira Wada
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Advanced Biomolecular Engineering, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
- Laboratory for Nonnatural Amino Acid Technology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan;
| |
Collapse
|
31
|
Özçelik C, Beğli Ö, Hınçer A, Ahan RE, Kesici MS, Oğuz O, Kasırga TS, Özçubukçu S, Şeker UÖŞ. Synergistic Screening of Peptide-Based Biotechnological Drug Candidates for Neurodegenerative Diseases Using Yeast Display and Phage Display. ACS Chem Neurosci 2023; 14:3609-3621. [PMID: 37638647 PMCID: PMC10557061 DOI: 10.1021/acschemneuro.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Peptide therapeutics are robust and promising molecules for treating diverse disease conditions. These molecules can be developed from naturally occurring or mimicking native peptides, through rational design and peptide libraries. We developed a new platform for the rapid screening of the peptide therapeutics for disease targets. In the course of the study, we aimed to employ our platform to screen a new generation of peptide therapeutic candidates against aggregation-prone protein targets. Two peptide drug candidates were screened for protein aggregation-prone diseases, namely, Parkinson's and Alzheimer's diseases. Currently, there are several therapeutic applications that are only effective in masking or slowing down symptom development. Nonetheless, different approaches are being developed for inhibiting amyloid aggregation in the secondary nucleation phase, which is critical for amyloid fibril formation. Instead of targeting secondary nucleated protein structures, we tried to inhibit the aggregation of monomeric amyloid units as a novel approach for halting the disease condition. To achieve this, we combined yeast surface display and phage display library platforms. We expressed α-synuclein, amyloid β40, and amyloid β42 on the yeast surface, and we selected peptides by using phage display library. After iterative biopanning cycles optimized for yeast cells, several peptides were selected for interaction studies. All of the peptides have been used for in vitro characterization methods, which are quartz crystal microbalance-dissipation (QCM-D) measurement, atomic force microscopy (AFM) imaging, dot-blotting, and ThT assay, and some of them have yielded promising results in blocking fibrillization. The rest of the peptides, although, interacted with amyloid units which made them usable as a sensor molecule candidate. Therefore, peptides selected by yeast surface display and phage display library combination are good choice for diverse disease-prone molecule inhibition, particularly those inhibiting fibrillization. Additionally, these selected peptides can be used as drugs and sensors to detect diseases quickly and halt disease progression.
Collapse
Affiliation(s)
- Cemile
Elif Özçelik
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Özge Beğli
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Ahmet Hınçer
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Recep Erdem Ahan
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Mehmet Seçkin Kesici
- Department
of Chemistry, Faculty of Science, Middle
East Technical University, Ankara 06800, Turkey
| | - Oğuzhan Oğuz
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Talip Serkan Kasırga
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Salih Özçubukçu
- Department
of Chemistry, Faculty of Science, Middle
East Technical University, Ankara 06800, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Interdisciplinary
Program in Neuroscience, Bilkent University, Ankara 06800, Turkey
| |
Collapse
|
32
|
Sørensen CV, Almeida JR, Bohn MF, Rivera-de-Torre E, Schoffelen S, Voldborg BG, Ljungars A, Vaiyapuri S, Laustsen AH. Discovery of a human monoclonal antibody that cross-neutralizes venom phospholipase A 2s from three different snake genera. Toxicon 2023; 234:107307. [PMID: 37783315 DOI: 10.1016/j.toxicon.2023.107307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Despite the considerable global impact of snakebite envenoming, available treatments remain suboptimal. Here, we report the discovery of a broadly-neutralizing human monoclonal antibody, using a phage display-based cross-panning strategy, capable of reducing the cytotoxic effects of venom phospholipase A2s from three different snake genera from different continents. This highlights the potential of utilizing monoclonal antibodies to develop more effective, safer, and globally accessible polyvalent antivenoms that can be widely used to treat snakebite envenoming.
