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Raybould MIJ, Turnbull OM, Suter A, Guloglu B, Deane CM. Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling. Commun Biol 2024; 7:62. [PMID: 38191620 PMCID: PMC10774428 DOI: 10.1038/s42003-023-05744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/26/2023] [Indexed: 01/10/2024] Open
Abstract
Antibodies with lambda light chains (λ-antibodies) are generally considered to be less developable than those with kappa light chains (κ-antibodies). Though this hypothesis has not been formally established, it has led to substantial systematic biases in drug discovery pipelines and thus contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged by λ-antibodies shows there is a functional cost to neglecting to consider them as potential lead candidates. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction, and apply it to evaluate developability risk profiles for κ-antibodies and λ-antibodies based on their surface physicochemical properties. We find that while human λ-antibodies on average have a higher risk of developability issues than κ-antibodies, a sizeable proportion are assigned lower-risk profiles by TAP and should represent more tractable candidates for therapeutic development. Through a comparative analysis of the low- and high-risk populations, we highlight opportunities for strategic design that TAP suggests would enrich for more developable λ-antibodies. Overall, we provide context to the differing developability of κ- and λ-antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Oliver M Turnbull
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Annabel Suter
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
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Guloglu B, Deane CM. Specific attributes of the V L domain influence both the structure and structural variability of CDR-H3 through steric effects. Front Immunol 2023; 14:1223802. [PMID: 37564639 PMCID: PMC10410447 DOI: 10.3389/fimmu.2023.1223802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
Antibodies, through their ability to target virtually any epitope, play a key role in driving the adaptive immune response in jawed vertebrates. The binding domains of standard antibodies are their variable light (VL) and heavy (VH) domains, both of which present analogous complementarity-determining region (CDR) loops. It has long been known that the VH CDRs contribute more heavily to the antigen-binding surface (paratope), with the CDR-H3 loop providing a major modality for the generation of diverse paratopes. Here, we provide evidence for an additional role of the VL domain as a modulator of CDR-H3 structure, using a diverse set of antibody crystal structures and a large set of molecular dynamics simulations. We show that specific attributes of the VL domain such as subtypes, CDR canonical forms and genes can influence the structural diversity of the CDR-H3 loop, and provide a physical model for how this effect occurs through inter-loop contacts and packing of CDRs against each other. Our results indicate that the rigid minor loops fine-tune the structure of CDR-H3, thereby contributing to the generation of surfaces complementary to the vast number of possible epitope topologies, and provide insights into the interdependent nature of CDR conformations, an understanding of which is important for the rational antibody design process.
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Affiliation(s)
- Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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Gordon GL, Capel HL, Guloglu B, Richardson E, Stafford RL, Deane CM. A comparison of the binding sites of antibodies and single-domain antibodies. Front Immunol 2023; 14:1231623. [PMID: 37533864 PMCID: PMC10392943 DOI: 10.3389/fimmu.2023.1231623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Antibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sdAbs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sdAbs, suggesting that they include non-specific interactions to achieve comparable affinity. Furthermore, the epitopes of sdAbs are only marginally less accessible than those of Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.
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Affiliation(s)
- Gemma L. Gordon
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Henriette L. Capel
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eve Richardson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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Moskovitz R, Pholcharee T, DonVito SM, Guloglu B, Lowe E, Mohring F, Moon RW, Higgins MK. Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax. Nat Commun 2023; 14:3637. [PMID: 37336887 DOI: 10.1038/s41467-023-39357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023] Open
Abstract
The symptoms of malaria occur during the blood stage of infection, when the parasite replicates within human red blood cells. The human malaria parasite, Plasmodium vivax, selectively invades reticulocytes in a process which requires an interaction between the ectodomain of the human DARC receptor and the Plasmodium vivax Duffy-binding protein, PvDBP. Previous studies have revealed that a small helical peptide from DARC binds to region II of PvDBP (PvDBP-RII). However, it is also known that sulphation of tyrosine residues on DARC affects its binding to PvDBP and these residues were not observed in previous structures. We therefore present the structure of PvDBP-RII bound to sulphated DARC peptide, showing that a sulphate on tyrosine 41 binds to a charged pocket on PvDBP-RII. We use molecular dynamics simulations, affinity measurements and growth-inhibition experiments in parasites to confirm the importance of this interaction. We also reveal the epitope for vaccine-elicited growth-inhibitory antibody DB1. This provides a complete understanding of the binding of PvDBP-RII to DARC and will guide the design of vaccines and therapeutics to target this essential interaction.
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Affiliation(s)
- Re'em Moskovitz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tossapol Pholcharee
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sophia M DonVito
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Bora Guloglu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Edward Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Franziska Mohring
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Robert W Moon
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Ko KT, Lennartz F, Mekhaiel D, Guloglu B, Marini A, Deuker DJ, Long CA, Jore MM, Miura K, Biswas S, Higgins MK. Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies. Nat Commun 2022; 13:5603. [PMID: 36153317 PMCID: PMC9509318 DOI: 10.1038/s41467-022-33379-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/14/2022] [Indexed: 12/05/2022] Open
Abstract
An effective malaria vaccine remains a global health priority and vaccine immunogens which prevent transmission of the parasite will have important roles in multi-component vaccines. One of the most promising candidates for inclusion in a transmission-blocking malaria vaccine is the gamete surface protein Pfs48/45, which is essential for development of the parasite in the mosquito midgut. Indeed, antibodies which bind Pfs48/45 can prevent transmission if ingested with the parasite as part of the mosquito bloodmeal. Here we present the structure of full-length Pfs48/45, showing its three domains to form a dynamic, planar, triangular arrangement. We reveal where transmission-blocking and non-blocking antibodies bind on Pfs48/45. Finally, we demonstrate that antibodies which bind across this molecule can be transmission-blocking. These studies will guide the development of future Pfs48/45-based vaccine immunogens. Pfs48/45, a surface protein of Plasmodium falciparum, is a promising anti-malarial vaccine candidate whose structure is not entirely resolved. Here, the authors present the structure of the full-length molecule, and characterise the binding and activity of transmission blocking antibodies.
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