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Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024; 19:1583-1592. [PMID: 38916527 PMCID: PMC11299430 DOI: 10.1021/acschembio.4c00236] [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] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
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Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Alexis D. Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Stéphane P. Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
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2
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Szkodny AC, Lee KH. A systemic approach to identifying sequence frameworks that decrease mAb production in a transient Chinese hamster ovary cell expression system. Biotechnol Prog 2024:e3466. [PMID: 38607316 DOI: 10.1002/btpr.3466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/17/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Monoclonal antibodies (mAbs) are often engineered at the sequence level for improved clinical performance yet are rarely evaluated prior to candidate selection for their "developability" characteristics, namely expression, which can necessitate additional resource investments to improve the manufacturing processes for problematic mAbs. A strong relationship between primary sequence and expression has emerged, with slight differences in amino acid sequence resulting in titers differing by up to an order of magnitude. Previous work on these "difficult-to-express" (DTE) mAbs has shown that these phenotypes are driven by post-translational bottlenecks in antibody folding, assembly, and secretion processes. However, it has been difficult to translate these findings across cell lines and products. This work presents a systematic approach to study the impact of sequence variation on mAb expression at a larger scale and under more industrially relevant conditions. The analysis found 91 mutations that decreased transient expression of an IgG1κ in Chinese hamster ovary (CHO) cells and revealed that mutations at inaccessible residues, especially those leading to decreases in residue hydrophobicity, are not favorable for high expression. This workflow can be used to better understand sequence determinants of mAb expression to improve candidate selection procedures and reduce process development timelines.
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Affiliation(s)
- Alana C Szkodny
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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3
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Arslan M, Uluçay T, Kale S, Kalyoncu S. Engineering of conserved residues near antibody heavy chain complementary determining region 3 (HCDR3) improves both affinity and stability. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140915. [PMID: 37059314 DOI: 10.1016/j.bbapap.2023.140915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Affinity and stability are crucial parameters in antibody development and engineering approaches. Although improvement in both metrics is desirable, trade-offs are almost unavoidable. Heavy chain complementarity determining region 3 (HCDR3) is the best-known region for antibody affinity but its impact on stability is often neglected. Here, we present a mutagenesis study of conserved residues near HCDR3 to elicit the role of this region in the affinity-stability trade-off. These key residues are positioned around the conserved salt bridge between VH-K94 and VH-D101 which is crucial for HCDR3 integrity. We show that the additional salt bridge at the stem of HCDR3 (VH-K94:VH-D101:VH-D102) has an extensive impact on this loop's conformation, therefore simultaneous improvement in both affinity and stability. We find that the disruption of π-π stacking near HCDR3 (VH-Y100E:VL-Y49) at the VH-VL interface cause an irrecoverable loss in stability even if it improves the affinity. Molecular simulations of putative rescue mutants exhibit complex and often non-additive effects. We confirm that our experimental measurements agree with the molecular dynamic simulations providing detailed insights for the spatial orientation of HCDR3. VH-V102 right next to HCDR3 salt bridge might be an ideal candidate to overcome affinity-stability trade-off.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balçova, 35340 Izmir, Turkey
| | - Tuğçe Uluçay
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey
| | - Sibel Kalyoncu
- Izmir Biomedicine and Genome Center, Balçova, 35340 Izmir, Turkey.
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4
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Structural mechanism of Fab domain dissociation as a measure of interface stability. J Comput Aided Mol Des 2023; 37:201-215. [PMID: 36918473 PMCID: PMC10049950 DOI: 10.1007/s10822-023-00501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.
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5
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Chang HJ, Zúñiga A, Conejero I, Voyvodic PL, Gracy J, Fajardo-Ruiz E, Cohen-Gonsaud M, Cambray G, Pageaux GP, Meszaros M, Meunier L, Bonnet J. Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples. Nat Commun 2021; 12:5216. [PMID: 34471137 PMCID: PMC8410942 DOI: 10.1038/s41467-021-25538-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial biosensors, or bactosensors, are promising agents for medical and environmental diagnostics. However, the lack of scalable frameworks to systematically program ligand detection limits their applications. Here we show how novel, clinically relevant sensing modalities can be introduced into bactosensors in a modular fashion. To do so, we have leveraged a synthetic receptor platform, termed EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) which supports the modular assembly of sensing modules onto a high-performance, generic signaling scaffold controlling gene expression in E. coli. We apply EMeRALD to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We improve the sensitivity and lower the limit-of-detection of the sensing module by directed evolution. We then engineer a colorimetric bactosensor detecting pathological bile salt levels in serum from patients having undergone liver transplant, providing an output detectable by the naked-eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes.