Collapse
Affiliation(s)
- Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
| | - José R Almeida
- School of Pharmacy, University of Reading, Reading, RG6 6UB, United Kingdom
| | - Markus-Frederik Bohn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Sanne Schoffelen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Bjørn G Voldborg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Sakthivel Vaiyapuri
- School of Pharmacy, University of Reading, Reading, RG6 6UB, United Kingdom.
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
| |
Collapse
|
33
|
Yu H, Mao G, Pei Z, Cen J, Meng W, Wang Y, Zhang S, Li S, Xu Q, Sun M, Xiao K. In Vitro Affinity Maturation of Nanobodies against Mpox Virus A29 Protein Based on Computer-Aided Design. Molecules 2023; 28:6838. [PMID: 37836685 PMCID: PMC10574621 DOI: 10.3390/molecules28196838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Mpox virus (MPXV), the most pathogenic zoonotic orthopoxvirus, caused worldwide concern during the SARS-CoV-2 epidemic. Growing evidence suggests that the MPXV surface protein A29 could be a specific diagnostic marker for immunological detection. In this study, a fully synthetic phage display library was screened, revealing two nanobodies (A1 and H8) that specifically recognize A29. Subsequently, an in vitro affinity maturation strategy based on computer-aided design was proposed by building and docking the A29 and A1 three-dimensional structures. Ligand-receptor binding and molecular dynamics simulations were performed to predict binding modes and key residues. Three mutant antibodies were predicted using the platform, increasing the affinity by approximately 10-fold compared with the parental form. These results will facilitate the application of computers in antibody optimization and reduce the cost of antibody development; moreover, the predicted antibodies provide a reference for establishing an immunological response against MPXV.
Collapse
Affiliation(s)
- Haiyang Yu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China;
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Guanchao Mao
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Zhipeng Pei
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Jinfeng Cen
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Wenqi Meng
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Yunqin Wang
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Shanshan Zhang
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Songling Li
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Qingqiang Xu
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Mingxue Sun
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
| | - Kai Xiao
- Lab of Toxicology and Pharmacology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (G.M.); (Z.P.); (J.C.); (W.M.); (Y.W.); (S.Z.); (S.L.)
- Marine Biomedical Science and Technology Innovation Platform of Lingang Special Area, Shanghai 201306, China
| |
Collapse
|
34
|
Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [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: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
Collapse
Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
35
|
León E, Ortiz V, Pérez A, Téllez J, Díaz GJ, Ramírez H MH, Contreras R LE. Anti-SpCas9 IgY Polyclonal Antibodies Production for CRISPR Research Use. ACS OMEGA 2023; 8:33809-33818. [PMID: 37744827 PMCID: PMC10515394 DOI: 10.1021/acsomega.3c04273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
The CRISPR/Cas adaptative immune system has been harnessed as an RNA-guided, programmable genome editing tool, allowing for diverse biotechnological applications. The implementation of the system relies on the ability to detect the Cas9 protein in biological samples. This task is facilitated by employing antibodies, which exhibit several advantageous features and applications in the context of tropical neglected diseases. This study reports a one-month immunization scheme with the Cas9 protein fromStreptococcus pyogenes to produce IgY polyclonal antibodies (anti-SpCas9), which can be rapidly isolated by combining yolk de-lipidation with protein salting out using pectin and ammonium sulfate, respectively. Immunodetection assays indicate that the antibodies are highly sensitive, specific, and useful for detecting the SpCas9 protein in promastigotes ofLeishmania braziliensisexpressing exogenous SpCas9. Thus, the simple method for producing anti-SpCas9 IgY antibodies will accelerate CRISPR/Cas-based studies in Leishmania spp. This approach serves as a valuable research tool in this parasite model and holds the potential for wide application in various other biological samples, promoting the implementation of the system. In fact, a bioinformatics approach based on the identification of antigenic determinants in the SpCas9 protein suggests the possibility of using the anti-SpCas9 IgY antibodies in applications such as Prime and Base editing.
