1
|
Liang WC, Xi H, Sun D, D’Ascenzo L, Zarzar J, Stephens N, Cook R, Li Y, Ye Z, Matsumoto M, Payandeh J, Masureel M, Wu Y. Structure- and machine learning-guided engineering demonstrate that a non-canonical disulfide in an anti-PD-1 rabbit antibody does not impede antibody developability. MAbs 2024; 16:2309685. [PMID: 38356181 PMCID: PMC10877986 DOI: 10.1080/19420862.2024.2309685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
Rabbits produce robust antibody responses and have unique features in their antibody repertoire that make them an attractive alternative to rodents for in vivo discovery. However, the frequent occurrence of a non-canonical disulfide bond between complementarity-determining region (CDR) H1 (C35a) and CDRH2 (C50) is often seen as a liability for therapeutic antibody development, despite limited reports of its effect on antibody binding, function, and stability. Here, we describe the discovery and humanization of a human-mouse cross-reactive anti-programmed cell death 1 (PD-1) monoclonal rabbit antibody, termed h1340.CC, which possesses this non-canonical disulfide bond. Initial removal of the non-canonical disulfide resulted in a loss of PD-1 affinity and cross-reactivity, which led us to explore protein engineering approaches to recover these. First, guided by the sequence of a related clone and the crystal structure of h1340.CC in complex with PD-1, we generated variant h1340.SA.LV with a potency and cross-reactivity similar to h1340.CC, but only partially recovered affinity. Side-by-side developability assessment of both h1340.CC and h1340.SA.LV indicate that they possess similar, favorable properties. Next, and prompted by recent developments in machine learning (ML)-guided protein engineering, we used an unbiased ML- and structure-guided approach to rapidly and efficiently generate a different variant with recovered affinity. Our case study thus indicates that, while the non-canonical inter-CDR disulfide bond found in rabbit antibodies does not necessarily constitute an obstacle to therapeutic antibody development, combining structure- and ML-guided approaches can provide a fast and efficient way to improve antibody properties and remove potential liabilities.
Collapse
Affiliation(s)
- Wei-Ching Liang
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| | - Hongkang Xi
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| | - Dawei Sun
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Luigi D’Ascenzo
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Jonathan Zarzar
- Department of Pharma Technical Development, Genentech Inc, South San Francisco, CA, USA
| | - Nicole Stephens
- Department of Pharma Technical Development, Genentech Inc, South San Francisco, CA, USA
| | - Ryan Cook
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Yinyin Li
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Zhengmao Ye
- Department of Biochemical and Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
- Discovery Science & Technology Department, Gilead Sciences Inc, Foster City, CA, USA
| | - Marissa Matsumoto
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
- Asher Biotherapeutics, South San Francisco, CA, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
- Exelixis Inc, Alameda, CA, USA
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc, South San Francisco, CA, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech Inc, South San Francisco, CA, USA
| |
Collapse
|
2
|
Mullin M, McClory J, Haynes W, Grace J, Robertson N, van Heeke G. Applications and challenges in designing VHH-based bispecific antibodies: leveraging machine learning solutions. MAbs 2024; 16:2341443. [PMID: 38666503 PMCID: PMC11057648 DOI: 10.1080/19420862.2024.2341443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/05/2024] [Indexed: 05/01/2024] Open
Abstract
The development of bispecific antibodies that bind at least two different targets relies on bringing together multiple binding domains with different binding properties and biophysical characteristics to produce a drug-like therapeutic. These building blocks play an important role in the overall quality of the molecule and can influence many important aspects from potency and specificity to stability and half-life. Single-domain antibodies, particularly camelid-derived variable heavy domain of heavy chain (VHH) antibodies, are becoming an increasingly popular choice for bispecific construction due to their single-domain modularity, favorable biophysical properties, and potential to work in multiple antibody formats. Here, we review the use of VHH domains as building blocks in the construction of multispecific antibodies and the challenges in creating optimized molecules. In addition to exploring traditional approaches to VHH development, we review the integration of machine learning techniques at various stages of the process. Specifically, the utilization of machine learning for structural prediction, lead identification, lead optimization, and humanization of VHH antibodies.
