1
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Xu J, Gong J, Bo X, Tong Y, Ren Z, Ni M. A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity. Biophys Chem 2024; 311:107253. [PMID: 38768531 DOI: 10.1016/j.bpc.2024.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/08/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between -0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.
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Affiliation(s)
- Jiayi Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jianting Gong
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Zilin Ren
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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2
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Shirvanizadeh N, Vihinen M. VariBench, new variation benchmark categories and data sets. FRONTIERS IN BIOINFORMATICS 2023; 3:1248732. [PMID: 37795169 PMCID: PMC10546188 DOI: 10.3389/fbinf.2023.1248732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Affiliation(s)
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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3
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Purisima EO, Corbeil CR, Gaudreault F, Wei W, Deprez C, Sulea T. Solvated interaction energy: from small-molecule to antibody drug design. Front Mol Biosci 2023; 10:1210576. [PMID: 37351549 PMCID: PMC10282643 DOI: 10.3389/fmolb.2023.1210576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Scoring functions are ubiquitous in structure-based drug design as an aid to predicting binding modes and estimating binding affinities. Ideally, a scoring function should be broadly applicable, obviating the need to recalibrate and refit its parameters for every new target and class of ligands. Traditionally, drugs have been small molecules, but in recent years biologics, particularly antibodies, have become an increasingly important if not dominant class of therapeutics. This makes the goal of having a transferable scoring function, i.e., one that spans the range of small-molecule to protein ligands, even more challenging. One such broadly applicable scoring function is the Solvated Interaction Energy (SIE), which has been developed and applied in our lab for the last 15 years, leading to several important applications. This physics-based method arose from efforts to understand the physics governing binding events, with particular care given to the role played by solvation. SIE has been used by us and many independent labs worldwide for virtual screening and discovery of novel small-molecule binders or optimization of known drugs. Moreover, without any retraining, it is found to be transferrable to predictions of antibody-antigen relative binding affinities and as accurate as functions trained on protein-protein binding affinities. SIE has been incorporated in conjunction with other scoring functions into ADAPT (Assisted Design of Antibody and Protein Therapeutics), our platform for affinity modulation of antibodies. Application of ADAPT resulted in the optimization of several antibodies with 10-to-100-fold improvements in binding affinity. Further applications included broadening the specificity of a single-domain antibody to be cross-reactive with virus variants of both SARS-CoV-1 and SARS-CoV-2, and the design of safer antibodies by engineering of a pH switch to make them more selective towards acidic tumors while sparing normal tissues at physiological pH.
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4
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Serra GM, Siqueira AS, de Molfetta FA, Santos AV, Xavier LP. In Silico Analysis of a GH3 β-Glucosidase from Microcystis aeruginosa CACIAM 03. Microorganisms 2023; 11:microorganisms11040998. [PMID: 37110421 PMCID: PMC10146135 DOI: 10.3390/microorganisms11040998] [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: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/28/2023] [Indexed: 04/29/2023] Open
Abstract
Cyanobacteria are rich sources of secondary metabolites and have the potential to be excellent industrial enzyme producers. β-glucosidases are extensively employed in processing biomass degradation as they mediate the most crucial step of bioconversion of cellobiose (CBI), hence controlling the efficiency and global rate of biomass hydrolysis. However, the production and availability of these enzymes derived from cyanobacteria remains limited. In this study, we evaluated the β-glucosidase from Microcystis aeruginosa CACIAM 03 (MaBgl3) and its potential for bioconversion of cellulosic biomass by analyzing primary/secondary structures, predicting physicochemical properties, homology modeling, molecular docking, and simulations of molecular dynamics (MD). The results showed that MaBgl3 derives from an N-terminal domain folded as a distorted β-barrel, which contains the conserved His-Asp catalytic dyad often found in glycosylases of the GH3 family. The molecular docking results showed relevant interactions with Asp81, Ala271 and Arg444 residues that contribute to the binding process during MD simulation. Moreover, the MD simulation of the MaBgl3 was stable, shown by analyzing the root mean square deviation (RMSD) values and observing favorable binding free energy in both complexes. In addition, experimental data suggest that MaBgl3 could be a potential enzyme for cellobiose-hydrolyzing degradation.