Collapse
Affiliation(s)
- Esteban León
- Facultad
de Ciencias, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| | - Valentina Ortiz
- Facultad
de Ciencias, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| | - Alexander Pérez
- Facultad
de Ciencias, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| | - Jair Téllez
- Escuela
de Pregrado, Dirección Académica, Universidad Nacional de Colombia, 202017 sede La Paz, Colombia
| | - Gonzalo J. Díaz
- Facultad
de Medicina Veterinaria y de Zootecnia, Laboratorio de Toxicología, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| | - María H. Ramírez H
- Facultad
de Ciencias, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| | - Luis E. Contreras R
- Facultad
de Ciencias, Universidad Nacional de Colombia, 111311 Bogotá, Colombia
| |
Collapse
|
36
|
Zhou Z, Liao B, Wang S, Tang J, Zhao H, Tong M, Li K, Xiong S. Improved Production of Anti-FGF-2 Nanobody Using Pichia pastoris and Its Effect on Antiproliferation of Keratinocytes and Alleviation of Psoriasis. Arch Immunol Ther Exp (Warsz) 2023; 71:20. [PMID: 37632545 DOI: 10.1007/s00005-023-00685-w] [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: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 08/28/2023]
Abstract
Fibroblast growth factor 2 (FGF-2) is not only an angiogenic factor, but also a mitogen for epidermal keratinocytes. FGF-2 has been shown to be positively immunoreactive in the basal layer of psoriatic lesions. In previous work, we used the Escherichia coli (E. coli) expression system to biosynthesize a biologically active anti-FGF-2 nanobody (Nb) screened by phage display technology, but the low yield limited its clinical application. In this study, we aimed to increase the yield of anti-FGF-2 Nb, and evaluate its therapeutic potential for psoriasis by inhibiting FGF-2-mediated mitogenic signaling in psoriatic epidermal keratinocytes. We demonstrated a 16-fold improvement in the yield of anti-FGF-2 Nb produced in the Pichia pastoris (P. pastoris) compared to the E. coli expression system. In vitro, the FGF-2-induced HaCaT cell model (FHCM) was established to mimic the key feature of keratinocyte overproliferation in psoriasis. Anti-FGF-2 Nb was able to effectively inhibit the proliferation and migration of FHCM. In vivo, anti-FGF-2 Nb attenuated the severity of imiquimod (IMQ)-induced psoriatic lesions in mice, and also improved the inflammatory microenvironment by inhibiting the secretion of inflammatory cytokines (IL-1β, IL-6, IL-23, and TNF-α), chemokines (CXCL1 and CCL20), and neutrophil infiltration in skin lesions. These were mainly related to the suppression of FGF-2-mediated mitogenic signaling in psoriatic keratinocytes. In conclusion, we have improved the production of anti-FGF-2 Nb and demonstrated the modality of attenuating the abnormal proliferative behavior of psoriatic keratinocytes by inhibiting FGF-2-mediated mitogenic signaling, which offers the possibility of treating psoriasis.
Collapse
Affiliation(s)
- Zhenlong Zhou
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, People's Republic of China
| | - Baixin Liao
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Shengli Wang
- Institute of Biomedical Transformation, School of Basic Medicine and Public Health, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Jian Tang
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Hui Zhao
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Mingjie Tong
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Keting Li
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Sheng Xiong
- Institute of Biomedicine and National Engineering Research Center of Genetic Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China.