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Affiliation(s)
- Hung-Ju Chang
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ana Zúñiga
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ismael Conejero
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
- Neuropsychiatry: Epidemiological and Clinical Research, Inserm Unit 1061, Montpellier, France
- Department of Psychiatry, CHU Nimes, University of Montpellier, Montpellier, France
| | - Peter L Voyvodic
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Jerome Gracy
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Elena Fajardo-Ruiz
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Georges-Philippe Pageaux
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Magdalena Meszaros
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Lucy Meunier
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France.
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6
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Hsu HJ, Tung CP, Yu CM, Chen CY, Chen HS, Huang YC, Tsai PH, Lin SI, Peng HP, Chiu YK, Tsou YL, Kuo WY, Jian JW, Hung FH, Hsieh CY, Hsiao M, Chuang SSH, Shen CN, Wang YA, Yang AS. Eradicating mesothelin-positive human gastric and pancreatic tumors in xenograft models with optimized anti-mesothelin antibody-drug conjugates from synthetic antibody libraries. Sci Rep 2021; 11:15430. [PMID: 34326410 PMCID: PMC8322431 DOI: 10.1038/s41598-021-94902-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023] Open
Abstract
Mesothelin (MSLN) is an attractive candidate of targeted therapy for several cancers, and hence there are increasing needs to develop MSLN-targeting strategies for cancer therapeutics. Antibody–drug conjugates (ADCs) targeting MSLN have been demonstrated to be a viable strategy in treating MSLN-positive cancers. However, developing antibodies as targeting modules in ADCs for toxic payload delivery to the tumor site but not to normal tissues is not a straightforward task with many potential hurdles. In this work, we established a high throughput engineering platform to develop and optimize anti-MSLN ADCs by characterizing more than 300 scFv CDR-variants and more than 50 IgG CDR-variants of a parent anti-MSLN antibody as candidates for ADCs. The results indicate that only a small portion of the complementarity determining region (CDR) residues are indispensable in the MSLN-specific targeting. Also, the enhancement of the hydrophilicity of the rest of the CDR residues could drastically increase the overall solubility of the optimized anti-MSLN antibodies, and thus substantially improve the efficacies of the ADCs in treating human gastric and pancreatic tumor xenograft models in mice. We demonstrated that the in vivo treatments with the optimized ADCs resulted in almost complete eradication of the xenograft tumors at the treatment endpoints, without detectable off-target toxicity because of the ADCs’ high specificity targeting the cell surface tumor-associated MSLN. The technological platform can be applied to optimize the antibody sequences for more effective targeting modules of ADCs, even when the candidate antibodies are not necessarily feasible for the ADC development due to the antibodies’ inferior solubility or affinity/specificity to the target antigen.
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Affiliation(s)
- Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chi-Yung Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Hong-Sen Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yu-Chuan Huang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Pei-Hsun Tsai
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Su-I Lin
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yi-Kai Chiu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yueh-Liang Tsou
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Wei-Ying Kuo
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Fei-Hung Hung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chiao-Yun Hsieh
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | | | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | | | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan.
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7
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Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains. J Biol Chem 2021; 296:100334. [PMID: 33508322 PMCID: PMC7949129 DOI: 10.1016/j.jbc.2021.100334] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Systemic light chain (AL) amyloidosis is a fatal protein misfolding disease in which excessive secretion, misfolding, and subsequent aggregation of free antibody light chains eventually lead to deposition of amyloid plaques in various organs. Patient-specific mutations in the antibody VL domain are closely linked to the disease, but the molecular mechanisms by which certain mutations induce misfolding and amyloid aggregation of antibody domains are still poorly understood. Here, we compare a patient VL domain with its nonamyloidogenic germline counterpart and show that, out of the five mutations present, two of them strongly destabilize the protein and induce amyloid fibril formation. Surprisingly, the decisive, disease-causing mutations are located in the highly variable complementarity determining regions (CDRs) but exhibit a strong impact on the dynamics of conserved core regions of the patient VL domain. This effect seems to be based on a deviation from the canonical CDR structures of CDR2 and CDR3 induced by the substitutions. The amyloid-driving mutations are not necessarily involved in propagating fibril formation by providing specific side chain interactions within the fibril structure. Rather, they destabilize the VL domain in a specific way, increasing the dynamics of framework regions, which can then change their conformation to form the fibril core. These findings reveal unexpected influences of CDR-framework interactions on antibody architecture, stability, and amyloid propensity.