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Affiliation(s)
- Gustavo Marques Serra
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará-UFPA, Belém 66075-10, Brazil
| | - Agenor Valadares Santos
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
| | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformações, Instituto de Ciências Biológicas, Universidade Federal do Pará-UFPA, Belém 66075-110, Brazil
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5
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Yang YX, Wang P, Zhu BT. Binding affinity prediction for antibody-protein antigen complexes: A machine learning analysis based on interface and surface areas. J Mol Graph Model 2023; 118:108364. [PMID: 36356467 DOI: 10.1016/j.jmgm.2022.108364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Specific antibodies can bind to protein antigens with high affinity and specificity, and this property makes them one of the best protein-based therapeutics. Accurate prediction of antibody‒protein antigen binding affinity is crucial for designing effective antibodies. The current predictive methods for protein‒protein binding affinity usually fail to predict the binding affinity of an antibody‒protein antigen complex with a comparable level of accuracy. Here, new models specific for antibody‒antigen binding affinity prediction are developed according to the different types of interface and surface areas present in antibody‒antigen complex. The contacts-based descriptors are also employed to construct or train different models specific for antibody‒protein antigen binding affinity prediction. The results of this study show that (i) the area-based descriptors are slightly better than the contacts-based descriptors in terms of the predictive power; (ii) the new models specific for antibody‒protein antigen binding affinity prediction are superior to the previously-used general models for predicting the protein‒protein binding affinities; (iii) the performances of the best area-based and contacts-based models developed in this work are better than the performances of a recently-developed graph-based model (i.e., CSM-AB) specific for antibody‒protein antigen binding affinity prediction. The new models developed in this work would not only help understand the mechanisms underlying antibody‒protein antigen interactions, but would also be of some applicable utility in the design and virtual screening of antibody-based therapeutics.
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Affiliation(s)
- Yong Xiao Yang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Pan Wang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Bao Ting Zhu
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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6
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Sulea T, Deprez C, Corbeil CR, Purisima EO. Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform. Methods Mol Biol 2023; 2552:361-374. [PMID: 36346603 DOI: 10.1007/978-1-0716-2609-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform guides the selection of mutants that improve/modulate the affinity of antibodies and other biologics. Predicted affinities are based on a consensus z-score from three scoring functions. Computational predictions are interleaved with experimental validation, significantly enhancing the robustness of the design and selection of mutants. A key step is an initial exhaustive virtual single-mutant scan that identifies hot spots and the mutations predicted to improve affinity. A small number of proposed single mutants are then produced and assayed. Only the validated single mutants (i.e., having improved affinity) are used to design double and higher-order mutants in subsequent rounds of design, avoiding the combinatorial explosion that arises from random mutagenesis. Typically, with a total of about 30-50 designed single, double, and triple mutants, affinity improvements of 10- to 100-fold are obtained.
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Affiliation(s)
- Traian Sulea
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Christophe Deprez
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Christopher R Corbeil
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Enrico O Purisima
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada.