| |
Collapse
|
37
|
Alassiri M, Lai JY, Ch'ng ACW, Choong YS, Alanazi A, Lim TS. Subtractive panning for the isolation of monoclonal PEPITEM peptide antibody by phage display. Sci Rep 2023; 13:13627. [PMID: 37604859 PMCID: PMC10442400 DOI: 10.1038/s41598-023-40630-7] [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: 03/28/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Antibody phage display is a key tool for the development of monoclonal antibodies against various targets. However, the development of anti-peptide antibodies is a challenging process due to the small size of peptides for binding. This makes anchoring of peptides a preferred approach for panning experiments. A common approach is by using streptavidin as the anchor protein to present biotinylated peptides for panning. Here, we propose the use of recombinant expression of the target peptide and an immunogenic protein as a fusion for panning. The peptide inhibitor of trans-endothelial migration (PEPITEM) peptide sequence was fused to the Mycobacterium tuberculosis (Mtb) α-crystalline (AC) as an anchor protein. The panning process was carried out by subtractive selection of the antibody library against the AC protein first, followed by binding to the library to PEPITEM fused AC (PEPI-AC). A unique monoclonal scFv antibodies with good specificity were identified. In conclusion, the use of an alternative anchor protein to present the peptide sequence coupled with subtractive panning allows for the identification of unique monoclonal antibodies against a peptide target.
Collapse
Affiliation(s)
- Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia.
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia.
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of the National Guard - Health Affairs, Riyadh, Kingdom of Saudi Arabia.
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Asma Alanazi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Kingdom of Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Kingdom of Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
| |
Collapse
|
38
|
Bauer J, Rajagopal N, Gupta P, Gupta P, Nixon AE, Kumar S. How can we discover developable antibody-based biotherapeutics? Front Mol Biosci 2023; 10:1221626. [PMID: 37609373 PMCID: PMC10441133 DOI: 10.3389/fmolb.2023.1221626] [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: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023] Open
Abstract
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals despite significant challenges and risks to their discovery and development. This review discusses the most frequently encountered hurdles in the research and development (R&D) of antibody-based biotherapeutics and proposes a conceptual framework called biopharmaceutical informatics. Our vision advocates for the syncretic use of computation and experimentation at every stage of biologic drug discovery, considering developability (manufacturability, safety, efficacy, and pharmacology) of potential drug candidates from the earliest stages of the drug discovery phase. The computational advances in recent years allow for more precise formulation of disease concepts, rapid identification, and validation of targets suitable for therapeutic intervention and discovery of potential biotherapeutics that can agonize or antagonize them. Furthermore, computational methods for de novo and epitope-specific antibody design are increasingly being developed, opening novel computationally driven opportunities for biologic drug discovery. Here, we review the opportunities and limitations of emerging computational approaches for optimizing antigens to generate robust immune responses, in silico generation of antibody sequences, discovery of potential antibody binders through virtual screening, assessment of hits, identification of lead drug candidates and their affinity maturation, and optimization for developability. The adoption of biopharmaceutical informatics across all aspects of drug discovery and development cycles should help bring affordable and effective biotherapeutics to patients more quickly.
Collapse
Affiliation(s)
- Joschka Bauer
- Early Stage Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
| | - Nandhini Rajagopal
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Priyanka Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Pankaj Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Andrew E. Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Sandeep Kumar
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| |
Collapse
|
39
|
Chang J, Rader C, Peng H. A mammalian cell display platform based on scFab transposition. Antib Ther 2023; 6:157-169. [PMID: 37492588 PMCID: PMC10365156 DOI: 10.1093/abt/tbad009] [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: 12/27/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 07/27/2023] Open
Abstract
In vitro display technologies have been successfully utilized for the discovery and evolution of monoclonal antibodies (mAbs) for diagnostic and therapeutic applications, with phage display and yeast display being the most commonly used platforms due to their simplicity and high efficiency. As their prokaryotic or lower eukaryotic host organisms typically have no or different post-translational modifications, several mammalian cell-based display and screening technologies for isolation and optimization of mAbs have emerged and are being developed. We report here a novel and useful mammalian cell display platform based on the PiggyBac transposon system to display mAbs in a single-chain Fab (scFab) format on the surface of HEK293F cells. Immune rabbit antibody libraries encompassing ~7 × 107 independent clones were generated in an all-in-one transposon vector, stably delivered into HEK293F cells and displayed as an scFab with rabbit variable and human constant domains. After one round of magnetic activated cell sorting and two rounds of fluorescence activated cell sorting, mAbs with high affinity in the subnanomolar range and cross-reactivity to the corresponding human and mouse antigens were identified, demonstrating the power of this platform for antibody discovery. We developed a highly efficient mammalian cell display platform based on the PiggyBac transposon system for antibody discovery, which could be further utilized for humanization as well as affinity and specificity maturation.