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8
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Beirão BCB, Raposo TP, Imamura LM, Ingberman M, Hupp T, Vojtěšek B, Argyle DJ. A blocking antibody against canine CSF-1R maturated by limited CDR mutagenesis. Antib Ther 2020; 3:193-204. [PMID: 33937625 PMCID: PMC7990251 DOI: 10.1093/abt/tbaa018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/02/2020] [Accepted: 07/29/2020] [Indexed: 01/15/2023] Open
Abstract
CSF-1R is a receptor mostly associated with the mononuclear phagocytic system. However, its expression within tumors has been linked with poor prognosis in both humans and dogs. Accordingly, several reports have demonstrated the beneficial effects of blocking CSF-1R in model systems of cancer. In this study, we generated a monoclonal antibody that could block CSF-1R in dogs as the first step to develop an anticancer drug for this species. Initially, an antibody was raised by the hybridoma methodology against the fragment responsible for receptor dimerization. mAb3.1, one of the resulting hybridoma clones, was able to bind macrophages in fixed tissues and was shown to inhibit cells of the mononuclear phagocytic line. Nevertheless, mAb 3.1 could not bind to some glycoforms of the receptor in its native form, while also demonstrating cross-reactivity with other proteins. To enhance binding properties of the mAb, five amino acids of the complementarity-determining region 2 of the variable heavy chain of mAb3.1 were mutated by PCR, and the variant scFv clones were screened by phage display. The selected scFv clones demonstrated improved binding to the native receptor as well as increased anti-macrophage activity. The resulting scFv antibody fragment presented here has the potential for use in cancer patients and in inflammatory diseases. Furthermore, this work provides insights into the use of such restricted mutations in antibody engineering.
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Affiliation(s)
- Breno C B Beirão
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh-Easter Bush, Midlothian, EH25 9RG, UK
| | - Teresa P Raposo
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh-Easter Bush, Midlothian, EH25 9RG, UK
| | - Louise M Imamura
- Department of Research and Development, Imunova Análises Biológicas, Curitiba, PR 80215-182, Brazil
| | - Max Ingberman
- Department of Research and Development, Imunova Análises Biológicas, Curitiba, PR 80215-182, Brazil
| | - Ted Hupp
- Cancer Research UK Edinburgh Centre MRC Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Bořivoj Vojtěšek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, 656 53, Czech Republic
| | - David J Argyle
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, The University of Edinburgh-Easter Bush, Midlothian, EH25 9RG, UK
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9
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A panel of anti-influenza virus nucleoprotein antibodies selected from phage-displayed synthetic antibody libraries with rapid diagnostic capability to distinguish diverse influenza virus subtypes. Sci Rep 2020; 10:13318. [PMID: 32770098 PMCID: PMC7414213 DOI: 10.1038/s41598-020-70135-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Immunoassays based on sandwich immuno-complexes of capture and detection antibodies simultaneously binding to the target analytes have been powerful technologies in molecular analyses. Recent developments in single molecule detection technologies enable the detection limit of the sandwich immunoassays approaching femtomolar (10-15 M), driving the needs of developing sensitive and specific antibodies for ever-increasingly broad applications in detecting and quantifying biomarkers. The key components underlying the sandwich immunoassays are antibody-based affinity reagents, for which the conventional sources are mono- or poly-clonal antibodies from immunized animals. The downsides of the animal-based antibodies as affinity reagents arise from the requirement of months of development timespan and limited choices of antibody candidates due to immunodominance of humoral immune responses in animals. Hence, developing animal antibodies capable of distinguishing highly related antigens could be challenging. To overcome the limitation imposed by the animal immune systems, we developed an in vitro methodology based on phage-displayed synthetic antibody libraries for diverse antibodies as affinity reagents against closely related influenza virus nucleoprotein (NP) subtypes, aiming to differentiating avian influenza virus (H5N1) from seasonal influenza viruses (H1N1 and H3N2), for which the NPs are closely related by 90-94% in terms of pairwise amino acid sequence identity. We applied the methodology to attain, within four weeks, a panel of IgGs with distinguishable specificities against a group of representative NPs with pairwise amino acid sequence identities up to more than 90%, and the antibodies derived from the antibody libraries without further affinity refinement had comparable affinity of mouse antibodies to the NPs with the detection limit less than 1 nM of viral NP from lysed virus with sandwich ELISA. The panel of IgGs were capable of rapidly distinguishing infections due to virulent avian influenza virus from infections of seasonal flu, in responding to a probable emergency scenario where avian influenza virus would be transmissible among humans overlapping with the seasonal influenza infections. The results indicate that the in vitro antibody development methodology enables developing diagnostic antibodies that would not otherwise be available from animal-based antibody technologies.
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10
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Pang WC, Ramli ANM, Hamid AAA. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 2020; 26:142. [PMID: 32417971 DOI: 10.1007/s00894-020-04398-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/28/2020] [Indexed: 12/25/2022]
Abstract
Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.