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7
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Wei W, Corbeil CR, Gaudreault F, Deprez C, Purisima EO, Sulea T. Antibody mutations favoring
pH
‐dependent binding in solid tumor microenvironments: Insights from large‐scale structure‐based calculations. Proteins 2022; 90:1538-1546. [DOI: 10.1002/prot.26340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/26/2022] [Accepted: 03/23/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Wanlei Wei
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Christopher R. Corbeil
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Francis Gaudreault
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Enrico O. Purisima
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Traian Sulea
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
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8
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Sulea T, Baardsnes J, Stuible M, Rohani N, Tran A, Parat M, Cepero Donates Y, Duchesne M, Plante P, Kour G, Durocher Y. Structure-based dual affinity optimization of a SARS-CoV-1/2 cross-reactive single-domain antibody. PLoS One 2022; 17:e0266250. [PMID: 35353868 PMCID: PMC8967028 DOI: 10.1371/journal.pone.0266250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
The SARS coronavirus 2 (SARS-CoV-2) spike (S) protein binding to the human ACE2 receptor is the molecular event that initiates viral entry into host cells and leads to infection and virus replication. There is a need for agents blocking viral entry into host cells that are cross-reactive with emerging virus variants. VHH-72 is an anti-SARS-CoV-1 single-domain antibody that also exhibits cross-specificity with SARS-CoV-2 but with decreased binding affinity. Here we applied a structure-based approach to affinity-mature VHH-72 for the SARS-CoV-2 spike protein while retaining the original affinity for SARS-CoV-1. This was achieved by employing the computational platform ADAPT in a constrained dual-affinity optimization mode as a means of broadening specificity. Select mutants designed by ADAPT were formatted as fusions with a human IgG1-Fc fragment. These mutants demonstrated improved binding to the SARS-CoV-2 spike protein due to decreased dissociation rates. Functional testing for virus neutralization revealed improvements relative to the parental VHH72-Fc up to 10-fold using a SARS-CoV-2 pseudotyped lentivirus and 20-fold against the SARS-CoV-2 authentic live virus (Wuhan variant). Binding and neutralization improvements were maintained for some other SARS-CoV-2 variants currently in circulation. These improved VHH-72 mutants are predicted to establish novel interactions with the S antigen. They will be useful, alone or as fusions with other functional modules, in the global quest for treatments of COVID-19 infections.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail:
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Pierre Plante
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Guneet Kour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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9
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Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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10
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Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences. Sci Rep 2021; 11:21362. [PMID: 34725391 PMCID: PMC8560851 DOI: 10.1038/s41598-021-00669-w] [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: 07/15/2021] [Accepted: 10/05/2021] [Indexed: 01/01/2023] Open
Abstract
The design of superior biologic therapeutics, including antibodies and engineered proteins, involves optimizing their specific ability to bind to disease-related molecular targets. Previously, we developed and applied the Assisted Design of Antibody and Protein Therapeutics (ADAPT) platform for virtual affinity maturation of antibodies (Vivcharuk et al. in PLoS One 12(7):e0181490, 10.1371/journal.pone.0181490, 2017). However, ADAPT is limited to point mutations of hot-spot residues in existing CDR loops. In this study, we explore the possibility of wholesale replacement of the entire H3 loop with no restriction to maintain the parental loop length. This complements other currently published studies that sample replacements for the CDR loops L1, L2, L3, H1 and H2. Given the immense sequence space theoretically available to H3, we focused on the virtual grafting of over 5000 human germline-derived H3 sequences from the IGMT/LIGM database increasing the diversity of the sequence space when compared to using crystalized H3 loop sequences. H3 loop conformations are generated and scored to identify optimized H3 sequences. Experimental testing of high-ranking H3 sequences grafted into the framework of the bH1 antibody against human VEGF-A led to the discovery of multiple hits, some of which had similar or better affinities relative to the parental antibody. In over 75% of the tested designs, the re-designed H3 loop contributed favorably to overall binding affinity. The hits also demonstrated good developability attributes such as high thermal stability and no aggregation. Crystal structures of select re-designed H3 variants were solved and indicated that although some deviations from predicted structures were seen in the more solvent accessible regions of the H3 loop, they did not significantly affect predicted affinity scores.
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11
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Riahi S, Lee JH, Wei S, Cost R, Masiero A, Prades C, Olfati-Saber R, Wendt M, Park A, Qiu Y, Zhou Y. Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers. Antib Ther 2021; 4:109-122. [PMID: 34396040 PMCID: PMC8344454 DOI: 10.1093/abt/tbab011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
As the COVID-19 pandemic continues to spread, hundreds of new initiatives including
studies on existing medicines are running to fight the disease. To deliver a potentially
immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new
collaborations and ways of sharing are required to create as many paths forward as
possible. Here, we leverage our expertise in computational antibody engineering to
rationally design/engineer three previously reported SARS-CoV neutralizing antibodies and
share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing
antibodies, m396, 80R and CR-3022 were chosen as templates due to their diversified
epitopes and confirmed neutralization potency against SARS-CoV (but not SARS-CoV-2 except
for CR3022). Structures of variable fragment (Fv) in complex with receptor binding domain
(RBD) from SARS-CoV or SARS-CoV-2 were subjected to our established in silico antibody
engineering platform to improve their binding affinity to SARS-CoV-2 and developability
profiles. The selected top mutations were ensembled into a focused library for each
antibody for further screening. In addition, we convert the selected binders with
different epitopes into the trispecific format, aiming to increase potency and to prevent
mutational escape. Lastly, to avoid antibody-induced virus activation or enhancement, we
suggest application of NNAS and DQ mutations to the Fc region to eliminate effector
functions and extend half-life.
