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Hutchings CJ, Sato AK. Phage display technology and its impact in the discovery of novel protein-based drugs. Expert Opin Drug Discov 2024; 19:887-915. [PMID: 39074492 DOI: 10.1080/17460441.2024.2367023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/07/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Phage display technology is a well-established versatile in vitro display technology that has been used for over 35 years to identify peptides and antibodies for use as reagents and therapeutics, as well as exploring the diversity of alternative scaffolds as another option to conventional therapeutic antibody discovery. Such successes have been responsible for spawning a range of biotechnology companies, as well as many complementary technologies devised to expedite the drug discovery process and resolve bottlenecks in the discovery workflow. AREAS COVERED In this perspective, the authors summarize the application of phage display for drug discovery and provide examples of protein-based drugs that have either been approved or are being developed in the clinic. The amenability of phage display to generate functional protein molecules to challenging targets and recent developments of strategies and techniques designed to harness the power of sampling diverse repertoires are highlighted. EXPERT OPINION Phage display is now routinely combined with cutting-edge technologies to deep-mine antibody-based repertoires, peptide, or alternative scaffold libraries generating a wealth of data that can be leveraged, e.g. via artificial intelligence, to enable the potential for clinical success in the discovery and development of protein-based therapeutics.
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2
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Hennigan JN, Menacho-Melgar R, Sarkar P, Golovsky M, Lynch MD. Scalable, robust, high-throughput expression & purification of nanobodies enabled by 2-stage dynamic control. Metab Eng 2024; 85:116-130. [PMID: 39059674 DOI: 10.1016/j.ymben.2024.07.012] [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: 02/05/2024] [Revised: 05/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024]
Abstract
Nanobodies are single-domain antibody fragments that have garnered considerable use as diagnostic and therapeutic agents as well as research tools. However, obtaining pure VHHs, like many proteins, can be laborious and inconsistent. High level cytoplasmic expression in E. coli can be challenging due to improper folding and insoluble aggregation caused by reduction of the conserved disulfide bond. We report a systems engineering approach leveraging engineered strains of E. coli, in combination with a two-stage process and simplified downstream purification, enabling improved, robust, soluble cytoplasmic nanobody expression, as well as rapid cell autolysis and purification. This approach relies on the dynamic control over the reduction potential of the cytoplasm, incorporates lysis enzymes for purification, and can also integrate dynamic expression of protein folding catalysts. Collectively, the engineered system results in more robust growth and protein expression, enabling efficient scalable nanobody production, and purification from high throughput microtiter plates, to routine shake flask cultures and larger instrumented bioreactors. We expect this system will expedite VHH development.
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Affiliation(s)
| | | | - Payel Sarkar
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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3
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Jahandar-Lashaki S, Farajnia S, Faraji-Barhagh A, Hosseini Z, Bakhtiyari N, Rahbarnia L. Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update. Mol Biotechnol 2024:10.1007/s12033-024-01195-6. [PMID: 38822912 DOI: 10.1007/s12033-024-01195-6] [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: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.
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Affiliation(s)
- Samaneh Jahandar-Lashaki
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Aref Faraji-Barhagh
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Hosseini
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasim Bakhtiyari
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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4
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Li X, Kulakova L, Jones K, Toth EA, Mitchell MK, Mendez Q, Weiner MP, Fuerst TR. Site-directed neutralizing antibodies targeting structural sites on SARS-CoV-2 spike protein. N Biotechnol 2024; 80:27-36. [PMID: 38128698 PMCID: PMC10954356 DOI: 10.1016/j.nbt.2023.12.004] [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: 07/03/2023] [Revised: 10/20/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
'Epivolve' (epitope evolution) is an innovative paratope-evolving technology using a haptenated peptide or protein immunogen as a means of directing the in vivo immune response to specifically targeted sites at a one amino acid residue resolution. Guided by protein structural analysis, Epivolve technology was tested to develop site-directed neutralizing antibodies (nAbs) in a systematic fashion against the SARS-CoV-2 Receptor Binding Domain (RBD). Thirteen solvent-exposed sites covering the ACE2 receptor-binding interface were targeted. Immunogens composed of each targeted site were used to immunize rabbits in separate cohorts. In vivo site-directed immune responses against all 13 targets were demonstrated by B cell secreted IgG and recombinant IgG testing. One site, SL13 (Y505) which mutates from tyrosine to histidine in the SARS-CoV-2 Omicron variant, was chosen as a proof-of-concept (PoC) model for further functional monoclonal antibody development. Epivolve technology demonstrated the capabilities of generating pan-variant antibodies and nAbs against the SARS-CoV-2 primary strain and the Omicron variant.