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Affiliation(s)
- Wei Cheng Pang
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia. .,Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
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11
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Stimple SD, Smith MD, Tessier PM. Directed evolution methods for overcoming trade-offs between protein activity and stability. AIChE J 2020; 66. [PMID: 32719568 DOI: 10.1002/aic.16814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Engineered proteins are being widely developed and employed in applications ranging from enzyme catalysts to therapeutic antibodies. Directed evolution, an iterative experimental process composed of mutagenesis and library screening, is a powerful technique for enhancing existing protein activities and generating entirely new ones not observed in nature. However, the process of accumulating mutations for enhanced protein activity requires chemical and structural changes that are often destabilizing, and low protein stability is a significant barrier to achieving large enhancements in activity during multiple rounds of directed evolution. Here we highlight advances in understanding the origins of protein activity/stability trade-offs for two important classes of proteins (enzymes and antibodies) as well as innovative experimental and computational methods for overcoming such trade-offs. These advances hold great potential for improving the generation of highly active and stable proteins that are needed to address key challenges related to human health, energy and the environment.
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Affiliation(s)
- Samuel D. Stimple
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Matthew D. Smith
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Biomedical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
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12
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Kunz P, Ortale A, Mücke N, Zinner K, Hoheisel JD. Nanobody stability engineering by employing the ΔTm shift; a comparison with apparent rate constants of heat-induced aggregation. Protein Eng Des Sel 2019; 32:241-249. [PMID: 31340035 DOI: 10.1093/protein/gzz017] [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: 03/17/2019] [Revised: 06/09/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
The antigen-binding domains of camelid heavy-chain antibodies, also called nanobodies, gained strong attention because of their unique functional and biophysical properties. They gave rise to an entire spectrum of applications in biotechnology, research and medicine. Despite several reports about reversibly refolding nanobodies, protein aggregation plays a major role in nanobody thermoresistance, asking for strategies to engineer their refolding behavior. Here, we use measurements of nanobody aggregation kinetics to validate structural features in the nanobody fold that are suppressing heat-induced nanobody aggregation. Furthermore, the kinetic measurements yielded a detailed insight into the concept of the ΔTm shift, a metric for protein aggregation propensities obtained from differential scanning fluorimetry measurements. By relating the equilibrium measurements of the ΔTm shift to the kinetic measurements of heat-induced nanobody aggregation, a distinct relationship could be identified that allows a prediction of nanobody aggregation rates from a simple equilibrium measurement of ΔTm.
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Affiliation(s)
- Patrick Kunz
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Aurelio Ortale
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Norbert Mücke
- Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Katinka Zinner
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany
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13
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Henderson R, Watts BE, Ergin HN, Anasti K, Parks R, Xia SM, Trama A, Liao HX, Saunders KO, Bonsignori M, Wiehe K, Haynes BF, Alam SM. Selection of immunoglobulin elbow region mutations impacts interdomain conformational flexibility in HIV-1 broadly neutralizing antibodies. Nat Commun 2019; 10:654. [PMID: 30737386 PMCID: PMC6368608 DOI: 10.1038/s41467-019-08415-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023] Open
Abstract
Somatic mutations within antibody variable and framework regions (FWR) can alter thermostability and structural flexibility, but their impact on functional potency is unclear. Here we study thermostability and use molecular dynamics (MD) simulations to assess the role of FWR mutations during maturation of HIV-1 broadly neutralizing antibodies (bnAbs). The tested bnAbs show lower thermostability than their unmutated ancestor antibodies. FWR mutations in the Fab elbow region are frequently observed in HIV-1 bnAbs and MD simulations show that such FWR mutations alter interdomain flexibility in two HIV-1 bnAbs. In a CD4-binding site lineage, reversion mutations result in a loss of neutralization potency in an early intermediate and affinity-matured bnAb against autologous and heterologous Tier-2 viruses, respectively. Elbow region reversion mutations in a glycan-V3 bnAb modestly reduces potency against an autologous virus isolate. Thus, selection of mutations in the Fab elbow region impacts interdomain conformational flexibility and paratope plasticity during bnAb development.
