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Alvarez JAE, Dean SN. TEMPRO: nanobody melting temperature estimation model using protein embeddings. Sci Rep 2024; 14:19074. [PMID: 39154093 PMCID: PMC11330463 DOI: 10.1038/s41598-024-70101-6] [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: 06/21/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024] Open
Abstract
Single-domain antibodies (sdAbs) or nanobodies have received widespread attention due to their small size (~ 15 kDa) and diverse applications in bio-derived therapeutics. As many modern biotechnology breakthroughs are applied to antibody engineering and design, nanobody thermostability or melting temperature (Tm) is crucial for their successful utilization. In this study, we present TEMPRO which is a predictive modeling approach for estimating the Tm of nanobodies using computational methods. Our methodology integrates various nanobody biophysical features to include Evolutionary Scale Modeling (ESM) embeddings, NetSurfP3 structural predictions, pLDDT scores per sdAb region from AlphaFold2, and each sequence's physicochemical characteristics. This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tm values from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tm of sdAbs with mean absolute error (MAE) of 4.03 °C and root mean squared error (RMSE) of 5.66 °C, thus offering a valuable tool for the optimization of nanobodies for various biomedical and therapeutic applications. Moreover, we have validated the models' performance using experimentally determined Tms from nanobodies not found in NbThermo. This predictive model not only enhances nanobody thermostability prediction, but also provides a useful perspective of using embeddings as a tool for facilitating a broader applicability of downstream protein analyses.
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Affiliation(s)
- Jerome Anthony E Alvarez
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Scott N Dean
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA.
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2
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Rodriguez Rodriguez ER, Nordvang RT, Petersson M, Rendsvig JKH, Arendrup EW, Fernández Quintero ML, Jenkins TP, Laustsen AH, Thrane SW. Fit-for-purpose heterodivalent single-domain antibody for gastrointestinal targeting of toxin B from Clostridium difficile. Protein Sci 2024; 33:e5035. [PMID: 38923049 PMCID: PMC11201815 DOI: 10.1002/pro.5035] [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: 12/11/2023] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024]
Abstract
Single-domain antibodies (sdAbs), such as VHHs, are increasingly being developed for gastrointestinal (GI) applications against pathogens to strengthen gut health. However, what constitutes a suitable developability profile for applying these proteins in a gastrointestinal setting remains poorly explored. Here, we describe an in vitro methodology for the identification of sdAb derivatives, more specifically divalent VHH constructs, that display extraordinary developability properties for oral delivery and functionality in the GI environment. We showcase this by developing a heterodivalent VHH construct that cross-inhibits the toxic activity of the glycosyltransferase domains (GTDs) from three different toxinotypes of cytotoxin B (TcdB) from lineages of Clostridium difficile. We show that the VHH construct possesses high stability and binding activity under gastric conditions, in the presence of bile salts, and at high temperatures. We suggest that the incorporation of early developability assessment could significantly aid in the efficient discovery of VHHs and related constructs fit for oral delivery and GI applications.
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Affiliation(s)
| | | | - Marcus Petersson
- Bactolife A/SCopenhagen EastDenmark
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | | | | | | | - Timothy P. Jenkins
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Andreas H. Laustsen
- Bactolife A/SCopenhagen EastDenmark
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
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3
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Liu ML, Liang XM, Jin MY, Huang HW, Luo L, Wang H, Shen X, Xu ZL. Food-Borne Biotoxin Neutralization in Vivo by Nanobodies: Current Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10753-10771. [PMID: 38706131 DOI: 10.1021/acs.jafc.4c02257] [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: 05/07/2024]
Abstract
Food-borne biotoxins from microbes, plants, or animals contaminate unclean, spoiled, and rotten foods, posing significant health risks. Neutralizing such toxins is vital for human health, especially after food poisoning. Nanobodies (Nbs), a type of single-domain antibodies derived from the genetic cloning of a variable domain of heavy chain antibodies (VHHs) in camels, offer unique advantages in toxin neutralization. Their small size, high stability, and precise binding enable effective neutralization. The use of Nbs in neutralizing food-borne biotoxins offers numerous benefits, and their genetic malleability allows tailored optimization for diverse toxins. As nanotechnology continues to evolve and improve, Nbs are poised to become increasingly efficient and safer tools for toxin neutralization, playing a pivotal role in safeguarding human health and environmental safety. This review not only highlights the efficacy of these agents in neutralizing toxins but also proposes innovative solutions to address their current challenges. It lays a solid foundation for their further development in this crucial field and propels their commercial application, thereby contributing significantly to advancements in this domain.
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Affiliation(s)
- Min-Ling Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Min Liang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Ming-Yu Jin
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
- School of Life and Health Technology, Dongguan, University of Technology, Dongguan 523808, China
| | - Hui-Wei Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lin Luo
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
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4
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Chen J, Yao G, Huang C, Shen Q, Miao J, Jia L. Biparatopic Nanobody-Based Immunosorbent for the Highly Selective Elimination of Tumor Necrosis Factor-α. ACS Biomater Sci Eng 2024; 10:1788-1795. [PMID: 38364210 DOI: 10.1021/acsbiomaterials.3c01765] [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: 02/18/2024]
Abstract
Removing the overexpressed TNF-α by hemoperfusion positively affects clinical treatments for diseases such as autoimmune disease and sepsis. However, clearance ratios of adsorbents targeting TNF-α were limited by the extremely low concentration of TNF-α (mostly <1000 ng/L in sepsis) and hydrophobic interactions. In this work, biparatopic nanobodies (NbC21) with a high affinity of 19.9 pM, which bind to two distinct sites of TNF-α, were constructed as high-affinity ligands for the immunosorbent. The theoretical maximum adsorption capacity estimated from the Langmuir isotherm was up to 18.22 mg/g gel. The prepared immunosorbent (NbC21-sorbent) had an outstanding TNF-α clearance ratio of approximately 96% during the dynamic adsorption test, with a sorbent-to-serum ratio of 1:1000. Additionally, it demonstrated favorable hemocompatibility and a prolonged storage capability. The results indicated that the biparatopic nanobody immunosorbent exhibited significant potential for clinical applications as it met the stringent criteria for both efficacy and safety.
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Affiliation(s)
- Jiewen Chen
- MOE Key Laboratory of Bio-Intelligent Manufacturing, Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Guangshuai Yao
- MOE Key Laboratory of Bio-Intelligent Manufacturing, Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Chundong Huang
- Kangyuan Biomedical Tech. (Dalian) Co., Ltd., Building 9, No. 57, Xinda Street, Dalian High-tech Zone, Dalian 116085, Liaoning, China
| | - Qidong Shen
- MOE Key Laboratory of Bio-Intelligent Manufacturing, Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Jian Miao
- The Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, Liaoning, China
| | - Lingyun Jia
- MOE Key Laboratory of Bio-Intelligent Manufacturing, Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116024, Liaoning, China
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Dhehibi A, Terrak M, Seddik MM, Hammadi M, Salhi I. Development of a bispecific Nanobody anti-F17 fimbria as a potential therapeutic tool. Protein Expr Purif 2024; 215:106411. [PMID: 38056514 DOI: 10.1016/j.pep.2023.106411] [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: 10/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
Pathogenic strains of Escherichia coli F17+ are associated with various intestinal and extra-intestinal pathologies, including diarrhea, and result in significant animal mortality. These infections rely on the expression of virulence factors, such as F17 fimbriae, for adhesion. F17 fimbriae form a protective layer on the surface of E. coli bacteria, consisting of a major structural subunit, F17A, and a minor functional subunit, F17G. Because of the evolution of bacterial resistance, conventional antibiotic treatments have limited efficacy. Therefore, there is a pressing need to develop novel therapeutic tools. In this study, we cloned and produced the F17G protein. We then immunized a camel with the purified F17G protein and constructed a VHH library consisting of 2 × 109 clones. The library was then screened against F17G protein using phage display technology. Through this process, we identified an anti-F17G nanobody that was subsequently linked, via a linker, to an anti-F17A nanobody, resulting in the creation of an effective bispecific nanobody. Comprehensive characterization of this bispecific nanobody demonstrated excellent production, specific binding capacity to both recombinant forms of the two F17 antigens and the E. coli F17+ strain, remarkable stability in camel serum, and superior resistance to pepsin protease. The successful generation of this bispecific nanobody with excellent production, specific binding capacity and stability highlights its potential as a valuable tool for fighting infections caused by pathogenic E. coli F17+ strain.