Collapse
Affiliation(s)
- Jing Chang
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, USA
| |
Collapse
|
40
|
Petersson M, Thrane SW, Gram L, Muyldermans S, Laustsen AH. Orally delivered single-domain antibodies against gastrointestinal pathogens. Trends Biotechnol 2023; 41:875-886. [PMID: 36774206 DOI: 10.1016/j.tibtech.2023.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023]
Abstract
Single-domain antibodies (sdAbs) are exceptionally stable fragments derived from the antigen-binding domains of immunoglobulins. They can withstand extreme pH, high temperature, and proteolysis, making them suitable for controlling gastrointestinal (GI) infections in humans and animals. sdAbs may function in their native soluble form, although different derived protein formats and the use of delivery vehicles can be useful for improved oral delivery. We discuss selected examples of the use of orally delivered sdAbs for protecting humans and animals against GI infections caused by pathogenic bacteria, viruses, and parasites. We finally provide perspectives on how sdAbs may be applied industrially and what challenges should be overcome for orally delivered sdAbs to reach the market.
Collapse
Affiliation(s)
- Marcus Petersson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Bactolife A/S, Copenhagen East, Denmark
| | | | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Serge Muyldermans
- Department of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Bactolife A/S, Copenhagen East, Denmark.
| |
Collapse
|
41
|
Sørensen CV, Ledsgaard L, Wildenauer HHK, Dahl CH, Ebersole TW, Bohn MF, Ljungars A, Jenkins TP, Laustsen AH. Cross-reactivity trends when selecting scFv antibodies against snake toxins using a phage display-based cross-panning strategy. Sci Rep 2023; 13:10181. [PMID: 37349546 PMCID: PMC10287648 DOI: 10.1038/s41598-023-37056-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Antibodies with cross-reactive binding and broad toxin-neutralizing capabilities are advantageous for treating indications such as infectious diseases and animal envenomings. Such antibodies have been successfully selected against closely related antigens using phage display technology. However, the mechanisms driving antibody cross-reactivity typically remain to be elucidated. Therefore, we sought to explore how a previously reported phage display-based cross-panning strategy drives the selection of cross-reactive antibodies using seven different snake toxins belonging to three protein (sub-)families: phospholipases A2, long-chain α-neurotoxins, and short-chain α-neurotoxins. We showcase how cross-panning can increase the chances of discovering cross-reactive single-chain variable fragments (scFvs) from phage display campaigns. Further, we find that the feasibility of discovering cross-reactive antibodies using cross-panning cannot easily be predicted by analyzing the sequence, structural, or surface similarity of the antigens alone. However, when antigens share the (exact) same functions, this seems to increase the chances of selecting cross-reactive antibodies, which may possibly be due to the existence of structurally similar motifs on the antigens.
Collapse
Affiliation(s)
- Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Helen H K Wildenauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Camilla H Dahl
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Tasja W Ebersole
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Markus-Frederik Bohn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| |
Collapse
|
42
|
Chen S, Liang Q, Zhuo Y, Hong Q. Human-murine chimeric autoantibodies with high affinity and specificity for systemic sclerosis. Front Immunol 2023; 14:1127849. [PMID: 37398644 PMCID: PMC10311643 DOI: 10.3389/fimmu.2023.1127849] [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: 12/20/2022] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Scleroderma 70 (Scl-70) is commonly used in the clinic for aiding systemic sclerosis (SSc) diagnosis due to its recognition as autoantibodies in the serum of SSc patients. However, obtaining sera positive for anti-Scl-70 antibody can be challenging; therefore, there is an urgent need to develop a specific, sensitive, and easily available reference for SSc diagnosis. In this study, murine-sourced scFv library were screened by phage display technology against human Scl-70, and the scFvs with high affinity were constructed into humanized antibodies for clinical application. Finally, ten high-affinity scFv fragments were obtained. Three fragments (2A, 2AB, and 2HD) were select for humanization. The physicochemical properties of the amino acid sequence, three-dimensional structural basis, and electrostatic potential distribution of the protein surface of different scFv fragments revealed differences in the electrostatic potential of their CDR regions determined their affinity for Scl-70 and expression. Notably, the specificity test showed the half-maximal effective concentration values of the three humanized antibodies were lower than that of positive patient serum. Moreover, these humanized antibodies showed high specificity for Scl-70 in diagnostic immunoassays for ANA. Among these three antibodies, 2A exhibited most positive electrostatic potential on the surface of the CDRs and highest affinity and specificity for Scl-70 but with least expression level; thus, it may provide new foundations for developing enhanced diagnostic strategies for SSc.