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Affiliation(s)
- Rory Henderson
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Brian E Watts
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hieu N Ergin
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kara Anasti
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Robert Parks
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Shi-Mao Xia
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ashley Trama
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Kevin O Saunders
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Mattia Bonsignori
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
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14
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Jian JW, Chen HS, Chiu YK, Peng HP, Tung CP, Chen IC, Yu CM, Tsou YL, Kuo WY, Hsu HJ, Yang AS. Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities. MAbs 2019; 11:373-387. [PMID: 30526270 PMCID: PMC6380391 DOI: 10.1080/19420862.2018.1550320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Antibodies provide immune protection by recognizing antigens of diverse chemical properties, but elucidating the amino acid sequence-function relationships underlying the specificity and affinity of antibody-antigen interactions remains challenging. We designed and constructed phage-displayed synthetic antibody libraries with enriched protein antigen-recognition propensities calculated with machine learning predictors, which indicated that the designed single-chain variable fragment variants were encoded with enhanced distributions of complementarity-determining region (CDR) hot spot residues with high protein antigen recognition propensities in comparison with those in the human antibody germline sequences. Antibodies derived directly from the synthetic antibody libraries, without affinity maturation cycles comparable to those in in vivo immune systems, bound to the corresponding protein antigen through diverse conformational or linear epitopes with specificity and affinity comparable to those of the affinity-matured antibodies from in vivo immune systems. The results indicated that more densely populated CDR hot spot residues were sustainable by the antibody structural frameworks and could be accompanied by enhanced functionalities in recognizing protein antigens. Our study results suggest that synthetic antibody libraries, which are not limited by the sequences found in antibodies in nature, could be designed with the guidance of the computational machine learning algorithms that are programmed to predict interaction propensities to molecules of diverse chemical properties, leading to antibodies with optimal characteristics pertinent to their medical applications.
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Affiliation(s)
- Jhih-Wei Jian
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan.,b Institute of Biomedical Informatics, National Yang-Ming University , Taipei , Taiwan.,c Bioinformatics Program, Taiwan International Graduate Program , Institute of Information Science, Academia Sinica , Taipei , Taiwan
| | - Hong-Sen Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yi-Kai Chiu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Pin Peng
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chao-Ping Tung
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Ing-Chien Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chung-Ming Yu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yueh-Liang Tsou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Wei-Ying Kuo
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Ju Hsu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - An-Suei Yang
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
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15
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Kuo WY, Hsu HJ, Wu CY, Chen HS, Chou YC, Tsou YL, Peng HP, Jian JW, Yu CM, Chiu YK, Chen IC, Tung CP, Hsiao M, Lin CL, Wang YA, Wang AHJ, Yang AS. Antibody-drug conjugates with HER2-targeting antibodies from synthetic antibody libraries are highly potent against HER2-positive human gastric tumor in xenograft models. MAbs 2018; 11:153-165. [PMID: 30365359 PMCID: PMC6343809 DOI: 10.1080/19420862.2018.1541370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HER2-ECD (human epidermal growth factor receptor 2 – extracellular domain) is a prominent therapeutic target validated for treating HER2-positive breast and gastric cancer, but HER2-specific therapeutic options for treating advanced gastric cancer remain limited. We have developed antibody-drug conjugates (ADCs), comprising IgG1 linked via valine-citrulline to monomethyl auristatin E, with potential to treat HER2-positive gastric cancer in humans. The antibodies optimally selected from the ADC discovery platform, which was developed to discover antibody candidates suitable for immunoconjugates from synthetic antibody libraries designed using antibody-antigen interaction principles, were demonstrated to be superior immunoconjugate targeting modules in terms of efficacy and off-target toxicity. In comparison with the two control humanized antibodies (trastuzumab and H32) derived from murine antibody repertoires, the antibodies derived from the synthetic antibody libraries had enhanced receptor-mediated internalization rate, which could result in ADCs with optimal efficacies. Along with the ADCs, two other forms of immunoconjugates (scFv-PE38KDEL and IgG1-AL1-PE38KDEL) were used to test the antibodies for delivering cytotoxic payloads to xenograft tumor models in vivo and to cultured cells in vitro. The in vivo experiments with the three forms of immunoconjugates revealed minimal off-target toxicities of the selected antibodies from the synthetic antibody libraries; the off-target toxicities of the control antibodies could have resulted from the antibodies’ propensity to target the liver in the animal models. Our ADC discovery platform and the knowledge gained from our in vivo tests on xenograft models with the three forms of immunoconjugates could be useful to anyone developing optimal ADC cancer therapeutics.