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Affiliation(s)
- Asma Dhehibi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia.
| | - Mohammed Terrak
- InBioS-Centre for Protein Engineering, University of Liege, B-4000, Liege, Belgium
| | - Mabrouk-Mouldi Seddik
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
| | - Mohamed Hammadi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
| | - Imed Salhi
- Livestock and Wildlife Laboratory (LR16IRA04), Arid Lands Institute (I.R.A), University of Gabès, Médenine, 4119, Tunisia
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Deng Y, Liu J, Lu Y, Fan X, Yang Y, Xu Y, Qin X, Nian R, Liu W. Novel Polystyrene-Binding Nanobody for Enhancing Immunoassays: Insights into Affinity, Immobilization, and Application Potential. Anal Chem 2024; 96:1597-1605. [PMID: 38235613 DOI: 10.1021/acs.analchem.3c04375] [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: 01/19/2024]
Abstract
Nanobodies, which represent the next generation of antibodies due to their unique properties, face a significant limitation in their poor physical adsorption on solid supports. In this study, we successfully discovered polystyrene binding nanobodies from a synthetic nanobody library. Notably, bivalent nanobody B2 exhibited high affinity for polystyrene (0.7 nM for ELISA saturation binding analysis and 15.6 nM for isothermal titration calorimetry), displaying a pH-dependent behavior. Remarkably, hydrophobic and electrostatic interactions contribute minimally to the binding process. Molecular modeling provided insights into the interaction between B2 and polystyrene, revealing that the Trp51 residue within the CDR2 loop formed an aromatic H-bond with polystyrene at a distance of 2.74 Å, thus explaining the observed reduction in B2 affinity caused by Trp51 mutations. To explore B2's potential in protein immobilization, we constructed a bispecific nanobody by fusing B2 to an anticarcinoembryonic antigen nanobody 11C12, which cannot be immobilized on polystyrene through passive adsorption. Remarkably, the fusion construct achieved effective immobilization on polystyrene within 5 min by passing the need for periplasmic protein purification despite its low expression level. Moreover, the fusion construct demonstrated excellent linearity in the chemiluminescent enzyme immunoassay. For the first time, this study reports a simplified and seamless platform for the oriented immobilization of nanobody. Importantly, the entire process eliminated the need for protein purification, enabling efficient and rapid immobilization of fusion proteins directly from crude cell extracts, even when the expression level was low. Our developed process dramatically reduced the processing time from 2.5 days to just 5 min.
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Affiliation(s)
- Yang Deng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, No 19(A), Yuquan Road, Beijing 100049, China
| | - Jinyan Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yaoping Lu
- WEGO Holding Co., Ltd., No. 18, Xingshan Road, Torch Hi-tech Science Park, Weihai 264210, China
| | - Xiying Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yuansheng Yang
- Agency for Science, Technology and Research (A*STAR), Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Yaozheng Xu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
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Chance R, Kang AS. Eukaryotic ribosome display for antibody discovery: A review. Hum Antibodies 2024; 32:107-120. [PMID: 38788063 DOI: 10.3233/hab-240001] [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: 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.
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8
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Mardani-Jouneghani R, Irani S, Habibi-Anbouhi M, Behdani M. Development and Characterization of a Novel Single-Chain Antibody Against B-Cell Activating Factor. Mol Biotechnol 2023; 65:1968-1978. [PMID: 36906729 DOI: 10.1007/s12033-023-00700-7] [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: 10/08/2022] [Accepted: 02/14/2023] [Indexed: 03/13/2023]
Abstract
As a member of the tumor necrosis factor (TNF) superfamily, the B-cell activating factor (BAFF) plays a crucial role in B-cell survival and differentiation. Overexpression of this protein has been closely linked to autoimmune disorders and some B-cell malignancies. Using monoclonal antibodies (mAbs) against the BAFF soluble domain appears to be a complementary treatment for some of these diseases. This study aimed to produce and develop a specific Nanobody (Nb), a variable camelid antibody domain, against the soluble domain of BAFF protein. After camel immunization with recombinant protein and preparing cDNA from total RNAs separated from camel lymphocytes, an Nb library was developed. Individual colonies capable of binding selectively to rBAFF were obtained by periplasmic-ELISA, sequenced, and expressed in a bacterial expression system. The specificity and affinity of selected Nb were determined and its target identification and functionality were evaluated using flow cytometry.
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Affiliation(s)
- Rasoul Mardani-Jouneghani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Biotechnology Research Centre, Venom and Biotherapeutics Molecules Laboratory, Pasteur Institute of Iran, Tehran, 1316543551, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Mahdi Behdani
- Biotechnology Research Centre, Venom and Biotherapeutics Molecules Laboratory, Pasteur Institute of Iran, Tehran, 1316543551, Iran.
- Zoonoses Research Centre, Pasteur Institute of Iran, Amol, Iran.
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Kim DY, Kandalaft H, Lowden MJ, Yang Q, Rossotti MA, Robotham A, Kelly JF, Hussack G, Schrag JD, Henry KA, Tanha J. Sequence tolerance of immunoglobulin variable domain framework regions to noncanonical intradomain disulfide linkages. J Biol Chem 2023; 299:105278. [PMID: 37742917 PMCID: PMC10641266 DOI: 10.1016/j.jbc.2023.105278] [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: 06/15/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Most immunoglobulin (Ig) domains bear only a single highly conserved canonical intradomain, inter-β-sheet disulfide linkage formed between Cys23-Cys104, and incorporation of rare noncanonical disulfide linkages at other locations can enhance Ig domain stability. Here, we exhaustively surveyed the sequence tolerance of Ig variable (V) domain framework regions (FRs) to noncanonical disulfide linkages. Starting from a destabilized VH domain lacking a Cys23-Cys104 disulfide linkage, we generated and screened phage-displayed libraries of engineered VHs, bearing all possible pairwise combinations of Cys residues in neighboring β-strands of the Ig fold FRs. This approach identified seven novel Cys pairs in VH FRs (Cys4-Cys25, Cys4-Cys118, Cys5-Cys120, Cys6-Cys119, Cys22-Cys88, Cys24-Cys86, and Cys45-Cys100; the international ImMunoGeneTics information system numbering), whose presence rescued domain folding and stability. Introduction of a subset of these noncanonical disulfide linkages (three intra-β-sheet: Cys4-Cys25, Cys22-Cys88, and Cys24-Cys86, and one inter-β-sheet: Cys6-Cys119) into a diverse panel of VH, VL, and VHH domains enhanced their thermostability and protease resistance without significantly impacting expression, solubility, or binding to cognate antigens. None of the noncanonical disulfide linkages identified were present in the natural human VH repertoire. These data reveal an unexpected permissiveness of Ig V domains to noncanonical disulfide linkages at diverse locations in FRs, absent in the human repertoire, whose presence is compatible with antigen recognition and improves domain stability. Our work represents the most complete assessment to date of the role of engineered noncanonical disulfide bonding within FRs in Ig V domain structure and function.
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Affiliation(s)
- Dae Young Kim
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Hiba Kandalaft
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Michael J Lowden
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Qingling Yang
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Martin A Rossotti
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - John F Kelly
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Greg Hussack
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Joseph D Schrag
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Quebec, Canada
| | - Kevin A Henry
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jamshid Tanha
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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10
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Kunz S, Durandy M, Seguin L, Feral CC. NANOBODY ® Molecule, a Giga Medical Tool in Nanodimensions. Int J Mol Sci 2023; 24:13229. [PMID: 37686035 PMCID: PMC10487883 DOI: 10.3390/ijms241713229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Although antibodies remain the most widely used tool for biomedical research, antibody technology is not flawless. Innovative alternatives, such as Nanobody® molecules, were developed to address the shortcomings of conventional antibodies. Nanobody® molecules are antigen-binding variable-domain fragments derived from the heavy-chain-only antibodies of camelids (VHH) and combine the advantageous properties of small molecules and monoclonal antibodies. Nanobody® molecules present a small size (~15 kDa, 4 nm long and 2.5 nm wide), high solubility, stability, specificity, and affinity, ease of cloning, and thermal and chemical resistance. Recombinant production in microorganisms is cost-effective, and VHH are also building blocks for multidomain constructs. These unique features led to numerous applications in fundamental research, diagnostics, and therapy. Nanobody® molecules are employed as biomarker probes and, when fused to radioisotopes or fluorophores, represent ideal non-invasive in vivo imaging agents. They can be used as neutralizing agents, receptor-ligand antagonists, or in targeted vehicle-based drug therapy. As early as 2018, the first Nanobody®, Cablivi (caplacizumab), a single-domain antibody (sdAb) drug developed by French pharmaceutical giant Sanofi for the treatment of adult patients with acquired thrombocytopenic purpura (aTTP), was launched. Nanobody® compounds are ideal tools for further development in clinics for diagnostic and therapeutic purposes.
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Affiliation(s)
- Sarah Kunz
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
- Department of Oncology, Sanofi Research Center, 94400 Vitry-sur-Seine, France
| | - Manon Durandy
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
| | - Laetitia Seguin
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
| | - Chloe C. Feral
- Université Côte d’Azur, CNRS UMR7284, INSERM U1081, IRCAN, 06107 Nice, France; (S.K.); (M.D.); (L.S.)
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11
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Hurley K, Cao M, Huang H, Wang Y. Targeted Alpha Therapy (TAT) with Single-Domain Antibodies (Nanobodies). Cancers (Basel) 2023; 15:3493. [PMID: 37444603 DOI: 10.3390/cancers15133493] [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: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The persistent threat of cancer necessitates the development of improved and more efficient therapeutic strategies that limit damage to healthy tissues. Targeted alpha therapy (TαT), a novel form of radioimmuno-therapy (RIT), utilizes a targeting vehicle, commonly antibodies, to deliver high-energy, but short-range, alpha-emitting particles specifically to cancer cells, thereby reducing toxicity to surrounding normal tissues. Although full-length antibodies are often employed as targeting vehicles for TαT, their high molecular weight and the presence of an Fc-region lead to a long blood half-life, increased bone marrow toxicity, and accumulation in other tissues such as the kidney, liver, and spleen. The discovery of single-domain antibodies (sdAbs), or nanobodies, naturally occurring in camelids and sharks, has introduced a novel antigen-specific vehicle for molecular imaging and TαT. Given that nanobodies are the smallest naturally occurring antigen-binding fragments, they exhibit shorter relative blood half-lives, enhanced tumor uptake, and equivalent or superior binding affinity and specificity. Nanobody technology could provide a viable solution for the off-target toxicity observed with full-length antibody-based TαT. Notably, the pharmacokinetic properties of nanobodies align better with the decay characteristics of many short-lived α-emitting radionuclides. This review aims to encapsulate recent advancements in the use of nanobodies as a vehicle for TαT.