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Affiliation(s)
- Saleh Riahi
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Jae Hyeon Lee
- Data & Data Science, Sanofi, Cambridge, MA, United States
| | - Shuai Wei
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Robert Cost
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | | | | | | | - Maria Wendt
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Anna Park
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Yu Qiu
- Large Molecule Research, Sanofi, Framingham, MA, United States
| | - Yanfeng Zhou
- Large Molecule Research, Sanofi, Framingham, MA, United States
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12
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Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure 2021; 29:606-621.e5. [PMID: 33539768 DOI: 10.1016/j.str.2021.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 11/15/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
Abstract
Accurate predictive modeling of antibody-antigen complex structures and structure-based antibody design remain major challenges in computational biology, with implications for biotherapeutics, immunity, and vaccines. Through a systematic search for high-resolution structures of antibody-antigen complexes and unbound antibody and antigen structures, in conjunction with identification of experimentally determined binding affinities, we have assembled a non-redundant set of test cases for antibody-antigen docking and affinity prediction. This benchmark more than doubles the number of antibody-antigen complexes and corresponding affinities available in our previous benchmarks, providing an unprecedented view of the determinants of antibody recognition and insights into molecular flexibility. Initial assessments of docking and affinity prediction tools highlight the challenges posed by this diverse set of cases, which includes camelid nanobodies, therapeutic monoclonal antibodies, and broadly neutralizing antibodies targeting viral glycoproteins. This dataset will enable development of advanced predictive modeling and design methods for this therapeutically relevant class of protein-protein interactions.
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Affiliation(s)
- Johnathan D Guest
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jing Zhou
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Iain Moal
- Computational Sciences, GlaxoSmithKline Research and Development, Stevenage SG1 2NY, UK
| | - Jeliazko R Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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13
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Sulea T, Rohani N, Baardsnes J, Corbeil CR, Deprez C, Cepero-Donates Y, Robert A, Schrag JD, Parat M, Duchesne M, Jaramillo ML, Purisima EO, Zwaagstra JC. Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment. MAbs 2021; 12:1682866. [PMID: 31777319 PMCID: PMC6927761 DOI: 10.1080/19420862.2019.1682866] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Recent development of monoclonal antibodies as mainstream anticancer agents demands further optimization of their safety for use in humans. Potent targeting and/or effector activities on normal tissues is an obvious toxicity concern. Optimization of specific tumor targeting could be achieved by taking advantage of the extracellular acidity of solid tumors relative to normal tissues. Here, we applied a structure-based computational approach to engineer anti-human epidermal growth factor receptor 2 (Her2) antibodies with selective binding in the acidic tumor microenvironment. We used an affinity maturation platform in which dual-pH histidine-scanning mutagenesis was implemented for pH selectivity optimization. Testing of a small set of designs for binding to the recombinant Her2 ectodomain led to the identification of antigen-binding fragment (Fab) variants with the desired pH-dependent binding behavior. Binding selectivity toward acidic pH was improved by as much as 25-fold relative to the parental bH1-Fab. In vitro experiments on cells expressing intact Her2 confirmed that designed variants formatted as IgG1/k full-size antibodies have high affinity and inhibit the growth of tumor spheroids at a level comparable to that of the benchmark anti-Her2 antibody trastuzumab (Herceptin®) at acidic pH, whereas these effects were significantly reduced at physiological pH. In contrast, both Herceptin and the parental bH1 antibody exhibited strong cell binding and growth inhibition irrespective of pH. This work demonstrates the feasibility of computational optimization of antibodies for selective targeting of the acidic environment such as that found in many solid tumors.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christopher R Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Maria L Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - John C Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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14