Collapse
|
3
|
ESKİER NE, ESKİER D, FİRUZAN E, UZUNLAR SKALYONCU. Physicochemical differences between camelid single-domain antibodies and mammalian antibodies. Turk J Biol 2023; 47:423-436. [PMID: 38681780 PMCID: PMC11045209 DOI: 10.55730/1300-0152.2676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/28/2023] [Accepted: 12/07/2023] [Indexed: 05/01/2024] Open
Abstract
Background/aim In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages, including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VHHs) and humans (VHs), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VHs and VHHs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity, while preserving stability, functionality, and antigen specificity. Materials and methods We obtained the VH and VHH sequences of various camelid and non-camelid mammalian antibodies from public databases and used multiple sequence alignment based on the Chothia numbering scheme. Aligned sequences were subjected to diverse analyses encompassing paratope length, binding prediction, motif, disulfide bridge, salt bridge profiling, and physicochemical characteristic distribution. Logistic Regression coupled with the Boruta - Random Forest algorithm facilitated the comprehensive examination of physicochemical properties. Results Our findings revealed longer, less variable paratope sequences in VHHs, along with specific antigen binding residues with increased binding potential compared to VHs. Although the VHs showed more heterogeneous noncanonical disulfide bond patterns, the VHHs had a higher number of noncanonical disulfide bridges. Intriguingly, a typical salt bridge between the 94th and 101st positions in the VHs had a very low encounter rate in the VHHs. Surprisingly, we also identified notable differences in the physicochemical patterns of mostly conserved frameworks (FWs), especially the FW2 and FW3 regions, between VHs and VHHs. Conclusion Our findings point to possible key sites in VHHs as candidate residues for nanobody engineering efforts.
Collapse
Affiliation(s)
- Nazlı Eda ESKİER
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir,
Turkiye
- İzmir Biomedicine and Genome Center, İzmir,
Turkiye
| | - Doğa ESKİER
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir,
Turkiye
- İzmir Biomedicine and Genome Center, İzmir,
Turkiye
| | - Esin FİRUZAN
- Department of Statistics, Faculty of Sciences, Dokuz Eylül University, İzmir,
Turkiye
| | | |
Collapse
|
4
|
Yamamoto K, Nagatoishi S, Matsunaga R, Nakakido M, Kuroda D, Tsumoto K. Conformational features and interaction mechanisms of V H H antibodies with β-hairpin CDR3: A case of Nb8-HigB2 interaction. Protein Sci 2023; 32:e4827. [PMID: 37916305 PMCID: PMC10661080 DOI: 10.1002/pro.4827] [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: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
The β-hairpin conformation is regarded as an important basic motif to form and regulate protein-protein interactions. Single-domain VH H antibodies are potential therapeutic and diagnostic tools, and the third complementarity-determining regions of the heavy chains (CDR3s) of these antibodies are critical for antigen recognition. Although the sequences and conformations of the CDR3s are diverse, CDR3s sometimes adopt β-hairpin conformations. However, characteristic features and interaction mechanisms of β-hairpin CDR3s remain to be fully elucidated. In this study, we investigated the molecular recognition of the anti-HigB2 VH H antibody Nb8, which has a CDR3 that forms a β-hairpin conformation. The interaction was analyzed by evaluation of alanine-scanning mutants, molecular dynamics simulations, and hydrogen/deuterium exchange mass spectrometry. These experiments demonstrated that positions 93 and 94 (Chothia numbering) in framework region 3, which is right outside CDR3 by definition, play pivotal roles in maintaining structural stability and binding properties of Nb8. These findings will facilitate the design and optimization of single-domain antibodies.