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Affiliation(s)
- Kate Hurley
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Meiyun Cao
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Haiming Huang
- Research Center, Forlong Biotechnology Inc., Suzhou 215004, China
| | - Yi Wang
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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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: 8] [Impact Index Per Article: 8.0] [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.
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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.
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13
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Yu S, Zhang L, Wang A, Jin Y, Zhou D. Nanobodies: the Potential Application in Bacterial Treatment and Diagnosis. Biochem Pharmacol 2023:115640. [PMID: 37315818 DOI: 10.1016/j.bcp.2023.115640] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023]
Abstract
An infection caused by bacteria is one of the main factors that poses a threat to human health. A recent report from the World Health Organization (WHO) has highlighted that bacteria that cause blood infections have become increasingly drug-resistant. Therefore, it is crucial to research and develop new techniques for detecting and treating these infections. Since their discovery, nanobodies have exhibited numerous outstanding biological properties. They are easy to express, modify, and have high stability, robust permeability and low immunogenicity, all of which indicate their potential as a substitute. Nanobodies have been utilized in a variety of studies on viruses and cancer. This article primarily focuses on nanobodies and introduces their characteristics and application in the diagnosis and treatment of bacterial infections.
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Affiliation(s)
- Siyuan Yu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Xianyang, China
| | - Lu Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Xianyang, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, China; Department of Animal Engineering, Yangling Vocational&Technical College, Xianyang, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Xianyang, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Xianyang, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, China.
| | - Dong Zhou
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Xianyang, China
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14
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Santos A, Macedo de Souza Brandão AP, Hryniewicz BM, Abreu H, Bach-Toledo L, Schuster da Silva S, Deller AE, Rogerio VZ, Baêta Rodrigues DS, Hiraiwa PM, Guimarães BG, Marchesi LF, Carvalho de Oliveira J, Gradia DF, Soares FLF, Zanchin NIT, Camargo de Oliveira C, Vidotti M. COVID-19 impedimetric biosensor based on polypyrrole nanotubes, nickel hydroxide and VHH antibody fragment: specific, sensitive, and rapid viral detection in saliva samples. MATERIALS TODAY. CHEMISTRY 2023; 30:101597. [PMID: 37284350 PMCID: PMC10236006 DOI: 10.1016/j.mtchem.2023.101597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/30/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023]
Abstract
SARS-CoV-2 rapid spread required urgent, accurate, and prompt diagnosis to control the virus dissemination and pandemic management. Several sensors were developed using different biorecognition elements to obtain high specificity and sensitivity. However, the task to achieve these parameters in combination with fast detection, simplicity, and portability to identify the biorecognition element even in low concentration remains a challenge. Therefore, we developed an electrochemical biosensor based on polypyrrole nanotubes coupled via Ni(OH)2 ligation to an engineered antigen-binding fragment of heavy chain-only antibodies (VHH) termed Sb#15. Herein we report Sb#15-His6 expression, purification, and characterization of its interaction with the receptor-binding domain (RBD) of SARS-CoV-2 in addition to the construction and validation of a biosensor. The recombinant Sb#15 is correctly folded and interacts with the RBD with a dissociation constant (KD) of 27.1 ± 6.4 nmol/L. The biosensing platform was developed using polypyrrole nanotubes and Ni(OH)2, which can properly orientate the immobilization of Sb#15-His6 at the electrode surface through His-tag interaction for the sensitive SARS-CoV-2 antigen detection. The quantification limit was determined as 0.01 pg/mL using recombinant RBD, which was expressively lower than commercial monoclonal antibodies. In pre-characterized saliva, both Omicron and Delta SARS-CoV-2 were accurately detected only in positive samples, meeting all the requirements recommended by the World Health Organization for in vitro diagnostics. A low sample volume of saliva is needed to perform the detection, providing results within 15 min without further sample preparations. In summary, a new perspective allying recombinant VHHs with biosensor development and real sample detection was explored, addressing the need for accurate, rapid, and sensitive biosensors.
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Affiliation(s)
- A Santos
- Laboratory of Inflammatory and Neoplastic Cells, Cell Biology Department, Section of Biological Sciences - Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - A P Macedo de Souza Brandão
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - B M Hryniewicz
- Grupo de Pesquisa em Macromoléculas e Interfaces, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - H Abreu
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics, Department of Genetics, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, Brazil
| | - L Bach-Toledo
- Grupo de Pesquisa em Macromoléculas e Interfaces, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
- Centro de Tecnologia da Informação Renato Archer (CTI), Rod. D. Pedro I, KM143.6, 13069-901, Campinas, SP, Brazil
| | - S Schuster da Silva
- Laboratory of Inflammatory and Neoplastic Cells, Cell Biology Department, Section of Biological Sciences - Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - A E Deller
- Grupo de Pesquisa em Macromoléculas e Interfaces, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - V Z Rogerio
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - D S Baêta Rodrigues
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - P M Hiraiwa
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - B G Guimarães
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - L F Marchesi
- Grupo de Estudos em Espectroscopia de Impedância Eletroquímica (GEIS), Universidade Tecnológica Federal Do Paraná, Rua Dr. Washington Subtil Chueire, 330 - Jd. Carvalho, CEP 84017-220, Ponta Grossa, PR, Brazil
| | - J Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics, Department of Genetics, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, Brazil
| | - D F Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Postgraduate Program in Genetics, Department of Genetics, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, Brazil
| | - F L F Soares
- Grupo de Pesquisa em Macromoléculas e Interfaces, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - N I T Zanchin
- Laboratory of Structural Biology and Protein Engineering, Carlos Chagas Institute, FIOCRUZ Paraná, 81350-010, Curitiba, PR, Brazil
| | - C Camargo de Oliveira
- Laboratory of Inflammatory and Neoplastic Cells, Cell Biology Department, Section of Biological Sciences - Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
| | - M Vidotti
- Grupo de Pesquisa em Macromoléculas e Interfaces, Universidade Federal do Paraná (UFPR), 81531-980, Curitiba, PR, Brazil
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15
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Valdés-Tresanco MS, Valdés-Tresanco ME, Molina-Abad E, Moreno E. NbThermo: a new thermostability database for nanobodies. Database (Oxford) 2023; 2023:baad021. [PMID: 37042467 PMCID: PMC10091358 DOI: 10.1093/database/baad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/08/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
We present NbThermo-a first-in-class database that collects melting temperatures (Tm), amino acid sequences and several other categories of useful data for hundreds of nanobodies (Nbs), compiled from an extensive literature search. This so-far unique database currently contains up-to-date, manually curated data for 564 Nbs. It represents a contribution to efforts aimed at developing new algorithms for reliable Tm prediction to assist Nb engineering for a wide range of applications of these unique biomolecules. Nbs from the two most common source organisms-llama and camel-show similar distributions of melting temperatures. A first exploratory research that takes advantage of this large data collection evidences that understanding the structural bases of Nb thermostability is a complex task, since there are no apparent differences in sequence patterns between the frameworks of Nbs with lower and higher melting temperatures, indicating that the highly variable loops play a relevant role in defining Nb thermostability. Database URL https://valdes-tresanco-ms.github.io/NbThermo.
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Affiliation(s)
- Mario S Valdés-Tresanco
- Faculty of Basic Sciences, University of Medellin, Cra. 87 No. 30-65, Medellin 050026, Colombia
| | - Mario E Valdés-Tresanco
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, 2500 University Drive N.W, Calgary, AB T2N 1N4, Canada
| | | | - Ernesto Moreno
- Faculty of Basic Sciences, University of Medellin, Cra. 87 No. 30-65, Medellin 050026, Colombia
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16
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Jin BK, Odongo S, Radwanska M, Magez S. NANOBODIES®: A Review of Diagnostic and Therapeutic Applications. Int J Mol Sci 2023; 24:5994. [PMID: 36983063 PMCID: PMC10057852 DOI: 10.3390/ijms24065994] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
NANOBODY® (a registered trademark of Ablynx N.V) molecules (Nbs), also referred to as single domain-based VHHs, are antibody fragments derived from heavy-chain only IgG antibodies found in the Camelidae family. Due to their small size, simple structure, high antigen binding affinity, and remarkable stability in extreme conditions, nanobodies possess the potential to overcome several of the limitations of conventional monoclonal antibodies. For many years, nanobodies have been of great interest in a wide variety of research fields, particularly in the diagnosis and treatment of diseases. This culminated in the approval of the world's first nanobody based drug (Caplacizumab) in 2018 with others following soon thereafter. This review will provide an overview, with examples, of (i) the structure and advantages of nanobodies compared to conventional monoclonal antibodies, (ii) methods used to generate and produce antigen-specific nanobodies, (iii) applications for diagnostics, and (iv) ongoing clinical trials for nanobody therapeutics as well as promising candidates for clinical development.