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Predicting antibody affinity changes upon mutations by combining multiple predictors. Sci Rep 2020; 10:19533. [PMID: 33177627 PMCID: PMC7658247 DOI: 10.1038/s41598-020-76369-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies are proteins working in our immune system with high affinity and specificity for target antigens, making them excellent tools for both biotherapeutic and bioengineering applications. The prediction of antibody affinity changes upon mutations (\documentclass[12pt]{minimal}
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\begin{document}$${{\Delta \Delta {\mathrm{G}}}}_{\mathrm{binding}}$$\end{document}ΔΔGbinding) is important for antibody engineering. Numerous computational methods have been proposed based on different approaches including molecular mechanics and machine learning. However, the accuracy by each individual predictor is not enough for efficient antibody development. In this study, we develop a new prediction method by combining multiple predictors based on machine learning. Our method was tested on the SiPMAB database, evaluating the Pearson’s correlation coefficient between predicted and experimental \documentclass[12pt]{minimal}
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\begin{document}$${{\Delta \Delta {\mathrm{G}}}}_{\mathrm{binding}}$$\end{document}ΔΔGbinding. Our method achieved higher accuracy (R = 0.69) than previous molecular mechanics or machine-learning based methods (R = 0.59) and the previous method using the average of multiple predictors (R = 0.64). Feature importance analysis indicated that the improved accuracy was obtained by combining predictors with different importance, which have different protocols for calculating energies and for generating mutant and unbound state structures. This study demonstrates that machine learning is a powerful framework for combining different approaches to predict antibody affinity changes.
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15
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Zwaagstra JC, Sulea T, Baardsnes J, Radinovic S, Cepero-Donates Y, Robert A, O’Connor-McCourt MD, Tikhomirov IA, Jaramillo ML. Binding and functional profiling of antibody mutants guides selection of optimal candidates as antibody drug conjugates. PLoS One 2019; 14:e0226593. [PMID: 31891584 PMCID: PMC6938348 DOI: 10.1371/journal.pone.0226593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/30/2019] [Indexed: 12/15/2022] Open
Abstract
An increasingly appreciated conundrum in the discovery of antibody drug conjugates (ADCs) is that an antibody that was selected primarily for strong binding to its cancer target may not serve as an optimal ADC. In this study, we performed mechanistic cell-based experiments to determine the correlation between antibody affinity, avidity, internalization and ADC efficacy. We used structure-guided design to assemble a panel of antibody mutants with predicted Her2 affinities ranging from higher to lower relative to the parent antibody, Herceptin. These antibodies were ranked for binding via SPR and via flow-cytometry on high-Her2 SKOV3 cells and low-Her2 MCF7 cells, the latter acting as a surrogate for low-Her2 normal cells. A subpanel of variants, representative of different Her2-binding affinities (2 strong, 2 moderate and 3 weak), were further screened via high-content imaging for internalization efficacies in high versus low-Her2 cells. Finally, these antibodies were evaluated in ADC cytotoxicity screening assays (using DM1 and MMAE secondary antibodies) and as antibody-drug conjugates (DM1 and PNU159682). Our results identified specific but weak Her2-binding variants as optimal candidates for developing DM1 and PNU ADCs since they exhibited high potencies (low to sub-nM) in high-Her2 SKOV3 cells and low toxicities in low-Her2 cells. The 2 strong-affinity variants were highly potent in SKOV3 cells but also showed significant toxicities in low-Her2 cells and therefore are predicted to be toxic in normal tissues. Our findings show that pharmacological profiling of an antibody library in multiple binding and functional assays allows for selection of optimal ADCs.