Collapse
Affiliation(s)
- Sunhui Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Department of Pharmacy, Fujian Provincial Hospital, Fuzhou, China
| | - Qiong Liang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Department of Pharmacy, Fujian Provincial Hospital, Fuzhou, China
| | - Yanhang Zhuo
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, China
| | - Qin Hong
- Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Key Laboratory of Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, China
| |
Collapse
|
43
|
Dong X, Zhang X, Du Y, Liu J, Zeng Q, Cao W, Wei Q, Ju H. Zirconium dioxide as electrochemiluminescence emitter for D-dimer determination based on dual-quenching sensing strategy. Biosens Bioelectron 2023; 236:115437. [PMID: 37263052 DOI: 10.1016/j.bios.2023.115437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/04/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
The ECL emission of simple and stable zirconium dioxide nanomaterials has always been a blank slate in the ECL sensors field. In this work, zirconium dioxide (ZrO2)-titanium dioxide (TiO2)-gold nanoparticle (AuNPs) composite (ZT-Au), a novel self-enhanced ECL emitter, was introduced the system of dual-quenching ECL immunosensor. The anodic luminescence of ZrO2 in the system of tripropylamine (TPrA) as a co-reagent was first reported and explored. Meanwhile, TiO2 was designed into the ECL scheme as a co-reaction accelerator to form the ZrO2/TPrA/TiO2 ternary system, which can efficiently amplify the ECL signal of the emitter. In addition, cuprous oxide-triaminophenol (Cu2O-APF) as the quencher was devoted to the dual-quenching sensing strategy. The dual-quenching mechanism that effectively boosted the immunosensor sensitivity was adequately investigated and conjectured in this paper. The sensing model based on the luminophor ZT-Au and the quencher Cu2O-APF was utilized for the detection of D-dimer, a reliable marker for the diagnosis and evaluation of thrombotic diseases. The short peptide ligands NARKFYKGC (NFC) with efficient biological affinity were used to site-directionally capture antibodies for adequately protecting the activity of antigen binding sites during the construction of the immunosensor. The implemented immunosensor was equipped with a broad linear range of 0.01-500 ng/mL and a low detection limit of 3.6 pg/mL. The original methodology opens up the field of vision for the detection of additional biomarkers.