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Affiliation(s)
- Bo-kyung Jin
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
| | - Steven Odongo
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
- Center for Biosecurity and Global Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala 7062, Uganda
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon 21985, Republic of Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
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17
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Kiyose N, Miyazaki N, Furuhata K, Ito Y. Sensitive immunoassay of Legionella using multivalent conjugates of engineered VHHs. J Biochem 2023; 173:185-195. [PMID: 36525357 DOI: 10.1093/jb/mvac102] [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: 03/18/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
VHH antibodies or nanobodies, which are antigen-binding domains of heavy chain antibodies from camelid species, have several advantageous characteristics, including compact molecular size, high productibility in bacteria and easy engineering for functional improvement. Focusing on these advantages of VHHs, we attempted to establish an immunoassay system for detection of Legionella, the causative pathogen of Legionnaires' disease. A VHH phage display library was constructed using cDNA from B cells of alpacas immunized with Legionella pneumophila serogroup1 (LpSG1). Through biopanning, two specific VHH clones were isolated and used to construct a Legionella detection system based on the latex agglutination assay. After engineering the VHHs and improving the assay system, the sensitive detection system was successfully established for the LpSG1 antigen. The immunoassay developed in this study should be useful in easy and sensitive detection of Legionella, the causative agent of Legionnaires' disease, which is a potentially fatal pneumonia.
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Key Words
- VHH.Abbreviations: Abs, antibodies; BSA, bovine serum albumin; CDR, complementarity determining region; CFU, colony forming unit; DBCO, dibenzylcyclooctyne; ELISA, enzyme-linked immunosorbent assay; FR, framework region; HcAbs, heavy chain antibodies; KLH, keyhole limpet hemocyanin; LpSG1, Legionella pneumophila serogroup1; MALDI-TOFMS, matrix assisted laser desorption/ionization time of flight mass spectrometry; NHS, N-hydroxysuccinimide; PBMC, peripheral blood mononuclear cells; PCR, polymerase chain reaction; RT-PCR, reverse transcription PCR; SDS-PAGE, sodium do-decyl sulphate-polyacrylamide gel electrophoresis; TMB, 3,3′,5,5′-tetramethylbenzidine solution
- alpaca
- antibody
- engineering
- immunoassay
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Affiliation(s)
- Norihiko Kiyose
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan.,ARK Resource Co., Ltd., 383-2, Nakahara-machi, Nishi-ku, Kumamoto 861-5271, Japan
| | - Nobuo Miyazaki
- ARK Resource Co., Ltd., 383-2, Nakahara-machi, Nishi-ku, Kumamoto 861-5271, Japan
| | - Katsunori Furuhata
- School of Life and Environmental Science, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201, Japan
| | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
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18
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Isolation of atrazine nanobodies enhanced by depletion of anti-carrier protein phages and performance comparison between the nanobody and monoclonal antibody derived from the same immunogen. Anal Chim Acta 2023; 1244:340848. [PMID: 36737149 DOI: 10.1016/j.aca.2023.340848] [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: 10/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
Nanobody, a single domain antibody, has been shown a great promise for immunoassay (IA) applications. To improve the panning efficiency so as to obtain a valuable nanobody, anti-carrier protein phages in a phage display library were depleted to enhance the selection of nanobodies against the herbicide atrazine by using immunomagnetic beads conjugated with bovine serum albumin (IMB-BSA). The depletion of anti-carrier protein phages from the atrazine phage display library tripled the number of atrazine positive phage clones after four rounds of panning. One of the most sensitive phage clones Nb3 selected from the IMB-BSA depleted library was used to compare the performance with the monoclonal antibody (mAb 5D9) developed from the same immunogen. The Nb3-based IA exhibited similar specificity with the mAb 5D9-based IA, but greater thermostability and organic solvent tolerance. The half-maximum inhibition concentration (IC50) of the former was 3.5-fold greater than that of the latter (36.7 ng/mL versus 10.2 ng/mL). Because the Nb3-based IA was more robust than the mAb 5D9-based IA, the method detection limit of the two assays was 7.8 ng/mL of atrazine in river samples. The depletion strategy can increase the chance to acquire high quality nanobody and can be applicable for effective development of nanobodies against other small molecules.
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19
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Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023; 15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023] Open
Abstract
Beyond potency, a good developability profile is a key attribute of a biological drug. Selecting and screening for such attributes early in the drug development process can save resources and avoid costly late-stage failures. Here, we review some of the most important developability properties that can be assessed early on for biologics. These include the influence of the source of the biologic, its biophysical and pharmacokinetic properties, and how well it can be expressed recombinantly. We furthermore present in silico, in vitro, and in vivo methods and techniques that can be exploited at different stages of the discovery process to identify molecules with liabilities and thereby facilitate the selection of the most optimal drug leads. Finally, we reflect on the most relevant developability parameters for injectable versus orally delivered biologics and provide an outlook toward what general trends are expected to rise in the development of biologics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine and Department of Pharmacology, University of Oslo, Oslo, Norway
| | | | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjørn Gunnar Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lise Marie Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Peter M. Tessier
- Department of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCafferty
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Babraham Research Campus, Cambridge, UK
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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20
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Raeisi H, Azimirad M, Nabavi-Rad A, Asadzadeh Aghdaei H, Yadegar A, Zali MR. Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective. Front Immunol 2022; 13:972930. [PMID: 36081500 PMCID: PMC9445313 DOI: 10.3389/fimmu.2022.972930] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile (C. difficile), known as the major cause of antibiotic-associated diarrhea, is regarded as one of the most common healthcare-associated bacterial infections worldwide. Due to the emergence of hypervirulent strains, development of new therapeutic methods for C. difficile infection (CDI) has become crucially important. In this context, antibodies have been introduced as valuable tools in the research and clinical environments, as far as the effectiveness of antibody therapy for CDI was reported in several clinical investigations. Hence, production of high-performance antibodies for treatment of CDI would be precious. Traditional approaches of antibody generation are based on hybridoma technology. Today, application of in vitro technologies for generating recombinant antibodies, like phage display, is considered as an appropriate alternative to hybridoma technology. These techniques can circumvent the limitations of the immune system and they can be exploited for production of antibodies against different types of biomolecules in particular active toxins. Additionally, DNA encoding antibodies is directly accessible in in vitro technologies, which enables the application of antibody engineering in order to increase their sensitivity and specificity. Here, we review the application of antibodies for CDI treatment with an emphasis on recombinant fragment antibodies. Also, this review highlights the current and future prospects of the aforementioned approaches for antibody-mediated therapy of CDI.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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21
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Fu Y, da Fonseca Rezende e Mello J, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley TB, Hsu A, Dandey V, Sharma K, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. PLoS One 2022; 17:e0272364. [PMID: 35947606 PMCID: PMC9365158 DOI: 10.1371/journal.pone.0272364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/18/2022] [Indexed: 01/11/2023] Open
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Ying Fu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Juliana da Fonseca Rezende e Mello
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Bryan D. Fleming
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Alex Renn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Catherine Z. Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Quinlin Hanson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Emily M. Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Robert Petrovich
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Richard T. Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas B. Stanley
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Allen Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Venkata Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Kedar Sharma
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - William Gillette
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Troy Taylor
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Nitya Ramakrishnan
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Shelley Perkins
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eunkeu Oh
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Kimihiro Susumu
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
- Jacobs Corporation, Hanover, Maryland, United States of America
| | - Mason Wolak
- Optical Sciences Division, Naval Research Laboratory, Washington, D.C., United States of America
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
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22
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Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies. Mar Drugs 2022; 20:md20060397. [PMID: 35736200 PMCID: PMC9230156 DOI: 10.3390/md20060397] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 01/29/2023] Open
Abstract
Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.
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23
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Li B, Qin X, Mi LZ. Nanobodies: from structure to applications in non-injectable and bispecific biotherapeutic development. NANOSCALE 2022; 14:7110-7122. [PMID: 35535618 DOI: 10.1039/d2nr00306f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The increasing demand for convenient, miniaturized and multifunctional antibodies necessitates the development of novel antigen-recognition molecules for biological and medical studies. Nanobodies, the functional variable regions of camelid heavy-chain-only antibodies, as a new tool, complement the conventional antibodies and are in the stage of rapid development. The outstanding advantages of nanobodies include a stable structure, easy production, excellent water solubility, high affinity toward antigens and low immunogenicity. With promising application potential, nanobodies are now increasingly applied to various studies, including protein structure analysis, microscopic imaging, medical diagnosis, and drug development. The approval of the first nanobody drug Caplacizumab by the FDA disclosed the therapeutic potential of nanobodies. The outbreak of COVID-19 accelerated the development of nanobody drugs in non-injectable and bispecific biotherapeutic applications. Herein, we reviewed recent studies on the nanobody structure, screening and their applications in protein structure analysis and nanobody drugs, especially on non-injectable nanobody and bispecific nanobody development.
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Affiliation(s)
- Bingxuan Li
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
| | - Xiaohong Qin
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China.