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Affiliation(s)
- John C. Zwaagstra
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail: (JZ); (MJ)
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Stevo Radinovic
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero-Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alma Robert
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | | | | | - Maria Luz. Jaramillo
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail: (JZ); (MJ)
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16
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Schrag JD, Picard MÈ, Gaudreault F, Gagnon LP, Baardsnes J, Manenda MS, Sheff J, Deprez C, Baptista C, Hogues H, Kelly JF, Purisima EO, Shi R, Sulea T. Binding symmetry and surface flexibility mediate antibody self-association. MAbs 2019; 11:1300-1318. [PMID: 31318308 PMCID: PMC6748613 DOI: 10.1080/19420862.2019.1632114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Solution stability is an important factor in the optimization of engineered biotherapeutic candidates such as monoclonal antibodies because of its possible effects on manufacturability, pharmacology, efficacy and safety. A detailed atomic understanding of the mechanisms governing self-association of natively folded protein monomers is required to devise predictive tools to guide screening and re-engineering along the drug development pipeline. We investigated pairs of affinity-matured full-size antibodies and observed drastically different propensities to aggregate from variants differing by a single amino-acid. Biophysical testing showed that antigen-binding fragments (Fabs) from the aggregating antibodies also reversibly associated with equilibrium dissociation constants in the low-micromolar range. Crystal structures (PDB accession codes 6MXR, 6MXS, 6MY4, 6MY5) and bottom-up hydrogen-exchange mass spectrometry revealed that Fab self-association occurs in a symmetric mode that involves the antigen complementarity-determining regions. Subtle local conformational changes incurred upon point mutation of monomeric variants foster formation of complementary polar interactions and hydrophobic contacts to generate a dimeric Fab interface. Testing of popular in silico tools generally indicated low reliabilities for predicting the aggregation propensities observed. A structure-aggregation data set is provided here in order to stimulate further improvements of in silico tools for prediction of native aggregation. Incorporation of intermolecular docking, conformational flexibility, and short-range packing interactions may all be necessary features of the ideal algorithm.
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Affiliation(s)
- Joseph D Schrag
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand , Québec City, QC G1V 0A6 , Canada
| | - Francis Gaudreault
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Louis-Patrick Gagnon
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Mahder S Manenda
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand , Québec City, QC G1V 0A6 , Canada
| | - Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada , Ottawa , ON K1A 0R6 , Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Cassio Baptista
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Hervé Hogues
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada , Ottawa , ON K1A 0R6 , Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand , Québec City, QC G1V 0A6 , Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada , Montreal , QC H4P 2R2 , Canada
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17
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Siqueira AS, Lima ARJ, Aguiar DCF, Santos AS, Vianez Júnior JLDSG, Gonçalves EC. Genomic screening of new putative antiviral lectins from Amazonian cyanobacteria based on a bioinformatics approach. Proteins 2018; 86:1047-1054. [PMID: 30035823 PMCID: PMC7167734 DOI: 10.1002/prot.25577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/21/2018] [Accepted: 06/22/2018] [Indexed: 12/11/2022]
Abstract
Lectins are proteins of nonimmune origin, which are capable of recognizing and binding to glycoconjugate moieties. Some of them can block the interaction of viral glycoproteins to the host cell receptors acting as antiviral agents. Although cyanobacterial lectins have presented broad biotechnological potential, little research has been directed to Amazonian Cyanobacterial diversity. In order to identify new antiviral lectins, we performed genomic analysis in seven cyanobacterial strains from Coleção Amazônica de Cianobactérias e Microalgas (CACIAM). We found 75 unique CDS presenting one or more lectin domains. Since almost all were annotated as hypothetical proteins, we used homology modeling and molecular dynamics simulations to evaluate the structural and functional properties of three CDS that were more similar to known antiviral lectins. Nostoc sp. CACIAM 19 as well as Tolypothrix sp. CACIAM 22 strains presented cyanovirin‐N homologues whose function was confirmed by binding free energy calculations. Asn, Glu, Thr, Lys, Leu, and Gly, which were described as binding residues for cyanovirin, were also observed on those structures. As for other known cyanovirins, those residues in both our models also made favorable interactions with dimannose. Finally, Alkalinema sp. CACIAM 70d presented one CDS, which was identified as a seven‐bladed beta‐propeller structure with binding sites predicted for sialic acid and N‐acetylglucosamine. Despite its singular structure, our analysis suggested this molecule as a new putative antiviral lectin. Overall, the identification and the characterization of new lectins and their homologues are a promising area in antiviral research, and Amazonian cyanobacteria present biotechnological potential to be explored in this regard.
