Citation: | Wei Ye, Xiaoyu Liu, Ruiting He, Liming Gou, Ming Lu, Gang Yang, Jiaqi Wen, Xufei Wang, Fang Liu, Sujuan Ma, Weifeng Qian, Shaochang Jia, Tong Ding, Luan Sun, Wei Gao. Improving antibody affinity through in vitro mutagenesis in complementarity determining regions[J]. The Journal of Biomedical Research, 2022, 36(3): 155-166. DOI: 10.7555/JBR.36.20220003 |
[1] |
Basu K, Green EM, Cheng Y, et al. Why recombinant antibodies—benefits and applications[J]. Curr Opin Biotechnol, 2019, 60: 153–158. doi: 10.1016/j.copbio.2019.01.012
|
[2] |
Lu RM, Hwang YC, Liu IJ, et al. Development of therapeutic antibodies for the treatment of diseases[J]. J Biomed Sci, 2020, 27(1): 1. doi: 10.1186/s12929-019-0592-z
|
[3] |
Urquhart L. Top companies and drugs by sales in 2020[J]. Nat Rev Drug Discov, 2021, 20(4): 253. doi: 10.1038/d41573-021-00050-6
|
[4] |
Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface[J]. Science, 1985, 228(4705): 1315–1317. doi: 10.1126/science.4001944
|
[5] |
Lerner RA, Kang AS, Bain JD, et al. Antibodies without immunization[J]. Science, 1992, 258(5086): 1313–1314. doi: 10.1126/science.1455226
|
[6] |
Bradbury ARM, Sidhu S, Dübel S, et al. Beyond natural antibodies: the power of in vitro display technologies[J]. Nat Biotechnol, 2011, 29(3): 245–254. doi: 10.1038/nbt.1791
|
[7] |
Roth KDR, Wenzel EV, Ruschig M, et al. Developing recombinant antibodies by phage display against infectious diseases and toxins for diagnostics and therapy[J]. Front Cell Infect Microbiol, 2021, 11: 697876. doi: 10.3389/fcimb.2021.697876
|
[8] |
Sun L, Gao F, Gao Z, et al. Shed antigen-induced blocking effect on CAR-T cells targeting Glypican-3 in hepatocellular carcinoma[J]. J Immunother Cancer, 2021, 9(4): e001875. doi: 10.1136/jitc-2020-001875
|
[9] |
Liu X, Gao F, Jiang L, et al. 32A9, a novel human antibody for designing an immunotoxin and CAR-T cells against glypican-3 in hepatocellular carcinoma[J]. J Transl Med, 2020, 18(1): 295. doi: 10.1186/s12967-020-02462-1
|
[10] |
Li N, Wei L, Liu X, et al. A frizzled-like cysteine-rich domain in Glypican-3 mediates wnt binding and regulates hepatocellular carcinoma tumor growth in mice[J]. Hepatology, 2019, 70(4): 1231–1245. doi: 10.1002/hep.30646
|
[11] |
Shi R, Shan C, Duan X, et al. A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2[J]. Nature, 2020, 584(7819): 120–124. doi: 10.1038/s41586-020-2381-y
|
[12] |
Walls AC, Park YJ, Tortorici MA, et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein[J]. Cell, 2020, 181(2): 281–292.e6. doi: 10.1016/j.cell.2020.02.058
|
[13] |
Wrapp D, Wang N, Corbett KS, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation[J]. Science, 2020, 367(6483): 1260–1263. doi: 10.1126/science.abb2507
|
[14] |
Gao W, Liu X, Gao F, et al. Neutralizing antibody for resisting novel coronavirus SARS-CoV-2 and application thereof (in Chinese): CN, 202010342471.6[P]. 2020-08-28.
|
[15] |
Gao W, Gou L, Lu M, et al. Anti-Glypican-3 acid-resistant fully-humanized antibody, immunotoxins thereof, chimeric antigen recipient cells thereof and application (in Chinese): CN, 202110303641.4[P]. 2021-07-06.