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24
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Valdés-Tresanco MS, Molina-Zapata A, Pose AG, Moreno E. Structural Insights into the Design of Synthetic Nanobody Libraries. Molecules 2022; 27:molecules27072198. [PMID: 35408597 PMCID: PMC9000494 DOI: 10.3390/molecules27072198] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022] Open
Abstract
Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability. Since this synthetic approach has important advantages over the use of animals, the recent advances are indeed encouraging. Here we review over a dozen synthetic nanobody libraries reported so far and discuss the different approaches followed in their construction and validation, with an emphasis on framework and hypervariable loop design as critical issues defining their potential as high-class nanobody sources.
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Affiliation(s)
- Mario S. Valdés-Tresanco
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia; (A.M.-Z.); (A.G.P.)
- Correspondence: (M.S.V.-T.); (E.M.)
| | - Andrea Molina-Zapata
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia; (A.M.-Z.); (A.G.P.)
- Grupo de Micología Médica y Experimental, Corporación para Investigaciones Biológicas (CIB), Medellin 050034, Colombia
| | - Alaín González Pose
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia; (A.M.-Z.); (A.G.P.)
| | - Ernesto Moreno
- Faculty of Basic Sciences, University of Medellin, Medellin 050026, Colombia; (A.M.-Z.); (A.G.P.)
- Correspondence: (M.S.V.-T.); (E.M.)
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25
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Development of spirulina for the manufacture and oral delivery of protein therapeutics. Nat Biotechnol 2022; 40:956-964. [PMID: 35314813 PMCID: PMC9200632 DOI: 10.1038/s41587-022-01249-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
The use of the edible photosynthetic cyanobacterium Arthrospira platensis (spirulina) as a biomanufacturing platform has been limited by a lack of genetic tools. Here we report genetic engineering methods for stable, high-level expression of bioactive proteins in spirulina, including large-scale, indoor cultivation and downstream processing methods. Following targeted integration of exogenous genes into the spirulina chromosome (chr), encoded protein biopharmaceuticals can represent as much as 15% of total biomass, require no purification before oral delivery and are stable without refrigeration and protected during gastric transit when encapsulated within dry spirulina. Oral delivery of a spirulina-expressed antibody targeting campylobacter-a major cause of infant mortality in the developing world-prevents disease in mice, and a phase 1 clinical trial demonstrated safety for human administration. Spirulina provides an advantageous system for the manufacture of orally delivered therapeutic proteins by combining the safety of a food-based production host with the accessible genetic manipulation and high productivity of microbial platforms.
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26
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Barakat S, Berksöz M, Zahedimaram P, Piepoli S, Erman B. Nanobodies as molecular imaging probes. Free Radic Biol Med 2022; 182:260-275. [PMID: 35240292 DOI: 10.1016/j.freeradbiomed.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Camelidae derived single-domain antibodies (sdAbs), commonly known as nanobodies (Nbs), are the smallest antibody fragments with full antigen-binding capacity. Owing to their desirable properties such as small size, high specificity, strong affinity, excellent stability, and modularity, nanobodies are on their way to overtake conventional antibodies in terms of popularity. To date, a broad range of nanobodies have been generated against different molecular targets with applications spanning basic research, diagnostics, and therapeutics. In the field of molecular imaging, nanobody-based probes have emerged as a powerful tool. Radioactive or fluorescently labeled nanobodies are now used to detect and track many targets in different biological systems using imaging techniques. In this review, we provide an overview of the use of nanobodies as molecular probes. Additionally, we discuss current techniques for the generation, conjugation, and intracellular delivery of nanobodies.
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Affiliation(s)
- Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Melike Berksöz
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Pegah Zahedimaram
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
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27
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Akbarian M, Khani A, Eghbalpour S, Uversky VN. Bioactive Peptides: Synthesis, Sources, Applications, and Proposed Mechanisms of Action. Int J Mol Sci 2022; 23:ijms23031445. [PMID: 35163367 PMCID: PMC8836030 DOI: 10.3390/ijms23031445] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Bioactive peptides are a group of biological molecules that are normally buried in the structure of parent proteins and become active after the cleavage of the proteins. Another group of peptides is actively produced and found in many microorganisms and the body of organisms. Today, many groups of bioactive peptides have been marketed chemically or recombinantly. This article reviews the various production methods and sources of these important/ubiquitous and useful biomolecules. Their applications, such as antimicrobial, antihypertensive, antioxidant activities, blood-lipid-lowering effect, opioid role, antiobesity, ability to bind minerals, antidiabetic, and antiaging effects, will be explored. The types of pathways proposed for bioactive applications will be in the next part of the article, and at the end, the future perspectives of bioactive peptides will be reviewed. Reading this article is recommended for researchers interested in various fields of physiology, microbiology, biochemistry, and nanotechnology and food industry professionals.
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Affiliation(s)
- Mohsen Akbarian
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan;
| | - Ali Khani
- Department of Radiation Sciences, Faculty of Applied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran;
| | - Sara Eghbalpour
- Department of Obstetrics and Gynecology Surgery, Babol University of Medical Sciences, Babol 4717647745, Iran;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-(813)-974-5816
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28
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Abstract
Humanization of therapeutic antibodies derived from animal immunizations is often required to minimize immunogenicity risks in humans, which can cause potentially harmful and serious side effects and reduce antibody efficacy. Humanization is typically applied to conventional monoclonal antibodies derived in rodents as well as single-domain antibodies isolated from camelids and sharks (VHHs and VNARs). A streamlined protocol is described here for sequence humanization of camelid VHHs, which represent a promising biotherapeutic format with many desirable attributes. From human framework selection and complementarity-determining region grafting strategies to empirical scoring for prioritization of back-mutations, step-by-step instructions, and templates are provided along with bioinformatics resources to assist each step of the humanization process. Alternative approaches, warnings, and caveats are also presented.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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29
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Laughlin TM, Horn JR. Engineering pH-Sensitive Single-Domain Antibodies. Methods Mol Biol 2022; 2446:269-298. [PMID: 35157278 PMCID: PMC9924069 DOI: 10.1007/978-1-0716-2075-5_13] [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: 11/28/2022]
Abstract
There is increasing interest in expanding an antibody beyond high affinity and specificity. One such feature is custom regulation of the binding event, such as pH-dependent control. Here, we provide a methodology for generating single-domain antibodies (sdAbs) that bind their antigen in a pH-dependent fashion. As each sdAb is unique, we start by providing the conceptual framework for designing a combinatorial histidine scanning library within a sdAb-antigen-binding interface. Methods are provided to create a phage display library, containing up to 1 × 1010 unique members where each permutation of histidine substitution is sampled within the confines of the specified interface region(s). Finally, we describe phage display protocols for the selection and analysis of unique pH-dependent sdAb clones.
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Affiliation(s)
- Tosha M. Laughlin
- Department of Chemistry and Biochemistry, Northern Illinois University
| | - James R. Horn
- Department of Chemistry and Biochemistry, Northern Illinois University,Corresponding author: James R. Horn, Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb IL 60115,
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30
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Fu Y, Mello JDFRE, Fleming BD, Renn A, Chen CZ, Hu X, Xu M, Gorshkov K, Hanson Q, Zheng W, Lee EM, Perera L, Petrovich R, Pradhan M, Eastman RT, Itkin Z, Stanley T, Hsu A, Dandey V, Gillette W, Taylor T, Ramakrishnan N, Perkins S, Esposito D, Oh E, Susumu K, Wolak M, Ferrer M, Hall MD, Borgnia MJ, Simeonov A. The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34729560 DOI: 10.1101/2021.10.22.465476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants. One-Sentence Summary A cost-effective, high-throughput, adaptable pipeline capable of identifying effective humanized nanobodies against SARS-CoV-2.
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31
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Wicke N, Bedford MR, Howarth M. Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid. Commun Biol 2021; 4:960. [PMID: 34381153 PMCID: PMC8358037 DOI: 10.1038/s42003-021-02487-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 07/23/2021] [Indexed: 02/04/2023] Open
Abstract
Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Two stable scaffold proteins (nanobody and nanofitin), previously developed to be protease-resistant, were completely digested in less than 10 min at 100-fold lower concentration of pepsin than found in the stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI's evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. Gastrobodies show resilience to exceptionally harsh conditions, which should provide a foundation for targeting and modulating function within the GI tract.
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Affiliation(s)
- Niels Wicke
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK.
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32
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Positive charge in the complementarity-determining regions of synthetic nanobody prevents aggregation. Biochem Biophys Res Commun 2021; 572:1-6. [PMID: 34332323 DOI: 10.1016/j.bbrc.2021.07.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 01/19/2023]
Abstract
In the past, specificity and affinity were the priority for synthetic antibody library. However, therapeutic antibodies need good stability for medical use. Through carefully adjust the chemical diversity in CDRs, one hopes to design a synthetic antibody library with good developability. Here we thoroughly analyzed 296 nanobody sequences and structures, constructed a fully-functional synthetic nanobody library, evaluated the relationship between aggregation and isoelectric point, and found that high-pI nanobodies were more resistant to aggregation than low-pIs. As we used the same framework for constructing the library, CDRs charge played a crucial role in mediating nanobody aggregation. We also analyzed the theoretical pI of 296 nanobodies from PDB, about 75% had basic pI, only 25% were acidic. Those results provided useful guidelines for designing next-generation synthetic nanobody libraries and for identifying potent and safe nanobody therapeutics.