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Affiliation(s)
- Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular – Instituto de Ciências BiológicasUniversidade Federal do ParáBelém‐PennsylvaniaBrazil
| | - Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular – Instituto de Ciências BiológicasUniversidade Federal do ParáBelém‐PennsylvaniaBrazil
| | - Delia Cristina Figueira Aguiar
- Laboratório de Tecnologia Biomolecular – Instituto de Ciências BiológicasUniversidade Federal do ParáBelém‐PennsylvaniaBrazil
| | - Alberdan Silva Santos
- Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular – Instituto de Ciências Naturais – Universidade Federal do ParáBelém‐PennsylvaniaBrazil
| | | | - Evonnildo Costa Gonçalves
- Laboratório de Tecnologia Biomolecular – Instituto de Ciências BiológicasUniversidade Federal do ParáBelém‐PennsylvaniaBrazil
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18
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Sulea T, Hussack G, Ryan S, Tanha J, Purisima EO. Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody. Sci Rep 2018; 8:2260. [PMID: 29396522 PMCID: PMC5797146 DOI: 10.1038/s41598-018-20599-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023] Open
Abstract
Assisted Design of Antibody and Protein Therapeutics (ADAPT) is an affinity maturation platform interleaving predictions and testing that was previously validated on monoclonal antibodies (mAbs). This study expands the applicability of ADAPT to single-domain antibodies (sdAbs), a promising class of recombinant antibody-based biologics. As a test case, we used the camelid sdAb A26.8, a VHH that binds Clostridium difficile toxin A (TcdA) relatively weakly but displays a reasonable level of TcdA neutralization. ADAPT-guided A26.8 affinity maturation resulted in an improvement of one order of magnitude by point mutations only, reaching an equilibrium dissociation constant (KD) of 2 nM, with the best binding mutants having similar or improved stabilities relative to the parent sdAb. This affinity improvement generated a 6-fold enhancement of efficacy at the cellular level; the A26.8 double-mutant T56R,T103R neutralizes TcdA cytotoxicity with an IC50 of 12 nM. The designed mutants with increased affinities are predicted to establish novel electrostatic interactions with the antigen. Almost full additivity of mutation effects is observed, except for positively charged residues introduced at adjacent positions. Furthermore, analysis of false-positive predictions points to general directions for improving the ADAPT platform. ADAPT guided the efficacy enhancement of an anti-toxin sdAb, an alternative therapeutic modality for C. difficile.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada.,Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada. .,Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada.
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Abstract
The immune systems protect our bodies from foreign molecules or antigens, where antibodies play important roles. Antibodies evolve over time upon antigen encounter by somatically mutating their genome sequences. The end result is a series of antibodies that display higher affinities and specificities to specific antigens. This process is called affinity maturation. Recent improvements in computer hardware and modeling algorithms now enable the rational design of protein structures and functions, and several works on computer-aided antibody design have been published. In this chapter, we briefly describe computational methods for antibody affinity maturation, focusing on methods for sampling antibody conformations and for scoring designed antibody variants. We also discuss lessons learned from the successful computer-aided design of antibodies.
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Affiliation(s)
- Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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20
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Vivcharuk V, Baardsnes J, Deprez C, Sulea T, Jaramillo M, Corbeil CR, Mullick A, Magoon J, Marcil A, Durocher Y, O’Connor-McCourt MD, Purisima EO. Assisted Design of Antibody and Protein Therapeutics (ADAPT). PLoS One 2017; 12:e0181490. [PMID: 28750054 PMCID: PMC5531539 DOI: 10.1371/journal.pone.0181490] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/30/2017] [Indexed: 11/19/2022] Open
Abstract
Effective biologic therapeutics require binding affinities that are fine-tuned to their disease-related molecular target. The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform aids in the selection of mutants that improve/modulate the affinity of antibodies and other biologics. It uses a consensus z-score from three scoring functions and interleaves computational predictions with experimental validation, significantly enhancing the robustness of the design and selection of mutants. The platform was tested on three antibody Fab-antigen systems that spanned a wide range of initial binding affinities: bH1-VEGF-A (44 nM), bH1-HER2 (3.6 nM) and Herceptin-HER2 (0.058 nM). Novel triple mutants were obtained that exhibited 104-, 46- and 32-fold improvements in binding affinity for each system, respectively. Moreover, for all three antibody-antigen systems over 90% of all the intermediate single and double mutants that were designed and tested showed higher affinities than the parent sequence. The contributions of the individual mutants to the change in binding affinity appear to be roughly additive when combined to form double and triple mutants. The new interactions introduced by the affinity-enhancing mutants included long-range electrostatics as well as short-range nonpolar interactions. This diversity in the types of new interactions formed by the mutants was reflected in SPR kinetics that showed that the enhancements in affinities arose from increasing on-rates, decreasing off-rates or a combination of the two effects, depending on the mutation. ADAPT is a very focused search of sequence space and required only 20-30 mutants for each system to be made and tested to achieve the affinity enhancements mentioned above.