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Affiliation(s)
- Xiaofeng Li
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA.
| | - Liudmila Kulakova
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Kezzia Jones
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | | | - Qiana Mendez
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Michael P Weiner
- Abbratech Inc., 25 Business Park Drive, Suite C, Branford, CT 06405, USA
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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5
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Yang ML, Yuan TZ, Chan KY, Ding L, Han Z, Franco H, Holliday C, Kannan S, Davidson E, Doranz BJ, Chandran K, Miller EH, Plante JA, Weaver SC, Cho E, Kailasan S, Marsalek L, Giang H, Abdiche Y, Sato AK. A VHH single-domain platform enabling discovery and development of monospecific antibodies and modular neutralizing bispecifics against SARS-CoV-2 variants. Antib Ther 2024; 7:164-176. [PMID: 38933534 PMCID: PMC11200683 DOI: 10.1093/abt/tbae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 06/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, escape coronavirus disease 2019 therapeutics and vaccines, and jeopardize public health. To combat SARS-CoV-2 antigenic escape, we developed a rapid, high-throughput pipeline to discover monospecific VHH antibodies and iteratively develop VHH-Fc-VHH bispecifics capable of neutralizing emerging SARS-CoV-2 variants. By panning VHH single-domain phage libraries against ancestral or beta spike proteins, we discovered high-affinity VHH antibodies with unique target epitopes. Combining two VHHs into a tetravalent bispecific construct conferred broad neutralization activity against multiple variants and was more resistant to antigenic escape than the monospecific antibody alone. Following the rise of the Omicron variant, a VHH in the original bispecific construct was replaced with another VHH discovered against the Omicron BA.1 receptor binding domain; the resulting bispecific exhibited neutralization against both BA.1 and BA.5 sublineage variants. A heavy chain-only tetravalent VHH-Fc-VHH bispecific platform derived from humanized synthetic libraries held a myriad of unique advantages: (i) synthetic preconstructed libraries minimized risk of liabilities and maximized discovery speed, (ii) VHH scaffolds allowed for a modular "plug-and-play" format that could be rapidly iterated upon as variants of concern arose, (iii) natural dimerization of single VHH-Fc-VHH polypeptides allowed for straightforward bispecific production and purification methods, and (iv) multivalent approaches enhanced avidity boosting effects and neutralization potency, and conferred more robust resistance to antigenic escape than monovalent approaches against specific variants. This iterative platform of rapid VHH discovery combined with modular bispecific design holds promise for long-term viral control efforts.
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Affiliation(s)
- Marisa L Yang
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Tom Z Yuan
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Kara Y Chan
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Lin Ding
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Zhen Han
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Hector Franco
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Carson Holliday
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Shruthi Kannan
- Integral Molecular, Philadelphia, PA 19104, United States
| | - Edgar Davidson
- Integral Molecular, Philadelphia, PA 19104, United States
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Emily Happy Miller
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Eunice Cho
- Integrated Biotherapeutics, Rockville, MD 20850, United States
| | - Shweta Kailasan
- Integrated Biotherapeutics, Rockville, MD 20850, United States
| | | | - Hoa Giang
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
| | - Yasmina Abdiche
- Revelar Biotherapeutics, Inc., Bethesda, MD 20817, United States
| | - Aaron K Sato
- Biopharma Department, Twist Bioscience, South San Francisco, CA 94080, United States
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Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024; 11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [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: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.
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Affiliation(s)
- Doo Nam Kim
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Andrew D McNaughton
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
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Lee RB, Maddineni S, Landry M, Diaz C, Tashfeen A, Yamada-Hunter SA, Mackall CL, Beinat C, Sunwoo JB, Cochran JR. An engineered NKp46 antibody for construction of multi-specific NK cell engagers. Protein Eng Des Sel 2024; 37:gzae013. [PMID: 39163262 PMCID: PMC11359164 DOI: 10.1093/protein/gzae013] [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: 04/10/2024] [Revised: 08/04/2024] [Indexed: 08/22/2024] Open
Abstract
Recent developments in cancer immunotherapy have highlighted the potential of harnessing natural killer (NK) cells in the treatment of neoplastic malignancies. Of these, bispecific antibodies, and NK cell engager (NKCE) protein therapeutics in particular, have been of interest. Here, we used phage display and yeast surface display to engineer RLN131, a unique cross-reactive antibody that binds to human, mouse, and cynomolgus NKp46, an activating receptor found on NK cells. RLN131 induced proliferation and activation of primary NK cells, and was used to create bispecific NKCE constructs of varying configurations and valency. All NKCEs were able to promote greater NK cell cytotoxicity against tumor cells than an unmodified anti-CD20 monoclonal antibody, and activity was observed irrespective of whether the constructs contained a functional Fc domain. Competition binding and fine epitope mapping studies were used to demonstrate that RLN131 binds to a conserved epitope on NKp46, underlying its species cross-reactivity.