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33
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Güttler T, Aksu M, Dickmanns A, Stegmann KM, Gregor K, Rees R, Taxer W, Rymarenko O, Schünemann J, Dienemann C, Gunkel P, Mussil B, Krull J, Teichmann U, Groß U, Cordes VC, Dobbelstein M, Görlich D. Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. EMBO J 2021; 40:e107985. [PMID: 34302370 PMCID: PMC8420576 DOI: 10.15252/embj.2021107985] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022] Open
Abstract
Monoclonal anti-SARS-CoV-2 immunoglobulins represent a treatment option for COVID-19. However, their production in mammalian cells is not scalable to meet the global demand. Single-domain (VHH) antibodies (also called nanobodies) provide an alternative suitable for microbial production. Using alpaca immune libraries against the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein, we isolated 45 infection-blocking VHH antibodies. These include nanobodies that can withstand 95°C. The most effective VHH antibody neutralizes SARS-CoV-2 at 17-50 pM concentration (0.2-0.7 µg per liter), binds the open and closed states of the Spike, and shows a tight RBD interaction in the X-ray and cryo-EM structures. The best VHH trimers neutralize even at 40 ng per liter. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. We also demonstrate neutralization of the Beta strain at low-picomolar VHH concentrations. We further discovered VHH antibodies that enforce native folding of the RBD in the E. coli cytosol, where its folding normally fails. Such "fold-promoting" nanobodies may allow for simplified production of vaccines and their adaptation to viral escape-mutations.
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Affiliation(s)
- Thomas Güttler
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Metin Aksu
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Antje Dickmanns
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Kim M Stegmann
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Kathrin Gregor
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Renate Rees
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Waltraud Taxer
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Oleh Rymarenko
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Philip Gunkel
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bianka Mussil
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jens Krull
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ulrike Teichmann
- Animal facility, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Uwe Groß
- Institute of Medical Microbiology and Virology, University Medical Center, Göttingen, Germany
| | - Volker C Cordes
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, GZMB, University Medical Center, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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34
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Sun S, Ding Z, Yang X, Zhao X, Zhao M, Gao L, Chen Q, Xie S, Liu A, Yin S, Xu Z, Lu X. Nanobody: A Small Antibody with Big Implications for Tumor Therapeutic Strategy. Int J Nanomedicine 2021; 16:2337-2356. [PMID: 33790553 PMCID: PMC7997558 DOI: 10.2147/ijn.s297631] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
The development of monoclonal antibody treatments for successful tumor-targeted therapies took several decades. However, the efficacy of antibody-based therapy is still confined and desperately needs further improvement. Nanobodies are the recombinant variable domains of heavy-chain-only antibodies, with many unique properties such as small size (~15kDa), excellent solubility, superior stability, ease of manufacture, quick clearance from blood, and deep tissue penetration, which gain increasing acceptance as therapeutical tools and are considered also as building blocks for chimeric antigen receptors as well as for targeted drug delivery. Thus, one of the promising novel developments that may address the deficiency of monoclonal antibody-based therapies is the utilization of nanobodies. This article provides readers the significant factors that the structural and biochemical properties of nanobodies and the research progress on nanobodies in the fields of tumor treatment, as well as their application prospect.
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Affiliation(s)
- Shuyang Sun
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Stomatology, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Ziqiang Ding
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Xiaomei Yang
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Xinyue Zhao
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Minlong Zhao
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Stomatology, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Li Gao
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Qu Chen
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Stomatology, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Shenxia Xie
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- Department of Pharmacology, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Aiqun Liu
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Shihua Yin
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
| | - Zhiping Xu
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Xiaoling Lu
- International Nanobody Research Center, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
- School of Stomatology, Guangxi Medical University, Nanning, Guangxi, 530021, People’s Republic of China
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35
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Simeon RA, Zeng Y, Chonira V, Aguirre AM, Lasagna M, Baloh M, Sorg JA, Tommos C, Chen Z. Protease-stable DARPins as promising oral therapeutics. Protein Eng Des Sel 2021; 34:gzab028. [PMID: 34882774 PMCID: PMC8861517 DOI: 10.1093/protein/gzab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/16/2021] [Accepted: 10/02/2021] [Indexed: 12/30/2022] Open
Abstract
Clostridioides difficile is an enteric bacterium whose exotoxins, TcdA and TcdB, inactivate small GTPases within the host cells, leading to bloody diarrhea. In prior work, our group engineered a panel of potent TcdB-neutralizing designed ankyrin repeat proteins (DARPin) as oral therapeutics against C. difficile infection. However, all these DARPins are highly susceptible to digestion by gut-resident proteases, i.e. trypsin and chymotrypsin. Close evaluation of the protein sequence revealed a large abundance of positively charged and aromatic residues in the DARPin scaffold. In this study, we significantly improved the protease stability of one of the DARPins, 1.4E, via protein engineering. Unlike 1.4E, whose anti-TcdB EC50 increased >83-fold after 1-hour incubation with trypsin (1 mg/ml) or chymotrypsin (0.5 mg/ml), the best progenies-T10-2 and T10b-exhibit similar anti-TcdB potency as their parent in PBS regardless of protease treatment. The superior protease stability of T10-2 and T10b is attributed to the removal of nearly all positively charged and aromatic residues except those directly engaged in target binding. Furthermore, T10-2 was found to retain significant toxin-neutralization ability in ex vivo cecum fluid and can be easily detected in mouse fecal samples upon oral administration. Both T10-2 and T10b enjoy a high thermo- and chemo-stability and can be expressed very efficiently in Escherichia coli (>100 mg/l in shaker flasks). We believe that, in additional to their potential as oral therapeutics against C. difficile infection, T10-2 and T10b can also serve as a new generation DARPin scaffold with superior protease stability.
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Affiliation(s)
- Rudo A Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | - Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | - Vikas Chonira
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | | | - Mauricio Lasagna
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843, USA
| | - Marko Baloh
- Department of Biology, Texas A&M University, 424 Nagle St, College Station, TX 77840, USA
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, 424 Nagle St, College Station, TX 77840, USA
| | - Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
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36
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Liu JL, Webb EM, Zabetakis D, Burke CW, Gardner CL, Glass PJ, Legler PM, Weger-Lucarelli J, Anderson GP, Goldman ER. Stabilization of a Broadly Neutralizing Anti-Chikungunya Virus Single Domain Antibody. Front Med (Lausanne) 2021; 8:626028. [PMID: 33585527 PMCID: PMC7876468 DOI: 10.3389/fmed.2021.626028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
A single domain antibody (clone CC3) previously found to neutralize a vaccine strain of the chikungunya virus (PRNT50 = 2. 5 ng/mL) was found to be broadly neutralizing. Clone CC3 is not only able to neutralize a wild-type (WT) strain of chikungunya virus (CHIKV), but also neutralizes WT strains of Mayaro virus (MAYV) and Ross River virus (RRV); both arthralgic, Old World alphaviruses. Interestingly, CC3 also demonstrated a degree of neutralizing activity against the New World alphavirus, Venezuelan equine encephalitis virus (VEEV); albeit both the vaccine strain, TC-83, and the parental, WT Trinidad donkey strain had PRNT50 values ~1,000-fold higher than that of CHIKV. However, no neutralization activity was observed with Western equine encephalitis virus (WEEV). Ten CC3 variants designed to possess a range of isoelectric points, both higher and lower, were constructed. This approach successfully identified several lower pI mutants which possessed improved thermal stabilities by as much as 10°C over the original CC3 (Tm = 62°C), and excellent refolding abilities while maintaining their capacity to bind and neutralize CHIKV.
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Affiliation(s)
- Jinny L Liu
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Emily M Webb
- Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Dan Zabetakis
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Crystal W Burke
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Christina L Gardner
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Pamela J Glass
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | | | - George P Anderson
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Ellen R Goldman
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
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37
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Se Thoe E, Fauzi A, Tang YQ, Chamyuang S, Chia AYY. A review on advances of treatment modalities for Alzheimer's disease. Life Sci 2021; 276:119129. [PMID: 33515559 DOI: 10.1016/j.lfs.2021.119129] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/10/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease which is mainly characterized by progressive impairment in cognition, emotion, language and memory in older population. Considering the impact of AD, formulations of pharmaceutical drugs and cholinesterase inhibitors have been widely propagated, receiving endorsement by FDA as a form of AD treatment. However, these medications were gradually discovered to be ineffective in removing the root of AD pathogenesis but merely targeting the symptoms so as to improve a patient's cognitive outcome. Hence, a search for better disease-modifying alternatives is put into motion. Having a clear understanding of the neuroprotective mechanisms and diverse properties undertaken by specific genes, antibodies and nanoparticles is central towards designing novel therapeutic agents. In this review, we provide a brief introduction on the background of Alzheimer's disease, the biology of blood-brain barrier, along with the potentials and drawbacks associated with current therapeutic treatment avenues pertaining to gene therapy, immunotherapy and nanotherapy for better diagnosis and management of Alzheimer's disease.
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Affiliation(s)
- Ewen Se Thoe
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 47500 Selangor, Malaysia
| | - Ayesha Fauzi
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 47500 Selangor, Malaysia
| | - Yin Quan Tang
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 47500 Selangor, Malaysia
| | - Sunita Chamyuang
- School of Science, Mae Fah Luang University, Chaing Rai 57100, Thailand; Microbial Products and Innovation Research Group, Mae Fah Luang University, Chaing Rai 57100, Thailand
| | - Adeline Yoke Yin Chia
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, 47500 Selangor, Malaysia.