Collapse
Affiliation(s)
- Xue Dong
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Xiaoyue Zhang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yu Du
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Jiajun Liu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Qingze Zeng
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Wei Cao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China; Department of Chemistry, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| |
Collapse
|
44
|
Song SH, Ghosh T, You DG, Joo H, Lee J, Lee J, Kim CH, Jeon J, Shin S, Park JH. Functionally Masked Antibody to Uncouple Immune-Related Toxicities in Checkpoint Blockade Cancer Therapy. ACS NANO 2023. [PMID: 37184643 DOI: 10.1021/acsnano.2c12532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Of the existing immunotherapy drugs in oncology, monoclonal antibodies targeting the immune checkpoint axis are preferred because of the durable responses observed in selected patients. However, the associated immune-related adverse events (irAEs), causing uncommon fatal events, often require specialized management and medication discontinuation. The study aim was to investigate our hypothesis that masking checkpoint antibodies with tumor microenvironment (TME)-responsive polymer chains can mitigate irAEs and selectively target tumors by limiting systemic exposure to patients. We devised a broadly applicable strategy that functionalizes immune checkpoint-blocking antibodies with a mildly acidic pH-cleavable poly(ethylene glycol) (PEG) shell to prevent inflammatory side effects in normal tissues. Conjugation of pH-sensitive PEG to anti-CD47 antibodies (αCD47) minimized antibody-cell interactions by inhibiting their binding ability and functionality at physiological pH, leading to prevention of αCD47-induced anemia in tumor-bearing mice. When conjugated to anti-CTLA-4 and anti-PD-1 antibodies, double checkpoint blockade-induced colitis was also ameliorated. Notably, removal of the protective shell in response to an acidic TME restored the checkpoint antibody activities, accompanied by effective tumor regression and long-term survival in the mouse model. Our results support a feasible strategy for antibody-based therapies to uncouple toxicity from efficacy and show the translational potential for cancer immunotherapy.
Collapse
Affiliation(s)
- Seok Ho Song
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Torsha Ghosh
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dong Gil You
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyeyeon Joo
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeongjin Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Jaeah Lee
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Chan Ho Kim
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jueun Jeon
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sol Shin
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea
| | - Jae Hyung Park
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| |
Collapse
|
45
|
Monti A, Vitagliano L, Caporale A, Ruvo M, Doti N. Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches. Int J Mol Sci 2023; 24:ijms24097842. [PMID: 37175549 PMCID: PMC10178479 DOI: 10.3390/ijms24097842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protein surfaces and the development of modulators of protein-protein interactions still represent a major challenge due to their highly dynamic and extensive interfacial areas. Over the years, multiple strategies including structural, computational, and combinatorial approaches have been developed to characterize PPI and to date, several successful examples of small molecules, antibodies, peptides, and aptamers able to modulate these interfaces have been determined. Notably, peptides are a particularly useful tool for inhibiting PPIs due to their exquisite potency, specificity, and selectivity. Here, after an overview of PPIs and of the commonly used approaches to identify and characterize them, we describe and evaluate the impact of chemical peptide libraries in medicinal chemistry with a special focus on the results achieved through recent applications of this methodology. Finally, we also discuss the role that this methodology can have in the framework of the opportunities, and challenges that the application of new predictive approaches based on artificial intelligence is generating in structural biology.
Collapse
Affiliation(s)
- Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), Strada Statale 14 km 163.5, Basovizza, 34149 Triese, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| |
Collapse
|
46
|
Choi HL, Yang HR, Shin HG, Hwang K, Kim JW, Lee JH, Ryu T, Jung Y, Lee S. Generation and Next-Generation Sequencing-Based Characterization of a Large Human Combinatorial Antibody Library. Int J Mol Sci 2023; 24:ijms24066011. [PMID: 36983085 PMCID: PMC10057307 DOI: 10.3390/ijms24066011] [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: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Antibody phage display is a key technology for the discovery and development of target-specific monoclonal antibodies (mAbs) for use in research, diagnostics, and therapy. The construction of a high-quality antibody library, with larger and more diverse antibody repertoires, is essential for the successful development of phage display-derived mAbs. In this study, a large human combinatorial single-chain variable fragment library (1.5 × 1011 colonies) was constructed from Epstein-Barr virus-infected human peripheral blood mononuclear cells stimulated with a combination of two of the activators of human B cells, the Toll-like receptor 7/8 agonist R848 and interleukin-2. Next-generation sequencing analysis with approximately 1.9 × 106 and 2.7 × 106 full-length sequences of heavy chain variable (VH) and κ light chain variable (Vκ) domains, respectively, revealed that the library consists of unique VH (approximately 94%) and Vκ (approximately 91%) sequences with greater diversity than germline sequences. Lastly, multiple unique mAbs with high affinity and broad cross-species reactivity could be isolated from the library against two therapeutically relevant target antigens, validating the library quality. These findings suggest that the novel antibody library we have developed may be useful for the rapid development of target-specific phage display-derived recombinant human mAbs for use in therapeutic and diagnostic applications.