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Affiliation(s)
- Robert B Lee
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
| | - Sainiteesh Maddineni
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Madeleine Landry
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, United States
| | - Celeste Diaz
- Cancer Biology Program, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Aanya Tashfeen
- Department of Electrical Engineering, Stanford University, 350 Jane Stanford Way, Stanford, CA, 94305, United States
| | - Sean A Yamada-Hunter
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Corinne Beinat
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, United States
| | - John B Sunwoo
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, United States
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, United States
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8
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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.
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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
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9
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State of the art in epitope mapping and opportunities in COVID-19. Future Sci OA 2023; 16:FSO832. [PMID: 36897962 PMCID: PMC9987558 DOI: 10.2144/fsoa-2022-0048] [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: 07/29/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The understanding of any disease calls for studying specific biological structures called epitopes. One important tool recently drawing attention and proving efficiency in both diagnosis and vaccine development is epitope mapping. Several techniques have been developed with the urge to provide precise epitope mapping for use in designing sensitive diagnostic tools and developing rpitope-based vaccines (EBVs) as well as therapeutics. In this review, we will discuss the state of the art in epitope mapping with a special emphasis on accomplishments and opportunities in combating COVID-19. These comprise SARS-CoV-2 variant analysis versus the currently available immune-based diagnostic tools and vaccines, immunological profile-based patient stratification, and finally, exploring novel epitope targets for potential prophylactic, therapeutic or diagnostic agents for COVID-19.
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Chang MR, Ke H, Losada Miguéns L, Coherd C, Nguyen K, Kamkaew M, Johnson R, Storm N, Honko A, Zhu Q, Griffiths A, Marasco WA. The variable conversion of neutralizing anti-SARS-CoV-2 single-chain antibodies to IgG provides insight into RBD epitope accessibility. Protein Eng Des Sel 2023; 36:gzad008. [PMID: 37561410 PMCID: PMC10505556 DOI: 10.1093/protein/gzad008] [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: 03/14/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 08/11/2023] Open
Abstract
Monoclonal antibody (mAb) therapies have rapidly become a powerful class of therapeutics with applications covering a diverse range of clinical indications. Though most widely used for the treatment of cancer, mAbs are also playing an increasing role in the defense of viral infections, most recently with palivizumab for prevention and treatment of severe RSV infections in neonatal and pediatric populations. In addition, during the COVID-19 pandemic, mAbs provided a bridge to the rollout of vaccines; however, their continued role as a therapeutic option for those at greatest risk of severe disease has become limited due to the emergence of neutralization resistant Omicron variants. Although there are many techniques for the identification of mAbs, including single B cell cloning and immunization of genetically engineered mice, the low cost, rapid throughput and technological simplicity of antibody phage display has led to its widespread adoption in mAb discovery efforts. Here we used our 27-billion-member naïve single-chain antibody (scFv) phage library to identify a panel of neutralizing anti-SARS-CoV-2 scFvs targeting diverse epitopes on the receptor binding domain (RBD). Although typically a routine process, we found that upon conversion to IgG, a number of our most potent clones failed to maintain their neutralization potency. Kinetic measurements confirmed similar affinity to the RBD; however, mechanistic studies provide evidence that the loss of neutralization is a result of structural limitations likely arising from initial choice of panning antigen. Thus this work highlights a risk of scFv-phage panning to mAb conversion and the importance of initial antigen selection.
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Affiliation(s)
- Matthew R Chang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hanzhong Ke
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Losada Miguéns
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christian Coherd
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Katrina Nguyen
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maliwan Kamkaew
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rebecca Johnson
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nadia Storm
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anna Honko
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Quan Zhu
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Wayne A Marasco
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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11
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Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Front Immunol 2022; 13:965446. [PMID: 36189235 PMCID: PMC9524272 DOI: 10.3389/fimmu.2022.965446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 1011 diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and 9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.
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Affiliation(s)
- Dmitri Dormeshkin
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National academy of Sciences of Belarus, Minsk, Belarus
- *Correspondence: Dmitri Dormeshkin,
| | - Michail Shapira
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National academy of Sciences of Belarus, Minsk, Belarus
| | - Simon Dubovik
- Department of Biology, Belarusian State University, Minsk, Belarus
| | - Anton Kavaleuski
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mikalai Katsin
- Imunovakcina, UAB, Vilnius, Lithuania
- Immunofusion, LLC, Minsk, Belarus
| | - Alexandr Migas
- Imunovakcina, UAB, Vilnius, Lithuania
- Immunofusion, LLC, Minsk, Belarus
| | | | - Sergei Semyonov
- Laboratory of Biosafety With Pathogens Collection, Republican Research and Practical Center for Epidemiology & Microbiology, Minsk, Belarus
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12
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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