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Intracellular Antibodies for Drug Discovery and as Drugs of the Future. Antibodies (Basel) 2023; 12:antib12010024. [PMID: 36975371 PMCID: PMC10044824 DOI: 10.3390/antib12010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
The application of antibodies in cells was first shown in the early 1990s, and subsequently, the field of intracellular antibodies has expanded to encompass antibody fragments and their use in target validation and as engineered molecules that can be fused to moieties (referred to as warheads) to replace the Fc effector region of a whole immunoglobulin to elicit intracellular responses, such as cell death pathways or protein degradation. These various forms of intracellular antibodies have largely been used as research tools to investigate function within cells by perturbing protein activity. New applications of such molecules are on the horizon, namely their use as drugs per se and as templates for small-molecule drug discovery. The former is a potential new pharmacology that could harness the power and flexibility of molecular biology to generate new classes of drugs (herein referred to as macrodrugs when used in the context of disease control). Delivery of engineered intracellular antibodies, and other antigen-binding macromolecules formats, into cells to produce a therapeutic effect could be applied to any therapeutic area where regulation, degradation or other kinds of manipulation of target proteins can produce a therapeutic effect. Further, employing single-domain antibody fragments as competitors in small-molecule screening has been shown to enable identification of drug hits from diverse chemical libraries. Compounds selected in this way can mimic the effects of the intracellular antibodies that have been used for target validation. The capability of intracellular antibodies to discriminate between closely related proteins lends a new dimension to drug screening and drug development.
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Yin M, Izadi M, Tenglin K, Viennet T, Zhai L, Zheng G, Arthanari H, Dassama LMK, Orkin SH. Evolution of nanobodies specific for BCL11A. Proc Natl Acad Sci U S A 2023; 120:e2218959120. [PMID: 36626555 PMCID: PMC9933118 DOI: 10.1073/pnas.2218959120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Transcription factors (TFs) control numerous genes that are directly relevant to many human disorders. However, developing specific reagents targeting TFs within intact cells is challenging due to the presence of highly disordered regions within these proteins. Intracellular antibodies offer opportunities to probe protein function and validate therapeutic targets. Here, we describe the optimization of nanobodies specific for BCL11A, a validated target for the treatment of hemoglobin disorders. We obtained first-generation nanobodies directed to a region of BCL11A comprising zinc fingers 4 to 6 (ZF456) from a synthetic yeast surface display library, and employed error-prone mutagenesis, structural determination, and molecular modeling to enhance binding affinity. Engineered nanobodies recognized ZF6 and mediated targeted protein degradation (TPD) of BCL11A protein in erythroid cells, leading to the anticipated reactivation of fetal hemoglobin (HbF) expression. Evolved nanobodies distinguished BCL11A from its close paralog BCL11B, which shares an identical DNA-binding specificity. Given the ease of manipulation of nanobodies and their exquisite specificity, nanobody-mediated TPD of TFs should be suitable for dissecting regulatory relationships of TFs and gene targets and validating therapeutic potential of proteins of interest.
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Affiliation(s)
- Maolu Yin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Manizheh Izadi
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Karin Tenglin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Liting Zhai
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ge Zheng
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Laura M. K. Dassama
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Stuart H. Orkin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
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Sorbara M, Cordelier P, Bery N. Antibody-Based Approaches to Target Pancreatic Tumours. Antibodies (Basel) 2022; 11:antib11030047. [PMID: 35892707 PMCID: PMC9326758 DOI: 10.3390/antib11030047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 02/01/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with a dismal prognosis. This is due to the difficulty to detect the disease at an early and curable stage. In addition, only limited treatment options are available, and they are confronted by mechanisms of resistance. Monoclonal antibody (mAb) molecules are highly specific biologics that can be directly used as a blocking agent or modified to deliver a drug payload depending on the desired outcome. They are widely used to target extracellular proteins, but they can also be employed to inhibit intracellular proteins, such as oncoproteins. While mAbs are a class of therapeutics that have been successfully employed to treat many cancers, they have shown only limited efficacy in pancreatic cancer as a monotherapy so far. In this review, we will discuss the challenges, opportunities and hopes to use mAbs for pancreatic cancer treatment, diagnostics and imagery.
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Bery N, Rabbitts T. A Cell-based Screening Method Using an Intracellular Antibody for Discovering Small Molecules Targeting Hard-to-drug Proteins. Bio Protoc 2022; 12:e4324. [DOI: 10.21769/bioprotoc.4324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022] Open
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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Targeting small GTPases and their downstream pathways with intracellular macromolecule binders to define alternative therapeutic strategies in cancer. Biochem Soc Trans 2021; 49:2021-2035. [PMID: 34623375 DOI: 10.1042/bst20201059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
The RAS superfamily of small GTPases regulates major physiological cellular processes. Mutation or deregulation of these small GTPases, their regulators and/or their effectors are associated with many diseases including cancer. Hence, targeting these classes of proteins is an important therapeutic strategy in cancer. This has been recently achieved with the approval of the first KRASG12C covalent inhibitors for the clinic. However, many other mutants and small GTPases are still considered as 'undruggable' with small molecule inhibitors because of a lack of well-defined pocket(s) at their surface. Therefore, alternative therapeutic strategies have been developed to target these proteins. In this review, we discuss the use of intracellular antibodies and derivatives - reagents that bind their antigen inside the cells - for the discovery of novel inhibitory mechanisms, targetable features and therapeutic strategies to inhibit small GTPases and their downstream pathways. These reagents are also versatile tools used to better understand the biological mechanisms regulated by small GTPases and to accelerate the drug discovery process.
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Canning P, Bataille C, Bery N, Milhas S, Hayes A, Raynaud F, Miller A, Rabbitts T. Competitive SPR using an intracellular anti-LMO2 antibody identifies novel LMO2-interacting compounds. J Immunol Methods 2021; 494:113051. [PMID: 33794223 PMCID: PMC8208243 DOI: 10.1016/j.jim.2021.113051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 01/13/2023]
Abstract
The use of intracellular antibodies as templates to derive surrogate compounds is an important objective because intracellular antibodies can be employed initially for target validation in pre-clinical assays and subsequently employed in compound library screens. LMO2 is a T cell oncogenic protein activated in the majority of T cell acute leukaemias. We have used an inhibitory intracellular antibody fragment as a competitor in a small molecule library screen using competitive surface plasmon resonance (cSPR) to identify compounds that bind to LMO2. We selected four compounds that bind to LMO2 but not when the anti-LMO2 intracellular antibody fragment is bound to it. These findings further illustrate the value of intracellular antibodies in the initial stages of drug discovery campaigns and more generally antibodies, or antibody fragments, can be the starting point for chemical compound development as surrogates of the antibody combining site.
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Affiliation(s)
- Peter Canning
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Carole Bataille
- Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sabine Milhas
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Angela Hayes
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Terry Rabbitts
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK.
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