|
[16] |
Ministro J, Manuel AM, Goncalves J. Therapeutic antibody engineering and selection strategies[J]. Adv Biochem Eng Biotechnol, 2020, 171: 55–86. doi: 10.1007/10_2019_116
|
[17] |
Barbas III CF, Bain JD, Hoekstra DM, et al. Semisynthetic combinatorial antibody libraries: a chemical solution to the diversity problem[J]. Proc Natl Acad Sci U S A, 1992, 89(10): 4457–4461. doi: 10.1073/pnas.89.10.4457
|
[18] |
Hoet RM, Cohen EH, Kent RB, et al. Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity-determining-region diversity[J]. Nat Biotechnol, 2005, 23(3): 344–348. doi: 10.1038/nbt1067
|
[19] |
De Wildt RMT, Mundy CR, Gorick BD, et al. Antibody arrays for high-throughput screening of antibody–antigen interactions[J]. Nat Biotechnol, 2000, 18(9): 989–994. doi: 10.1038/79494
|
[20] |
Hoogenboom HR. Selecting and screening recombinant antibody libraries[J]. Nat Biotechnol, 2005, 23(9): 1105–1116. doi: 10.1038/nbt1126
|
[21] |
Tabasinezhad M, Talebkhan Y, Wenzel W, et al. Trends in therapeutic antibody affinity maturation: from in-vitro towards next-generation sequencing approaches[J]. Immunol Lett, 2019, 212: 106–113. doi: 10.1016/j.imlet.2019.06.009
|
[22] |
Wark KL, Hudson PJ. Latest technologies for the enhancement of antibody affinity[J]. Adv Drug Deliv Rev, 2006, 58(5-6): 657–670. doi: 10.1016/j.addr.2006.01.025
|
[23] |
Tiller KE, Chowdhury R, Li T, et al. Facile affinity maturation of antibody variable domains using natural diversity mutagenesis[J]. Front Immunol, 2017, 8: 986. doi: 10.3389/fimmu.2017.00986
|
[24] |
Xu JL, Davis MM. Diversity in the CDR3 region of VH is sufficient for most antibody specificities[J]. Immunity, 2000, 13(1): 37–45. doi: 10.1016/S1074-7613(00)00006-6
|
[25] |
Lippow SM, Wittrup KD, Tidor B. Computational design of antibody-affinity improvement beyond in vivo maturation[J]. Nat Biotechnol, 2007, 25(10): 1171–1176. doi: 10.1038/nbt1336
|
[26] |
Kuroda D, Shirai H, Jacobson MP, et al. Computer-aided antibody design[J]. Protein Eng Des Sel, 2012, 25(10): 507–521. doi: 10.1093/protein/gzs024
|
[27] |
Pérez AMW, Sormanni P, Andersen JS, et al. In vitro and in silico assessment of the developability of a designed monoclonal antibody library[J]. MAbs, 2019, 11(2): 388–400. doi: 10.1080/19420862.2018.1556082
|
[28] |
Silva D, Santos G, Barroca M, et al. Inverse PCR for point mutation introduction[J]. Methods Mol Biol, 2017, 1620: 87–100. doi: 10.1007/978-1-4939-7060-5_5
|
[29] |
Nie J, Li Q, Wu J, et al. Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2[J]. Emerg Microbes Infect, 2020, 9(1): 680–686. doi: 10.1080/22221751.2020.1743767
|
[30] |
Xiong H, Wu Y, Cao J, et al. Robust neutralization assay based on SARS-CoV-2 S-protein-bearing vesicular stomatitis virus (VSV) pseudovirus and ACE2-overexpressing BHK21 cells[J]. Emerg Microbes Infect, 2020, 9(1): 2105–2113. doi: 10.1080/22221751.2020.1815589
|
[31] |
Hwang JK, Wang C, Du Z, et al. Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies[J]. Proc Natl Acad Sci U S A, 2017, 114(32): 8614–8619. doi: 10.1073/pnas.1709203114
|
[32] |
Kepler TB, Liao H, Alam SM, et al. Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies[J]. Cell Host Microbe, 2014, 16(3): 304–313. doi: 10.1016/j.chom.2014.08.006
|
[33] |
MacCallum RM, Martin ACR, Thornton JM. Antibody-antigen interactions: contact analysis and binding site topography[J]. J Mol Biol, 1996, 262(5): 732–745. doi: 10.1006/jmbi.1996.0548
|
[34] |
Skamaki K, Emond S, Chodorge M, et al. In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region[J]. Proc Natl Acad Sci U S A, 2020, 117(44): 27307–27318. doi: 10.1073/pnas.2002954117
|
[35] |
Wei L, Chahwan R, Wang S, et al. Overlapping hotspots in CDRs are critical sites for V region diversification[J]. Proc Natl Acad Sci U S A, 2015, 112(7): E728–E737. doi: 10.1073/pnas.1500788112
|
[36] |
Jackson JR, Sathe G, Rosenberg M, et al. In vitro antibody maturation. Improvement of a high affinity, neutralizing antibody against IL-1 beta[J]. J Immunol, 1995, 154(7): 3310–3319. https://pubmed.ncbi.nlm.nih.gov/7897213/
|
[37] |