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38
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Wang W, Yuan J, Jiang C. Applications of nanobodies in plant science and biotechnology. PLANT MOLECULAR BIOLOGY 2021; 105:43-53. [PMID: 33037986 PMCID: PMC7547553 DOI: 10.1007/s11103-020-01082-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/05/2020] [Indexed: 05/15/2023]
Abstract
Present review summarizes the current applications of nanobodies in plant science and biotechnology, including plant expression of nanobodies, plant biotechnological applications, nanobody-based immunodetection, and nanobody-mediated resistance against plant pathogens. Nanobodies (Nbs) are variable domains of heavy chain-only antibodies (HCAbs) isolated from camelids. In spite of their single domain structure, nanobodies display many unique features, such as small size, high stability, and cryptic epitopes accessibility, which make them ideal for sophisticated applications in plants and animals. In this review, we summarize the current applications of nanobodies in plant science and biotechnology, focusing on nanobody expression in plants, plant biotechnological applications, determination of plant toxins and pathogens, and nanobody-mediated resistance against plant pathogens. Prospects and challenges of nanobody applications in plants are also discussed.
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Affiliation(s)
- Wenyi Wang
- Institute for Medical Biology and Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, Hubei, China.
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China.
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China.
| | - Jumao Yuan
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
| | - Changan Jiang
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Chinese Academy of Sciences, Zhuhai, Guangdong Province, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province, China
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39
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Payandeh Z, Rahbar MR, Jahangiri A, Hashemi ZS, Zakeri A, Jafarisani M, Rasaee MJ, Khalili S. Design of an engineered ACE2 as a novel therapeutics against COVID-19. J Theor Biol 2020; 505:110425. [PMID: 32735992 PMCID: PMC7387268 DOI: 10.1016/j.jtbi.2020.110425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/05/2020] [Accepted: 07/27/2020] [Indexed: 01/02/2023]
Abstract
The interaction between the angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in virus entry into the host cells. Since recombinant ACE2 protein has been suggested as an anti-SARS-CoV-2 therapeutic agent, this study was conducted to design an ACE2 protein with more desirable properties. In this regard, the amino acids with central roles in enzymatic activity of the ACE2 were substituted. Moreover, saturation mutagenesis at the interaction interface between the ACE2 and RBD was performed to increase their interaction affinity. The best mutations to increase the structural and thermal stability of the ACE2 were also selected based on B factors and mutation effects. The obtained resulted revealed that the Arg273Gln and Thr445Gly mutation have drastically reduced the binding affinity of the angiotensin-II into the active site of ACE2. The Thr27Arg mutation was determined to be the most potent mutation to increase the binding affinity. The Asp427Arg mutation was done to decrease the flexibility of the region with high B factor. The Pro451Met mutation along with the Gly448Trp mutation was predicted to increase the thermodynamic stability and thermostability of the ACE2. The designed therapeutic ACE2 would have no enzymatic activity while it could bear stronger interaction with Spike glycoprotein of the SARS-CoV-2. Moreover, decreased in vivo enzymatic degradation would be anticipated due to increased thermostability. This engineered ACE2 could be exploited as a novel therapeutic agent against COVID-19 after necessary evaluations.
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Affiliation(s)
- Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Moslem Jafarisani
- Clinical Biochemistry, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
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40
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Gao Y, Zhu J, Lu H. Single domain antibody-based vectors in the delivery of biologics across the blood-brain barrier: a review. Drug Deliv Transl Res 2020; 11:1818-1828. [PMID: 33155179 DOI: 10.1007/s13346-020-00873-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
Biologics are a promising and effective method for the treatment of central nervous system (CNS) diseases. The blood-brain barrier (BBB) is a natural barrier for the delivery of biologics into the brain, which decreases the effective concentration of drugs in the CNS. A range of strategies has been explored to transport biologics across the BBB endothelium, typically via receptor-mediated transcytosis (RMT), which involving molecules for endogenous BBB receptors to be fused with biologics. This review emphasized a category of novel alternative RMT-targeting vectors: single domain antibodies (sdAb). SdAbs are a unique category of antibodies derived from naturally occurring heavy-chain-only antibodies. Herein, we describe their properties, mechanisms, modifications, and translational perspectives for their ability to transmigrate across the BBB in vitro and in vivo in detail.
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Affiliation(s)
- Yang Gao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huili Lu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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41
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Sawant MS, Streu CN, Wu L, Tessier PM. Toward Drug-Like Multispecific Antibodies by Design. Int J Mol Sci 2020; 21:E7496. [PMID: 33053650 PMCID: PMC7589779 DOI: 10.3390/ijms21207496] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.
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Affiliation(s)
- Manali S. Sawant
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Craig N. Streu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, Albion College, Albion, MI 49224, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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42
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Yu X, Xu Q, Wu Y, Jiang H, Wei W, Zulipikaer A, Guo Y, Jirimutu, Chen J. Nanobodies derived from Camelids represent versatile biomolecules for biomedical applications. Biomater Sci 2020; 8:3559-3573. [PMID: 32490444 DOI: 10.1039/d0bm00574f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nanobodies are antigen binding variable domains of heavy-chain antibodies without light-chains, and these biomolecules occur naturally in the serum of Camelidae species. Nanobodies have a compact structure and low molecular weight when compared with antibodies, and are the smallest active antigen-binding fragments. Because of their remarkable stability and manipulable characteristics, nanobodies have been incorporated into biomaterials and used as molecular recognition and tracing agents, drug delivery systems, molecular imaging tools and disease therapeutics. This review summarizes recent progress in this field focusing on nanobodies as versatile biomolecules for biomedical applications.
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Affiliation(s)
- Xinyu Yu
- Center for Global Health, School of Public Health, Nanjing Medical University, 211166 Nanjing, China.
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43
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A compact nanobody-DNAzyme conjugate enables antigen detection and signal amplification. N Biotechnol 2020; 56:1-8. [DOI: 10.1016/j.nbt.2019.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022]
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44
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van Faassen H, Ryan S, Henry KA, Raphael S, Yang Q, Rossotti MA, Brunette E, Jiang S, Haqqani AS, Sulea T, MacKenzie CR, Tanha J, Hussack G. Serum albumin‐binding V
H
Hs with variable pH sensitivities enable tailored half‐life extension of biologics. FASEB J 2020; 34:8155-8171. [DOI: 10.1096/fj.201903231r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Henk van Faassen
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Qingling Yang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Martin A. Rossotti
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Susan Jiang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Arsalan S. Haqqani
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre National Research Council Canada Montréal QC Canada
| | - C. Roger MacKenzie
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
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45
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Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020; 477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.
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Affiliation(s)
- Aaron M. Collier
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Yuliya Nemtsova
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Narendra Kuber
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | | | - Anurag Modak
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
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46
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Hollander MR, Jansen MF, Hopman LHGA, Dolk E, van de Ven PM, Knaapen P, Horrevoets AJ, Lutgens E, van Royen N. Stimulation of Collateral Vessel Growth by Inhibition of Galectin 2 in Mice Using a Single-Domain Llama-Derived Antibody. J Am Heart Assoc 2019; 8:e012806. [PMID: 31594443 PMCID: PMC6818022 DOI: 10.1161/jaha.119.012806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background In the presence of arterial stenosis, collateral artery growth (arteriogenesis) can alleviate ischemia and preserve tissue function. In patients with poorly developed collateral arteries, Gal‐2 (galectin 2) expression is increased. In vivo administration of Gal‐2 inhibits arteriogenesis. Blocking of Gal‐2 potentially stimulates arteriogenesis. This study aims to investigate the effect of Gal‐2 inhibition on arteriogenesis and macrophage polarization using specific single‐domain antibodies. Methods and Results Llamas were immunized with Gal‐2 to develop anti–Gal‐2 antibodies. Binding of Gal‐2 to monocytes and binding inhibition of antibodies were quantified. To test arteriogenesis in vivo, Western diet‐fed LDLR.(low‐density lipoprotein receptor)–null Leiden mice underwent femoral artery ligation and received treatment with llama antibodies 2H8 or 2C10 or with vehicle. Perfusion restoration was measured with laser Doppler imaging. In the hind limb, arterioles and macrophage subtypes were characterized by histology, together with aortic atherosclerosis. Llama‐derived antibodies 2H8 and 2C10 strongly inhibited the binding of Gal‐2 to monocytes (93% and 99%, respectively). Treatment with these antibodies significantly increased perfusion restoration at 14 days (relative to sham, vehicle: 41.3±2.7%; 2H8: 53.1±3.4%, P=0.016; 2C10: 52.0±3.8%, P=0.049). In mice treated with 2H8 or 2C10, the mean arteriolar diameter was larger compared with control (vehicle: 17.25±4.97 μm; 2H8: 17.71±5.01 μm; 2C10: 17.84±4.98 μm; P<0.001). Perivascular macrophages showed a higher fraction of the M2 phenotype in both antibody‐treated animals (vehicle: 0.49±0.24; 2H8: 0.73±0.15, P=0.007; 2C10: 0.75±0.18, P=0.006). In vitro antibody treatment decreased the expression of M1‐associated cytokines compared with control (P<0.05 for each). Atherosclerotic lesion size was comparable between groups (overall P=0.59). Conclusions Inhibition of Gal‐2 induces a proarteriogenic M2 phenotype in macrophages, improves collateral artery growth, and increases perfusion restoration in a murine hind limb model.