Collapse
Affiliation(s)
- Koichi Yamamoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
| | - Ryo Matsunaga
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Kuroda
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Yamazaki T, Nagatoishi S, Yamawaki T, Nozawa T, Matsunaga R, Nakakido M, Caaveiro JMM, Nakagawa I, Tsumoto K. Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J Biol Chem 2023; 299:105254. [PMID: 37716701 PMCID: PMC10582769 DOI: 10.1016/j.jbc.2023.105254] [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: 04/09/2023] [Revised: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Listeriosis, caused by infection with Listeria monocytogenes, is a severe disease with a high mortality rate. The L. monocytogenes virulence factor, internalin family protein InlA, which binds to the host receptor E-cadherin, is necessary to invade host cells. Here, we isolated two single-domain antibodies (VHHs) that bind to InlA with picomolar affinities from an alpaca immune library using the phage display method. These InlA-specific VHHs inhibited the binding of InlA to the extracellular domains of E-cadherin in vitro as shown by biophysical interaction analysis. Furthermore, we determined that the VHHs inhibited the invasion of L. monocytogenes into host cells in culture. High-resolution X-ray structure analyses of the complexes of VHHs with InlA revealed that the VHHs bind to the same binding site as E-cadherin against InlA. We conclude that these VHHs have the potential for use as drugs to treat listeriosis.
Collapse
Affiliation(s)
- Taichi Yamazaki
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Tsukushi Yamawaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takashi Nozawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jose M M Caaveiro
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
7
|
Sharma P, Joshi RV, Pritchard R, Xu K, Eicher MA. Therapeutic Antibodies in Medicine. Molecules 2023; 28:6438. [PMID: 37764213 PMCID: PMC10535987 DOI: 10.3390/molecules28186438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/05/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Antibody engineering has developed into a wide-reaching field, impacting a multitude of industries, most notably healthcare and diagnostics. The seminal work on developing the first monoclonal antibody four decades ago has witnessed exponential growth in the last 10-15 years, where regulators have approved monoclonal antibodies as therapeutics and for several diagnostic applications, including the remarkable attention it garnered during the pandemic. In recent years, antibodies have become the fastest-growing class of biological drugs approved for the treatment of a wide range of diseases, from cancer to autoimmune conditions. This review discusses the field of therapeutic antibodies as it stands today. It summarizes and outlines the clinical relevance and application of therapeutic antibodies in treating a landscape of diseases in different disciplines of medicine. It discusses the nomenclature, various approaches to antibody therapies, and the evolution of antibody therapeutics. It also discusses the risk profile and adverse immune reactions associated with the antibodies and sheds light on future applications and perspectives in antibody drug discovery.
Collapse
Affiliation(s)
- Prerna Sharma
- Geisinger Commonwealth School of Medicine, Scranton, PA 18509, USA
| | | | | | | | | |
Collapse
|
8
|
Bahrami Dizicheh Z, Chen IL, Koenig P. VHH CDR-H3 conformation is determined by VH germline usage. Commun Biol 2023; 6:864. [PMID: 37598276 PMCID: PMC10439903 DOI: 10.1038/s42003-023-05241-y] [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: 12/29/2022] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
VHHs or nanobodies are single antigen binding domains originating from camelid heavy-chain antibodies. They are used as diagnostic and research tools and in a variety of therapeutic molecules. Analyzing variable domain structures from llama and alpaca we found that VHHs can be classified into two large structural clusters based on their CDR-H3 conformation. Extended CDR-H3 loops protrude into the solvent, whereas kinked CDR-H3 loops fold back onto framework regions. Both major families have distinct properties in terms of their CDR-H3 secondary structure, how their CDR-H3 interacts with the framework region and how they bind to antigens. We show that the CDR-H3 conformation of VHHs correlates with the germline from which the antibodies are derived: IGHV3-3 derived antibodies almost exclusively adopt a kinked CDR-H3 conformation while the CDR-H3 adopts an extended structure in most IGHV3S53 derived antibodies. We do not observe any bias stemming from V(D)J recombination in llama immune repertoires, suggesting that the correlation is the result of selection processes during B-cell development. Our findings demonstrate a previously undescribed impact of germline usage on antigen interaction and contribute to a better understanding on how properties of the antibody framework shape the immune repertoire.