Rajpal A, Beyaz N, Haber L, et al. A general method for greatly improving the affinity of antibodies by using combinatorial libraries[J]. Proc Natl Acad Sci U S A, 2005, 102(24): 8466–8471. doi: 10.1073/pnas.0503543102
|
[38] |
Steidl S, Ratsch O, Brocks B, et al. In vitro affinity maturation of human GM-CSF antibodies by targeted CDR-diversification[J]. Mol Immunol, 2008, 46(1): 135–144. doi: 10.1016/j.molimm.2008.07.013
|
[39] |
Rawat P, Sharma D, Srivastava A, et al. Exploring antibody repurposing for COVID-19: beyond presumed roles of therapeutic antibodies[J]. Sci Rep, 2021, 11(1): 10220. doi: 10.1038/s41598-021-89621-6
|
[40] |
Sharma D, Rawat P, Janakiraman V, et al. Elucidating important structural features for the binding affinity of spike - SARS-CoV-2 neutralizing antibody complexes[J]. Proteins, 2022, 90(3): 824–834. doi: 10.1002/prot.26277
|
[1] | Liu Shuying, Lu Shan. Antibody responses in COVID-19 patients[J]. The Journal of Biomedical Research, 2020, 34(6): 410-415. DOI: 10.7555/JBR.34.20200134 |
[2] | Kaibo Lin, Shikun Zhang, Jieli Chen, Ding Yang, Mengyi Zhu, Eugene Yujun Xu. Generation and functional characterization of a conditional Pumilio2 null allele[J]. The Journal of Biomedical Research, 2018, 32(6): 434-441. DOI: 10.7555/JBR.32.20170117 |
[3] | Fengzhen Wang, Mingwan Zhang, Dongsheng Zhang, Yuan Huang, Li Chen, Sunmin Jiang, Kun Shi, Rui Li. Preparation, optimization, and characterization of chitosancoated solid lipid nanoparticles for ocular drug delivery[J]. The Journal of Biomedical Research, 2018, 32(6): 411-423. DOI: 10.7555/JBR.32.20160170 |
[4] | Christopher J. Danford, Zemin Yao, Z. Gordon Jiang. Non-alcoholic fatty liver disease: a narrative review of genetics[J]. The Journal of Biomedical Research, 2018, 32(6): 389-400. DOI: 10.7555/JBR.32.20180045 |
[5] | Seo-jin Park, Kyoung-Ha So, Sang-Hwan Hyun. Effect of zeaxanthin on porcine embryonic development during in vitro maturation[J]. The Journal of Biomedical Research, 2017, 31(2): 154-161. DOI: 10.7555/JBR.31.20160079 |
[6] | Min Xue, Yuanyuan Guo, Qin Yan, Di Qin, Chun Lu. Preparation and application of polyclonal antibodies against KSHV v-cyclin[J]. The Journal of Biomedical Research, 2013, 27(5): 421-429. DOI: 10.7555/JBR.27.20120085 |
[7] | Aixia Zhang, Brian Cao. Generation and characterization of an anti-GP73 monoclonal antibody for immunoblotting and sandwich ELISA[J]. The Journal of Biomedical Research, 2012, 26(6): 467-473. DOI: 10.7555/JBR.26.20120057 |
[8] | Shuangshuang Wang, Ping Zhao, Brian Cao. Development and optimization of an antibody array method for potential cancer biomarker detection[J]. The Journal of Biomedical Research, 2011, 25(1): 63-70. DOI: 10.1016/S1674-8301(11)60008-0 |
[9] | Xinjian Liu, Xiaomin Feng, Qi Tang, Zhongcan Wang, Zhenning Qiu, Yuhua Li, Changjun Wang, Zhenqing Feng, Jin Zhu, Xiaohong Guan. Characterization and potential diagnostic application of monoclonal antibodies specific to rabies virus[J]. The Journal of Biomedical Research, 2010, 24(5): 395-403. DOI: 10.1016/S1674-8301(10)60053-X |
[10] | Sundeep?S.?Tumber, Hong?Liu. Epidural abscess after multiple lumbar punctures for labour epidural catheter placement[J]. The Journal of Biomedical Research, 2010, 24(4): 332-335. DOI: 10.1016/S1674-8301(10)60046-2 |
1. | Langyan S, Bhardwaj R, Kumari J, et al. Nutritional Diversity in Native Germplasm of Maize Collected From Three Different Fragile Ecosystems of India. Front Nutr, 2022, 9: 812599. DOI:10.3389/fnut.2022.812599 |
2. | Juvinao-Quintero DL, Cardenas A, Perron P, et al. Associations between an integrated component of maternal glycemic regulation in pregnancy and cord blood DNA methylation. Epigenomics, 2021, 13(18): 1459-1472. DOI:10.2217/epi-2021-0220 |
3. | Zhang J, Wu X. Predict Health Care Accessibility for Texas Medicaid Gap. Healthcare (Basel), 2021, 9(9): 1214. DOI:10.3390/healthcare9091214 |
4. | Ayati M, Koyutürk M. PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases. PLoS Comput Biol, 2016, 12(11): e1005195. DOI:10.1371/journal.pcbi.1005195 |
5. | Zhang Q, Zhao Y, Zhang R, et al. A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies. PLoS One, 2016, 11(6): e0156895. DOI:10.1371/journal.pone.0156895 |