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Affiliation(s)
- Victor Vivcharuk
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Jason Baardsnes
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Christophe Deprez
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Traian Sulea
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Maria Jaramillo
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | | | - Alaka Mullick
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Joanne Magoon
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Anne Marcil
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | - Yves Durocher
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
| | | | - Enrico O. Purisima
- Human Health Therapeutics, National Research Council Canada, Montreal, QC, Canada
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21
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Siqueira AS, Jerônimo Lima AR, de Souza RC, Santos AS, da Silva Gonçalves Vianez Júnior JL, Gonçalves EC. Anti-dengue virus activity of scytovirin and evaluation of point mutation effects by molecular dynamics and binding free energy calculations. Biochem Biophys Res Commun 2017; 490:1033-1038. [PMID: 28666874 DOI: 10.1016/j.bbrc.2017.06.160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 01/21/2023]
Abstract
The absence of a specific treatment against DENV has led to intensive research into developing strategies for curing the infection. One lectin with high antiviral activity is scytovirin, which was isolated from the cyanobacterium Scytonema varium and has proven activity against HIV and Zaire Ebola Virus. To achieve the results presented here, we tested the affinity of full-length scytovirin, SD1 and SD2 separately, and six SD1 mutants for DENV glycoprotein E carbohydrate by Molecular Dynamics (MD) simulations and binding free energy calculations. It was possible to identify the key residues for protein-ligand interaction such as Glu10, Ala11, Pro17, Ans18, Arg30, Thr41, Ser42 and Arg43, which also has importance action against HIV. All binding free energy calculations showed negative values to ΔGbind of protein-DENV carbohydrate complexation. Additionally, these results are similar to the values of scytovirin and HIV gp120 carbohydrate complexation (-32.20 kcal/mol). Furthermore, we found that SD1 individually has more affinity to the carbohydrate and the Asn9, Glu10, Asn18, Arg30 and Arg43 demonstrated an important role in this matter. We also found that mutant G48R has better affinity (-34.10 kcal/mol) for the DENV carbohydrate than the wild type protein (-27.15 kcal/mol).
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Affiliation(s)
- Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas -Universidade Federal do Pará, Belém-PA, Brazil.
| | - Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas -Universidade Federal do Pará, Belém-PA, Brazil
| | | | - Alberdan Silva Santos
- Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Naturais - Universidade Federal do Pará, Belém-PA, Brazil
| | | | - Evonnildo Costa Gonçalves
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas -Universidade Federal do Pará, Belém-PA, Brazil
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22
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Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Sci Rep 2016; 6:39774. [PMID: 28008969 PMCID: PMC5180089 DOI: 10.1038/srep39774] [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: 09/09/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022] Open
Abstract
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
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23
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Henry KA, Sulea T, van Faassen H, Hussack G, Purisima EO, MacKenzie CR, Arbabi-Ghahroudi M. A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies. PLoS One 2016; 11:e0163113. [PMID: 27631624 PMCID: PMC5025174 DOI: 10.1371/journal.pone.0163113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/04/2016] [Indexed: 12/21/2022] Open
Abstract
Staphylococcal protein A (SpA) and streptococcal protein G (SpG) affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs) in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs) are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species.
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Affiliation(s)
- Kevin A. Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Traian Sulea
- Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada, H4P 2R2
| | - Henk van Faassen
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Greg Hussack
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Enrico O. Purisima
- Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada, H4P 2R2
| | - C. Roger MacKenzie
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6
- * E-mail:
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