Collapse
Affiliation(s)
- Zahra Bahrami Dizicheh
- 23andMe, Inc. Therapeutics, 349 Oyster Point Boulevard, South San Francisco, CA, 94080, USA
| | - I-Ling Chen
- 23andMe, Inc. Therapeutics, 349 Oyster Point Boulevard, South San Francisco, CA, 94080, USA
| | - Patrick Koenig
- 23andMe, Inc. Therapeutics, 349 Oyster Point Boulevard, South San Francisco, CA, 94080, USA.
| |
Collapse
|
9
|
Ferraz MVF, Neto JCS, Lins RD, Teixeira ES. An artificial neural network model to predict structure-based protein-protein free energy of binding from Rosetta-calculated properties. Phys Chem Chem Phys 2023; 25:7257-7267. [PMID: 36810523 DOI: 10.1039/d2cp05644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The prediction of the free energy (ΔG) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its centrality in understanding protein association phenomena and protein engineering, the ΔG of binding is a daunting quantity to obtain theoretically. In this work, we devise a novel Artificial Neural Network (ANN) model to predict the ΔG of binding for a given three-dimensional structure of a protein-protein complex with Rosetta-calculated properties. Our model was tested using two data sets, and it presented a root-mean-square error ranging from 1.67 kcal mol-1 to 2.45 kcal mol-1, showing a better performance compared to the available state-of-the-art tools. Validation of the model for a variety of protein-protein complexes is showcased.
Collapse
Affiliation(s)
- Matheus V F Ferraz
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, FIOCRUZ, Recife, PE, Brazil.,Department of Fundamental Chemistry, Federal University of Pernambuco, UFPE, Recife, PE, Brazil.,Heidelberg Institute for Theoretical Studies, HITS, Heidelberg, Germany
| | - José C S Neto
- Recife Center for Advanced Studies and Systems, CESAR, Recife, PE, Brazil.
| | - Roberto D Lins
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, FIOCRUZ, Recife, PE, Brazil.,Department of Fundamental Chemistry, Federal University of Pernambuco, UFPE, Recife, PE, Brazil
| | - Erico S Teixeira
- Recife Center for Advanced Studies and Systems, CESAR, Recife, PE, Brazil.
| |
Collapse
|
10
|
Li Y, Jin T, Liu N, Wang J, Qin Z, Yin S, Zhang Y, Fu Z, Wu Y, Wang Y, Liu Y, Yang M, Pang A, Sun J, Wang Y, Yang X. A short peptide exerts neuroprotective effects on cerebral ischemia-reperfusion injury by reducing inflammation via the miR-6328/IKKβ/NF-κB axis. J Neuroinflammation 2023; 20:53. [PMID: 36855153 PMCID: PMC9972639 DOI: 10.1186/s12974-023-02739-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Despite considerable efforts, ischemic stroke (IS) remains a challenging clinical problem. Therefore, the discovery of effective therapeutic and targeted drugs based on the underlying molecular mechanism is crucial for effective IS treatment. METHODS A cDNA-encoding peptide was cloned from RNA extracted from Rana limnocharis skin, and the mature amino acid sequence was predicted and synthesized. Hemolysis and acute toxicity of the peptide were tested. Furthermore, its neuroprotective properties were evaluated using a middle cerebral artery occlusion/reperfusion (MCAO/R) model in rats and an oxygen-glucose deprivation/reperfusion (OGD/R) model in neuron-like PC12 cells. The underlying molecular mechanisms were explored using microRNA (miRNA) sequencing, quantitative real-time polymerase chain reaction, dual-luciferase reporter gene assay, and western blotting. RESULTS A new peptide (NP1) with an amino acid sequence of 'FLPAAICLVIKTC' was identified. NP1 showed no obvious toxicities in vivo and in vitro and was able to cross the blood-brain barrier. Intraperitoneal administration of NP1 (10 nmol/kg) effectively reduced the volume of cerebral infarction and relieved neurological dysfunction in MCAO/R model rats. Moreover, NP1 significantly alleviated the decrease in viability and increase in apoptosis of neuron-like PC12 cells induced by OGD/R. NP1 effectively