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For: 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] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/30/2017] [Indexed: 11/19/2022]  Open
Number Cited by Other Article(s)
1
Chen Y, Zha J, Xu S, Shao J, Liu X, Li D, Zhang X. Structure-Based Optimization of One Neutralizing Antibody against SARS-CoV-2 Variants Bearing the L452R Mutation. Viruses 2024;16:566. [PMID: 38675908 PMCID: PMC11053997 DOI: 10.3390/v16040566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]  Open
2
Gallo E. The rise of big data: deep sequencing-driven computational methods are transforming the landscape of synthetic antibody design. J Biomed Sci 2024;31:29. [PMID: 38491519 PMCID: PMC10943851 DOI: 10.1186/s12929-024-01018-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024]  Open
3
Lv Y, Gong H, Liu X, Hao J, Xu L, Sun Z, Yu C, Xu L. A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment. PLoS Comput Biol 2024;20:e1011984. [PMID: 38536788 PMCID: PMC10971747 DOI: 10.1371/journal.pcbi.1011984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/10/2024] [Indexed: 04/05/2024]  Open
4
Gaudreault F, Corbeil CR, Sulea T. Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2. Sci Rep 2023;13:15107. [PMID: 37704686 PMCID: PMC10499836 DOI: 10.1038/s41598-023-42090-5] [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: 02/03/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]  Open
5
Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023;247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [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: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
6
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
7
Soler MA, Minovski N, Rocchia W, Fortuna S. Replica-exchange optimization of antibody fragments. Comput Biol Chem 2023;103:107819. [PMID: 36657284 DOI: 10.1016/j.compbiolchem.2023.107819] [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: 10/10/2022] [Revised: 12/16/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
8
Sheff J, Kelly J, Foss M, Brunette E, Kemmerich K, van Faassen H, Raphael S, Hussack G, Comamala G, Rand K, Stanimirovic DB. Epitope mapping of a blood-brain barrier crossing antibody targeting the cysteine-rich region of IGF1R using hydrogen-exchange mass spectrometry enabled by electrochemical reduction. J Biochem 2023;173:95-105. [PMID: 36346120 DOI: 10.1093/jb/mvac088] [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: 08/03/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022]  Open
9
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]
10
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]
11
Bai Z, Wang J, Li J, Yuan H, Wang P, Zhang M, Feng Y, Cao X, Cao X, Kang G, de Marco A, Huang H. Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations. Comput Struct Biotechnol J 2022;21:601-613. [PMID: 36659922 PMCID: PMC9822835 DOI: 10.1016/j.csbj.2022.12.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]  Open
12
Ye C, Hu W, Gaeta B. Prediction of Antibody-Antigen Binding via Machine Learning: Development of Data Sets and Evaluation of Methods. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022;3:e29404. [PMID: 38935962 PMCID: PMC11135222 DOI: 10.2196/29404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/23/2021] [Accepted: 10/18/2022] [Indexed: 06/29/2024]
13
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]
14
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
15
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
16
Computational and Rational Design of Single-Chain Antibody against Tick-Borne Encephalitis Virus for Modifying Its Specificity. Viruses 2021;13:v13081494. [PMID: 34452359 PMCID: PMC8402911 DOI: 10.3390/v13081494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022]  Open
17
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
18
Vajda S, Porter KA, Kozakov D. Progress toward improved understanding of antibody maturation. Curr Opin Struct Biol 2021;67:226-231. [PMID: 33610066 DOI: 10.1016/j.sbi.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
19
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
20
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
21
Hu M, Kang G, Cheng X, Wang J, Li R, Bai Z, Yang D, Huang H. In vitro affinity maturation to improve the efficacy of a hypoxia-inducible factor 1α single-domain intrabody. Biochem Biophys Res Commun 2020;529:936-942. [PMID: 32819602 DOI: 10.1016/j.bbrc.2020.06.097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022]
22
de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020;172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
23
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
24
Homology Modeling-Based in Silico Affinity Maturation Improves the Affinity of a Nanobody. Int J Mol Sci 2019;20:ijms20174187. [PMID: 31461846 PMCID: PMC6747709 DOI: 10.3390/ijms20174187] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/08/2023]  Open
25
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
26
Outlier Detection and Smoothing Process for Water Level Data Measured by Ultrasonic Sensor in Stream Flows. WATER 2019. [DOI: 10.3390/w11050951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
27
Cannon DA, Shan L, Du Q, Shirinian L, Rickert KW, Rosenthal KL, Korade M, van Vlerken-Ysla LE, Buchanan A, Vaughan TJ, Damschroder MM, Popovic B. Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design. PLoS Comput Biol 2019;15:e1006980. [PMID: 31042706 PMCID: PMC6513101 DOI: 10.1371/journal.pcbi.1006980] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/13/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023]  Open
28
Sharmeen N, Sulea T, Whiteway M, Wu C. The adaptor protein Ste50 directly modulates yeast MAPK signaling specificity through differential connections of its RA domain. Mol Biol Cell 2019;30:794-807. [PMID: 30650049 PMCID: PMC6589780 DOI: 10.1091/mbc.e18-11-0708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
29
Hogues H, Gaudreault F, Corbeil CR, Deprez C, Sulea T, Purisima EO. ProPOSE: Direct Exhaustive Protein-Protein Docking with Side Chain Flexibility. J Chem Theory Comput 2018;14:4938-4947. [PMID: 30107730 DOI: 10.1021/acs.jctc.8b00225] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
30
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
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