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Affiliation(s)
- Maurits R Hollander
- Department of Cardiology VU University Medical Centre Amsterdam The Netherlands
| | - Matthijs F Jansen
- Department of Cardiology VU University Medical Centre Amsterdam The Netherlands.,Department of Medical Biochemistry Academic Medical Centre Amsterdam The Netherlands
| | - Luuk H G A Hopman
- Department of Cardiology VU University Medical Centre Amsterdam The Netherlands
| | | | - Peter M van de Ven
- Department of Epidemiology and Biostatistics VU University Amsterdam The Netherlands
| | - Paul Knaapen
- Department of Cardiology VU University Medical Centre Amsterdam The Netherlands
| | - Anton J Horrevoets
- Department of Molecular Cell Biology and Immunology VU Medical Center Amsterdam The Netherlands
| | - Esther Lutgens
- Department of Medical Biochemistry Academic Medical Centre Amsterdam The Netherlands.,Institute for Cardiovascular Prevention (IPEK) Ludwig Maximilian's University Munich Germany
| | - Niels van Royen
- Department of Cardiology VU University Medical Centre Amsterdam The Netherlands.,Department of Cardiology Radboud University Medical Center Nijmegen The Netherlands
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47
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Li D, Ji F, Huang C, Jia L. High Expression Achievement of Active and Robust Anti-β2 microglobulin Nanobodies via E.coli Hosts Selection. Molecules 2019; 24:molecules24162860. [PMID: 31394739 PMCID: PMC6720793 DOI: 10.3390/molecules24162860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
Nanobodies (VHHs) overcome many of the drawbacks of conventional antibodies, and the related technologies represent state-of-the-art and advanced applications in scientific research, pharmaceuticals, and therapies. In terms of productivity and economic cost, the cytoplasmic expression of VHHs in Escherichia coli (E. coli) is a good process for their recombinant production. The cytoplasmic environment of the host is critical to the affinity and stability of the recombinant VHHs in soluble form, yet the effects have not been studied. For this purpose, recombinant anti-β2 microglobulin VHHs were constructed and expressed in four commercialized E. coli hosts, including BL21 (DE3), Rosetta-gami B (DE3) pLysS, Origami 2 (DE3) and SHuffle T7 Express. The results showed that anti-β2 microglobulin (β2MG) VHHs expressed in different hosts exhibited distinctive differences in the affinity and structural characteristics. The VHHs expressed in Rosetta-gami B (DE3) pLysS possessed not only the greatest affinity of (equilibrium dissociation constant) KD = 4.68 × 10−8 M but also the highest yields compared with the VHHs expressed in BL21 (DE3), Origami 2 (DE3) and SHuffle T7 Express. In addition, the VHHs expressed in Rosetta-gami B (DE3) pLysS were more stable than the VHHs expressed in the rest three hosts. Thus far, we have successfully realized the high expression of the active and robust anti-β2MG VHHs in Rosetta-gami B (DE3) pLysS. The underlying principle of our study is able to guide the expression strategies of nanobodies on the context of industrial large-scale production.
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Affiliation(s)
- Da Li
- Liaoning Key Laboratory of Molecular Recognition and imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, China
| | - Chundong Huang
- Liaoning Key Laboratory of Molecular Recognition and imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and imaging, School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian 116023, China.
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48
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Kim DY, Kandalaft H, Hussack G, Raphael S, Ding W, Kelly JF, Henry KA, Tanha J. Evaluation of a noncanonical Cys40-Cys55 disulfide linkage for stabilization of single-domain antibodies. Protein Sci 2019; 28:881-888. [PMID: 30803088 DOI: 10.1002/pro.3595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/01/2019] [Accepted: 02/21/2019] [Indexed: 12/27/2022]
Abstract
Incorporation of noncanonical disulfide linkages into single-domain antibodies (sdAbs) has been shown to enhance thermostability and other properties. Here, we evaluated the effects of introducing a novel disulfide linkage formed between Cys residues at IMGT positions 40 and 55 on the melting temperatures (T m s), reversibility of thermal unfolding, solubility, and antigen-binding affinities of three types of sdAbs (VH H, VH , and VL domains). The Cys40-Cys55 disulfide linkage was tolerated by 9/9 VH Hs, 12/12 VH s, and 2/11 VL s tested and its formation was confirmed by mass spectrometry. Using circular dichroism, we found that the Cys40-Cys55 disulfide linkage increased sdAb T m by an average of 10.0°C (range: 0-21.8°C). However, enhanced thermostability came at the cost of a partial loss of refolding ability upon thermal denaturation as well as, for some sdAbs, significantly decreased solubility and antigen-binding affinity. Thus, Cys40/Cys55 can be added to the panel of known locations for introducing stabilizing noncanonical disulfide linkages into antibody variable domains, although its effects should be tested empirically for individual sdAbs.
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Affiliation(s)
- Dae Young Kim
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Hiba Kandalaft
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Wen Ding
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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49
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D'Eall C, Pon RA, Rossotti MA, Krahn N, Spearman M, Callaghan D, van Faassen H, Hussack G, Stetefeld J, Butler M, Durocher Y, Zhang J, Henry KA, Tanha J. Modulating antibody-dependent cellular cytotoxicity of epidermal growth factor receptor-specific heavy-chain antibodies through hinge engineering. Immunol Cell Biol 2019; 97:526-537. [PMID: 30680791 DOI: 10.1111/imcb.12238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 01/20/2023]
Abstract
Human IgG1 and IgG3 antibodies (Abs) can mediate Ab-dependent cellular cytotoxicity (ADCC), and engineering of the Ab Fc (point mutation; defucosylation) has been shown to affect ADCC by modulating affinity for FcRγIIIa. In the absence of a CH 1 domain, many camelid heavy-chain Abs (HCAbs) naturally bear very long and flexible hinge regions connecting their VH H and CH 2 domains. To better understand the influence of hinge length and structure on HCAb ADCC, we produced a series of hinge-engineered epidermal growth factor receptor (EGFR)-specific chimeric camelid VH H-human Fc Abs and characterized their affinities for recombinant EGFR and FcRγIIIa, their binding to EGFR-positive tumor cells, and their ability to elicit ADCC. In the case of one chimeric HCAb (EG2-hFc), we found that variants bearing longer hinges (IgG3 or camelid hinge regions) showed dramatically improved ADCC in comparison with a variant bearing the human IgG1 hinge, in similar fashion to a variant with reduced CH 2 fucosylation. Conversely, an EG2-hFc variant bearing a truncated human IgG1 upper hinge region failed to elicit ADCC. However, there was no consistent association between hinge length and ADCC for four similarly engineered chimeric HCAbs directed against distinct EGFR epitopes. These findings demonstrate that the ADCC of some HCAbs can be modulated simply by varying the length of the Ab hinge. Although this effect appears to be heavily epitope-dependent, this strategy may be useful to consider during the design of VH H-based therapeutic Abs for cancer.
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Affiliation(s)
- Calvin D'Eall
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Robert A Pon
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Natalie Krahn
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Maureen Spearman
- Department of Microbiology, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Deborah Callaghan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Ave, Montréal, QC, H4P 2R2, Canada
| | - Jianbing Zhang
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Kevin A Henry
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
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50
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He L, Tai W, Li J, Chen Y, Gao Y, Li J, Sun S, Zhou Y, Du L, Zhao G. Enhanced Ability of Oligomeric Nanobodies Targeting MERS Coronavirus Receptor-Binding Domain. Viruses 2019; 11:v11020166. [PMID: 30791410 PMCID: PMC6410414 DOI: 10.3390/v11020166] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022] Open
Abstract
Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV), an infectious coronavirus first reported in 2012, has a mortality rate greater than 35%. Therapeutic antibodies are key tools for preventing and treating MERS-CoV infection, but to date no such agents have been approved for treatment of this virus. Nanobodies (Nbs) are camelid heavy chain variable domains with properties distinct from those of conventional antibodies and antibody fragments. We generated two oligomeric Nbs by linking two or three monomeric Nbs (Mono-Nbs) targeting the MERS-CoV receptor-binding domain (RBD), and compared their RBD-binding affinity, RBD⁻receptor binding inhibition, stability, and neutralizing and cross-neutralizing activity against MERS-CoV. Relative to Mono-Nb, dimeric Nb (Di-Nb) and trimeric Nb (Tri-Nb) had significantly greater ability to bind MERS-CoV RBD proteins with or without mutations in the RBD, thereby potently blocking RBD⁻MERS-CoV receptor binding. The engineered oligomeric Nbs were very stable under extreme conditions, including low or high pH, protease (pepsin), chaotropic denaturant (urea), and high temperature. Importantly, Di-Nb and Tri-Nb exerted significantly elevated broad-spectrum neutralizing activity against at least 19 human and camel MERS-CoV strains isolated in different countries and years. Overall, the engineered Nbs could be developed into effective therapeutic agents for prevention and treatment of MERS-CoV infection.
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Affiliation(s)
- Lei He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Wanbo Tai
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Jiangfan Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Yuehong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Yaning Gao
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Junfeng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
- Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China.
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
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