suppressed inflammation by reducing interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) levels in vitro and in vivo. Furthermore, NP1 up-regulated the expression of miR-6328, which, in turn, down-regulated kappa B kinase β (IKKβ). IKKβ reduced the phosphorylation of nuclear factor-kappa B p65 (NF-κB p65) and inhibitor of NF-κB (I-κB), thereby inhibiting activation of the NF-κB pathway. CONCLUSIONS The newly discovered non-toxic peptide NP1 ('FLPAAICLVIKTC') exerted neuroprotective effects on cerebral ischemia-reperfusion injury by reducing inflammation via the miR-6328/IKKβ/NF-κB axis. Our findings not only provide an exogenous peptide drug candidate and endogenous small nucleic acid drug candidate but also a new drug target for the treatment of IS. This study highlights the importance of peptides in the development of new drugs, elucidation of pathological mechanisms, and discovery of new drug targets.
Collapse
Affiliation(s)
- Yilin Li
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Tao Jin
- Department of Orthopedics, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, 650032 Yunnan China
| | - Naixin Liu
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Junsong Wang
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Zihan Qin
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Saige Yin
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yingxuan Zhang
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Zhe Fu
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yutong Wu
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yinglei Wang
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yixiang Liu
- grid.413059.a0000 0000 9952 9510Key Laboratory of Chemistry in Ethnic Medicinal Resources and Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission and Ministry of Education, School of Ethnic Medicine, Yunnan Minzu University, Kunming, 650504 Yunnan China
| | - Meifeng Yang
- grid.285847.40000 0000 9588 0960Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Ailan Pang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, 650031, Yunnan, China.
| | - Jun Sun
- Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, Yunnan, China.
| | - Ying Wang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources and Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission and Ministry of Education, School of Ethnic Medicine, Yunnan Minzu University, Kunming, 650504, Yunnan, China.
| | - Xinwang Yang
- Department of Anatomy and Histology and Embryology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, 650500, Yunnan, China.
| |
Collapse
|
11
|
Abstract
The immune systems protect vertebrates from foreign molecules or antigens, and antibodies are important mediators of this system. The sequences and structural features of antibodies vary depending on species. Many of antibodies from vertebrates, including camelids, have both heavy and light chain variable domains, but camelids also have antibodies that lack the light chains. In antibodies that lack light chains, the C-terminal variable region is called the VHH domain. Antibodies recognize antigens through six complementarity-determining regions (CDRs). The third CDR of the heavy chain (CDR-H3) is at the center of the antigen-binding site and is diverse in terms of sequence and structure. Due to the importance of antibodies in basic science as well as in medical applications, there have been many studies of CDR-H3s of antibodies that possess both light and heavy chains. However, nature of CDR-H3s of single-domain VHH antibodies is less well studied. In this chapter, we describe current knowledge of sequence-structure-function correlations of single-domain VHH antibodies with emphasis on CDR-H3. Based on the 370 crystal structures in the Protein Data Bank, we also attempt structural classification of CDR-H3 in single-domain VHH antibodies and discuss lessons learned from the ever-increasing number of the structures.