Collapse
Affiliation(s)
- Hye Lim Choi
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Kyusang Hwang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ji Woong Kim
- Department of Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech Inc., Seoul 08507, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
| |
Collapse
|
47
|
He S, Wang J, Chen H, Qian Z, Hu K, Shi B, Wang J. A Competitive Panning Method Reveals an Anti-SARS-CoV-2 Nanobody Specific for an RBD-ACE2 Binding Site. Vaccines (Basel) 2023; 11:vaccines11020371. [PMID: 36851249 PMCID: PMC9964001 DOI: 10.3390/vaccines11020371] [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: 11/07/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 02/09/2023] Open
Abstract
Most neutralizing antibodies neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by directly blocking the interactions between the spike glycoprotein receptor-binding domain (RBD) and its receptor, human angiotensin-converting enzyme 2 (ACE2). Here, we report a novel nanobody (Nb) identified by an RBD-ACE2 competitive panning method that could specifically bind to the RBD of SARS-CoV-2 with a high affinity (EC50 = 0.03 nM) and successfully block the binding between the RBD and ACE2 recombinant protein. A structural simulation of the RBD-VHH complex also supports a mechanism of the Nb to block the interaction between the RBD and ACE2. A pseudovirus assay of the Nb showed it could neutralize the WT pseudovirus with high potency (IC50 = 0.026 μg/mL). Furthermore, we measured its binding to phages displaying RBDs of different SARS-CoV-2 variants and found that it could bind to recombinant phages displaying the RBD of beta and delta variants. This study also provides a method of phage library competitive panning, which could be useful for directly screening high-affinity antibodies targeting important functional regions.
Collapse
Affiliation(s)
- Siqi He
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jiali Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hanyi Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Keping Hu
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Andes Antibody Technology Hengshui LL Company, Hengshui 053000, China
| | - Bingjie Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen 518118, China
- Correspondence: ; Tel.: +86-10-5291-2186
| |
Collapse
|
48
|
Ljungars A, Laustsen AH. Neutralization capacity of recombinant antivenoms based on monoclonal antibodies and nanobodies. Toxicon 2023; 222:106991. [PMID: 36481349 DOI: 10.1016/j.toxicon.2022.106991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
| |
Collapse
|
49
|
Giang KA, Sidhu SS, Nilvebrant J. Construction of Synthetic Antibody Phage Display Libraries. Methods Mol Biol 2023; 2702:59-75. [PMID: 37679615 DOI: 10.1007/978-1-0716-3381-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Synthetic antibody libraries provide a vast resource of renewable antibody reagents that can rival natural antibodies and be rapidly isolated through controlled in vitro selections. Use of highly optimized human frameworks enables the incorporation of defined diversity at positions that are most likely to contribute to antigen recognition. This protocol describes the construction of synthetic antibody libraries based on a single engineered human autonomous variable heavy domain scaffold with diversity in all three complementarity-determining regions. The resulting libraries can be used to generate recombinant domain antibodies targeting a wide range of protein antigens using phage display. Furthermore, analogous methods can be used to construct antibody libraries based on larger antibody fragments or second-generation libraries aimed to fine-tune antibody characteristics including affinity, specificity, and manufacturability. The procedures rely on standard reagents and equipment available in most molecular biology laboratories.
Collapse
Affiliation(s)
- Kim Anh Giang
- Division of Protein Engineering, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Sachdev S Sidhu
- School of Pharmacy, University of Waterloo, Kitchener, ON, Canada
| | - Johan Nilvebrant
- Division of Protein Engineering, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
50
|
Zhai Y, Yu H, Liu X, Zhang M, Han R, Yin C, Liu X, Li H, Li J, Song X. Visual detection of Staphylococcus aureus based on immunomagnetic separation and polymerase spiral reaction. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|