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Affiliation(s)
- Wei-Ying Kuo
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Ju Hsu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chun-Yi Wu
- b Department of Biomedical Imaging and Radiological Science, College of Medicine , China Medical University , Taichung , Taiwan
| | - Hong-Sen Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yu-Chi Chou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yueh-Liang Tsou
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hung-Pin Peng
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Jhih-Wei Jian
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan.,c Institute of Biomedical Informatics , National Yang-Ming University , Taipei , Taiwan.,d Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science , Academia Sinica , Taipei , Taiwan
| | - Chung-Ming Yu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Yi-Kai Chiu
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Ing-Chien Chen
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chao-Ping Tung
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Michael Hsiao
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Chia-Lung Lin
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | | | - Andrew H-J Wang
- f Institute of Biological Chemistry , Academia Sinica , Taipei , Taiwan
| | - An-Suei Yang
- a Genomics Research Center , Academia Sinica , Taipei , Taiwan
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16
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High throughput discovery of influenza virus neutralizing antibodies from phage-displayed synthetic antibody libraries. Sci Rep 2017; 7:14455. [PMID: 29089574 PMCID: PMC5663709 DOI: 10.1038/s41598-017-14823-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/16/2017] [Indexed: 12/18/2022] Open
Abstract
Pandemic and epidemic outbreaks of influenza A virus (IAV) infection pose severe challenges to human society. Passive immunotherapy with recombinant neutralizing antibodies can potentially mitigate the threats of IAV infection. With a high throughput neutralizing antibody discovery platform, we produced artificial anti-hemagglutinin (HA) IAV-neutralizing IgGs from phage-displayed synthetic scFv libraries without necessitating prior memory of antibody-antigen interactions or relying on affinity maturation essential for in vivo immune systems to generate highly specific neutralizing antibodies. At least two thirds of the epitope groups of the artificial anti-HA antibodies resemble those of natural protective anti-HA antibodies, providing alternatives to neutralizing antibodies from natural antibody repertoires. With continuing advancement in designing and constructing synthetic scFv libraries, this technological platform is useful in mitigating not only the threats of IAV pandemics but also those from other newly emerging viral infections.
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Abstract
BACKGROUND Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. METHODS We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. RESULTS Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. CONCLUSIONS The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. GENERAL SIGNIFICANCE This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods.
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18
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Su CTT, Ling WL, Lua WH, Poh JJ, Gan SKE. The role of Antibody Vκ Framework 3 region towards Antigen binding: Effects on recombinant production and Protein L binding. Sci Rep 2017. [PMID: 28630463 PMCID: PMC5476676 DOI: 10.1038/s41598-017-02756-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antibody research has traditionally focused on heavy chains, often neglecting the important complementary role of light chains in antibody formation and secretion. In the light chain, the complementarity-determining region 3 (VL-CDR3) is specifically implicated in disease states. By modulating VL-CDR3 exposure on the scaffold through deletions in the framework region 3 (VL-FWR3), we further investigated the effects on secretion in recombinant production and antigen binding kinetics. Our random deletions of two residues in the VL-FWR3 of a Trastuzumab model showed that the single deletions could impact recombinant production without significant effect on Her2 binding. When both the selected residues were deleted, antibody secretion was additively decreased, and so was Her2 binding kinetics. Interestingly, we also found allosteric effects on the Protein L binding site at VL-FWR1 elicited by these deletions in VL- FWR3. Together, these findings demonstrate the importance of light chain FWR3 in antigen binding, recombinant production, and antibody purification using Protein L.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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19
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Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding. Proc Natl Acad Sci U S A 2017; 114:E486-E495. [PMID: 28057863 DOI: 10.1073/pnas.1613231114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo.
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20
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Kwong PD, Chuang G, DeKosky BJ, Gindin T, Georgiev IS, Lemmin T, Schramm CA, Sheng Z, Soto C, Yang A, Mascola JR, Shapiro L. Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1. Immunol Rev 2017; 275:108-128. [PMID: 28133812 PMCID: PMC5516196 DOI: 10.1111/imr.12480] [Citation(s) in RCA: 28] [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] [Indexed: 12/16/2022]
Abstract
Numerous antibodies have been identified from HIV-1-infected donors that neutralize diverse strains of HIV-1. These antibodies may provide the basis for a B cell-mediated HIV-1 vaccine. However, it has been unclear how to elicit similar antibodies by vaccination. To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies. As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway, and prevalence of broadly neutralizing antibody lineages (Antibodyomics1, 2, 4, and 6). We also incorporated large-scale robotic analyses of serum neutralization to identify and quantify neutralizing antibodies in donor cohorts (Antibodyomics3). Statistical analyses furnish another layer of insight (Antibodyomics5), with physical characteristics of antibodies and their targets through molecular dynamics simulations (Antibodyomics7) and free energy perturbation analyses (Antibodyomics8) providing information-rich output. Functional interrogation of individual antibodies (Antibodyomics9) and synthetic antibody libraries (Antibodyomics10) also yields multi-dimensional data by which to understand and improve antibodies. Antibodyomics, described here, thus comprise resolution-enhancing tools, which collectively embody an information-driven discovery engine aimed toward the development of effective B cell-based vaccines.