Collapse
Affiliation(s)
- Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
12
|
Liu Y, Yi L, Li Y, Wang Z, Jirimutu. Characterization of heavy-chain antibody gene repertoires in Bactrian camels. J Genet Genomics 2023; 50:38-45. [PMID: 35500746 DOI: 10.1016/j.jgg.2022.04.010] [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: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023]
Abstract
Camelids are the only mammals that can produce functional heavy-chain antibodies (HCAbs). Although HCAbs were discovered over 30 years ago, the antibody gene repertoire of Bactrian camels remains largely underexplored. To characterize the diversity of variable genes of HCAbs (VHHs), germline and rearranged VHH repertoires are constructed. Phylogenetics analysis shows that all camelid VHH genes are derived from a common ancestor and the nucleotide diversity of VHHs is similar across all camelid species. While species-specific hallmark sites are identified, the non-canonical cysteines specific to VHHs are distinct in Bactrian camels and dromedaries compared with alpacas. Though low divergence at the germline repertoire between wild and domestic Bactrian camels, higher expression of VHHs is observed in some wild Bactrian camels than that of domestic ones. This study not only adds our understanding of VHH repertoire diversity across camelids, but also provides useful resources for HCAb engineering.
Collapse
Affiliation(s)
- Yuexing Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yi
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, China
| | - Yixue Li
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Guangzhou Laboratory, Guangzhou, Guangdong 510005, China; Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jirimutu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, College of Food Science and Engineering, Inner Mongolia Agricultural University, Huhhot, Inner Mongolia 010018, China; Inner Mongolia Institute of Camel Research, West Alax, Inner Mongolia 737399, China.
| |
Collapse
|
13
|
Hong J, Kwon HJ, Cachau R, Chen CZ, Butay KJ, Duan Z, Li D, Ren H, Liang T, Zhu J, Dandey VP, Martin NP, Esposito D, Ortega-Rodriguez U, Xu M, Borgnia MJ, Xie H, Ho M. Dromedary camel nanobodies broadly neutralize SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2022; 119:e2201433119. [PMID: 35476528 PMCID: PMC9170159 DOI: 10.1073/pnas.2201433119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/24/2022] [Indexed: 01/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is a trimer of S1/S2 heterodimers with three receptor-binding domains (RBDs) at the S1 subunit for human angiotensin-converting enzyme 2 (hACE2). Due to their small size, nanobodies can recognize protein cavities that are not accessible to conventional antibodies. To isolate high-affinity nanobodies, large libraries with great diversity are highly desirable. Dromedary camels (Camelus dromedarius) are natural reservoirs of coronaviruses like Middle East respiratory syndrome CoV (MERS-CoV) that are transmitted to humans. Here, we built large dromedary camel VHH phage libraries to isolate nanobodies that broadly neutralize SARS-CoV-2 variants. We isolated two VHH nanobodies, NCI-CoV-7A3 (7A3) and NCI-CoV-8A2 (8A2), which have a high affinity for the RBD via targeting nonoverlapping epitopes and show broad neutralization activity against SARS-CoV-2 and its emerging variants of concern. Cryoelectron microscopy (cryo-EM) complex structures revealed that 8A2 binds the RBD in its up mode with a long CDR3 loop directly involved in the ACE2 binding residues and that 7A3 targets a deeply buried region that uniquely extends from the S1 subunit to the apex of the S2 subunit regardless of the conformational state of the RBD. At a dose of ≥5 mg/kg, 7A3 efficiently protected transgenic mice expressing hACE2 from the lethal challenge of variants B.1.351 or B.1.617.2, suggesting its therapeutic use against COVID-19 variants. The dromedary camel VHH phage libraries could be helpful as a unique platform ready for quickly isolating potent nanobodies against future emerging viruses.
Collapse
Affiliation(s)
- Jessica Hong
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| | - Hyung Joon Kwon
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993
| | - Raul Cachau
- Data Science and Information Technology Program, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Catherine Z. Chen
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Kevin John Butay
- Molecular Microscopy Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
| | - Zhijian Duan
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| | - Dan Li
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| | - Hua Ren
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| | - Tianyuzhou Liang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| | - Jianghai Zhu
- Data Science and Information Technology Program, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Venkata P. Dandey
- Molecular Microscopy Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
| | - Negin P. Martin
- Viral Vector Core, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Uriel Ortega-Rodriguez
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993
| | - Miao Xu
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Mario J. Borgnia
- Molecular Microscopy Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709
| | - Hang Xie
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
- Antibody Engineering Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20891
| |
Collapse
|
14
|
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.
Collapse
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.)
| |
Collapse
|
15
|
Birchenough HL, Nivia HDR, Jowitt TA. Interaction standards for biophysics: anti-lysozyme nanobodies. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:333-343. [PMID: 33839878 PMCID: PMC8189969 DOI: 10.1007/s00249-021-01524-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/01/2021] [Accepted: 03/22/2021] [Indexed: 11/25/2022]
Abstract
There is a significant demand in the molecular biophysics community for robust standard samples. They are required by researchers, instrument developers and pharmaceutical companies for instrumental quality control, methodological development and in the design and validation of devices, diagnostics and instrumentation. To-date there has been no clear consensus on the need and type of standards that should be available and different research groups and instrument manufacturers use different standard systems which significantly hinders comparative analysis. One of the major objectives of the Association of Resources for Biophysical Research in Europe (ARBRE) is to establish a common set of standard samples that can be used throughout the biophysics community and instrument developers. A survey was circulated among ARBRE members to ascertain the requirements of laboratories when using standard systems and the results are documented in this article. In summary, the major requirements are protein samples which are cheap, relatively small, stable and have different binding strengths. We have developed a panel of sdAb’s or ‘nanobodies’ against hen-egg white lysozyme with different binding strengths and suitable stability characteristics. Here we show the results of the survey, the selection procedure, validation and final selection of a panel of nanobody interaction standards.
Collapse
Affiliation(s)
- Holly L Birchenough
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology Medicine and Health, University of Manchester, Manchester, England
| | - Hilda D Ruiz Nivia
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology Medicine and Health, University of Manchester, Manchester, England
| | - Thomas A Jowitt
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology Medicine and Health, University of Manchester, Manchester, England.
| |
Collapse
|
16
|
Mendoza MN, Jian M, King MT, Brooks CL. Role of a noncanonical disulfide bond in the stability, affinity, and flexibility of a VHH specific for the Listeria virulence factor InlB. Protein Sci 2020; 29:1004-1017. [PMID: 31981247 DOI: 10.1002/pro.3831] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/29/2022]
Abstract
A distinguishing feature of camel (Camelus dromedarius) VHH domains are noncanonical disulfide bonds between CDR1 and CDR3. The disulfide bond may provide an evolutionary advantage, as one of the cysteines in the bond is germline encoded. It has been hypothesized that this additional disulfide bond may play a role in binding affinity by reducing the entropic penalty associated with immobilization of a long CDR3 loop upon antigen binding. To examine the role of a noncanonical disulfide bond on antigen binding and the biophysical properties of a VHH domain, we have used the VHH R303, which binds the Listeria virulence factor InlB as a model. Using site directed mutagenesis, we produced a double mutant of R303 (C33A/C102A) to remove the extra disulfide bond of the VHH R303. Antigen binding was not affected by loss of the disulfide bond, however the mutant VHH displayed reduced thermal stability (Tm = 12°C lower than wild-type), and a loss of the ability to fold reversibly due to heat induced aggregation. X-ray structures of the mutant alone and in complex with InlB showed no major changes in the structure. B-factor analysis of the structures suggested that the loss of the disulfide bond elicited no major change on the flexibility of the CDR loops, and revealed no evidence of loop immobilization upon antigen binding. These results suggest that the noncanonical disulfide bond found in camel VHH may have evolved to stabilize the biophysical properties of the domain, rather than playing a significant role in antigen binding.
Collapse
Affiliation(s)
- Matthew N Mendoza
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Mike Jian
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Moeko T King
- Department of Chemistry, California State University Fresno, Fresno, California
| | - Cory L Brooks
- Department of Chemistry, California State University Fresno, Fresno, California
| |
Collapse
|