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Affiliation(s)
- Peter D. Kwong
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Gwo‐Yu Chuang
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Brandon J. DeKosky
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Tatyana Gindin
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
| | - Ivelin S. Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTNUSA
| | - Thomas Lemmin
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCAUSA
| | - Chaim A. Schramm
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Zizhang Sheng
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Cinque Soto
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - An‐Suei Yang
- Genomics Research CenterAcademia SinicaTaipeiTaiwan
| | - John R. Mascola
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Lawrence Shapiro
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
- Department of Biochemistry & Molecular BiophysicsColumbia UniversityNew YorkNYUSA
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
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21
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van Rosmalen M, Janssen BMG, Hendrikse NM, van der Linden AJ, Pieters PA, Wanders D, de Greef TFA, Merkx M. Affinity Maturation of a Cyclic Peptide Handle for Therapeutic Antibodies Using Deep Mutational Scanning. J Biol Chem 2016; 292:1477-1489. [PMID: 27974464 DOI: 10.1074/jbc.m116.764225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/29/2016] [Indexed: 11/06/2022] Open
Abstract
Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging, and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning. Deep sequencing was used to construct a fitness landscape of this protein-peptide interaction, and four mutations were identified that together improved the affinity for cetuximab 10-fold to 15 nm Importantly, the increased affinity translated into enhanced cetuximab-mediated recruitment to EGF receptor-overexpressing cancer cells. Although in silico Rosetta simulations correctly identified positions that were tolerant to mutation, modeling did not accurately predict the affinity-enhancing mutations. The experimental approach reported here should be generally applicable and could be used to develop meditope peptides with low nanomolar affinity for other therapeutic antibodies.
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Affiliation(s)
- Martijn van Rosmalen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Brian M G Janssen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Natalie M Hendrikse
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Dave Wanders
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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22
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High throughput cytotoxicity screening of anti-HER2 immunotoxins conjugated with antibody fragments from phage-displayed synthetic antibody libraries. Sci Rep 2016; 6:31878. [PMID: 27550798 PMCID: PMC4994030 DOI: 10.1038/srep31878] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/29/2016] [Indexed: 02/07/2023] Open
Abstract
Immunotoxins are an important class of antibody-based therapeutics. The potency of the immunotoxins depends on the antibody fragments as the guiding modules targeting designated molecules on cell surfaces. Phage-displayed synthetic antibody scFv libraries provide abundant antibody fragment candidates as targeting modules for the immunoconjugates, but the discovery of optimally functional immunoconjugates is limited by the scFv-payload conjugation procedure. In this work, cytotoxicity screening of non-covalently assembled immunotoxins was developed in high throughput format to discover highly functional synthetic antibody fragments for delivering toxin payloads. The principles governing the efficiency of the antibodies as targeting modules have been elucidated from large volume of cytotoxicity data: (a) epitope and paratope of the antibody-based targeting module are major determinants for the potency of the immunotoxins; (b) immunotoxins with bivalent antibody-based targeting modules are generally superior in cytotoxic potency to those with corresponding monovalent targeting module; and (c) the potency of the immunotoxins is positively correlated with the densities of the cell surface antigen. These findings suggest that screening against the target cells with a large pool of antibodies from synthetic antibody libraries without the limitations of natural antibody responses can lead to optimal potency and minimal off-target toxicity of the immunoconjugates.
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23
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Lee CC, Julian MC, Tiller KE, Meng F, DuConge SE, Akter R, Raleigh DP, Tessier PM. Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide. J Biol Chem 2015; 291:2858-73. [PMID: 26601942 DOI: 10.1074/jbc.m115.682336] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/25/2022] Open
Abstract
Antibodies with conformational specificity are important for detecting and interfering with polypeptide aggregation linked to several human disorders. We are developing a motif-grafting approach for designing lead antibody candidates specific for amyloid-forming polypeptides such as the Alzheimer peptide (Aβ). This approach involves grafting amyloidogenic peptide segments into the complementarity-determining regions (CDRs) of single-domain (VH) antibodies. Here we have investigated the impact of polar mutations inserted at the edges of a large hydrophobic Aβ42 peptide segment (Aβ residues 17-42) in CDR3 on the solubility and conformational specificity of the corresponding VH domains. We find that VH expression and solubility are strongly enhanced by introducing multiple negatively charged or asparagine residues at the edges of CDR3, whereas other polar mutations are less effective (glutamine and serine) or ineffective (threonine, lysine, and arginine). Moreover, Aβ VH domains with negatively charged CDR3 mutations show significant preference for recognizing Aβ fibrils relative to Aβ monomers, whereas the same VH domains with other polar CDR3 mutations recognize both Aβ conformers. We observe similar behavior for a VH domain grafted with a large hydrophobic peptide from islet amyloid polypeptide (residues 8-37) that contains negatively charged mutations at the edges of CDR3. These findings highlight the sensitivity of antibody binding and solubility to residues at the edges of CDRs, and provide guidelines for designing other grafted antibody fragments with hydrophobic binding loops.
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Affiliation(s)
- Christine C Lee
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Mark C Julian
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Kathryn E Tiller
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Fanling Meng
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Sarah E DuConge
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Rehana Akter
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Daniel P Raleigh
- the Department of Chemistry, Stony Brook University, Stony Brook, New York 11794
| | - Peter M Tessier
- From the Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 and
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Tung CP, Chen IC, Yu CM, Peng HP, Jian JW, Ma SH, Lee YC, Jan JT, Yang AS. Discovering neutralizing antibodies targeting the stem epitope of H1N1 influenza hemagglutinin with synthetic phage-displayed antibody libraries. Sci Rep 2015; 5:15053. [PMID: 26456860 PMCID: PMC4601012 DOI: 10.1038/srep15053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/15/2015] [Indexed: 11/09/2022] Open
Abstract
Broadly neutralizing antibodies developed from the IGHV1-69 germline gene are known to bind to the stem region of hemagglutinin in diverse influenza viruses but the sequence determinants for the antigen recognition, including neutralization potency and binding affinity, are not clearly understood. Such understanding could inform designs of synthetic antibody libraries targeting the stem epitope on hemagglutinin, leading to artificially designed antibodies that are functionally advantageous over antibodies from natural antibody repertoires. In this work, the sequence space of the complementarity determining regions of a broadly neutralizing antibody (F10) targeting the stem epitope on the hemagglutinin of a strain of H1N1 influenza virus was systematically explored; the elucidated antibody-hemagglutinin recognition principles were used to design a phage-displayed antibody library, which was then used to discover neutralizing antibodies against another strain of H1N1 virus. More than 1000 functional antibody candidates were selected from the antibody library and were shown to neutralize the corresponding strain of influenza virus with up to 7 folds higher potency comparing with the parent F10 antibody. The antibody library could be used to discover functionally effective antibodies against other H1N1 influenza viruses, supporting the notion that target-specific antibody libraries can be designed and constructed with systematic sequence-function information.
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Affiliation(s)
- Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 112.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 115
| | - Shiou-Hwa Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
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Julian MC, Lee CC, Tiller KE, Rabia LA, Day EK, Schick AJ, Tessier PM. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies. Protein Eng Des Sel 2015; 28:339-50. [PMID: 26386257 DOI: 10.1093/protein/gzv050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments.
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Affiliation(s)
- Mark C Julian
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christine C Lee
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kathryn E Tiller
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lilia A Rabia
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Evan K Day
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Arthur J Schick
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Chen HS, Hou SC, Jian JW, Goh KS, Shen ST, Lee YC, You JJ, Peng HP, Kuo WC, Chen ST, Peng MC, Wang AHJ, Yu CM, Chen IC, Tung CP, Chen TH, Ping Chiu K, Ma C, Yuan Wu C, Lin SW, Yang AS. Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens. Sci Rep 2015. [PMID: 26202883 PMCID: PMC5378893 DOI: 10.1038/srep12411] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Humoral immunity against diverse pathogens is rapidly elicited from natural antibody repertoires of limited complexity. But the organizing principles underlying the antibody repertoires that facilitate this immunity are not well-understood. We used HER2 as a model immunogen and reverse-engineered murine antibody response through constructing an artificial antibody library encoded with rudimentary sequence and structural characteristics learned from high throughput sequencing of antibody variable domains. Antibodies selected in vitro from the phage-displayed synthetic antibody library bound to the model immunogen with high affinity and specificities, which reproduced the specificities of natural antibody responses. We conclude that natural antibody structural repertoires are shaped to allow functional antibodies to be encoded efficiently, within the complexity limit of an individual antibody repertoire, to bind to diverse protein antigens with high specificity and affinity. Phage-displayed synthetic antibody libraries, in conjunction with high-throughput sequencing, can thus be designed to replicate natural antibody responses and to generate novel antibodies against diverse antigens.
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Affiliation(s)
- Hong-Sen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Shin-Chen Hou
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhih-Wei Jian
- 1] Genomics Research Center, Academia Sinica, Taipei, Taiwan 115 [2] Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan 112 [3] Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan 115
| | - King-Siang Goh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - San-Tai Shen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Jhong-Jhe You
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Wen-Chih Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Shui-Tsung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Ming-Chi Peng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan 115
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