Antibody Engineering Towards Enhancement of Spike Protein SARS-COV-2 -m396 Binding Affinity
Regeneration, Reconstruction & Restoration (Triple R),
Vol. 5 (2020),
24 March 2020
,
Page e24
https://doi.org/10.22037/rrr.v5i.32838
Abstract
Introduction: The SARS-COV-2 is a non-segmented positive-sense RNA virus that belongs to the genus Beta Coronavirus. The envelope-anchored trimeric spike protein on the virus surface is considered to be the key protein for the viral entry into the host cells. The angiotensin-converting enzyme 2 (ACE2) is reported to be the effective human receptor for SARS-COV-2. ACE2 receptor can be prevented by neutralizing antibodies such as m396 targeting the virus receptor-binding site.
Material and Methods: Considering the importance of computational docking, and in silico affinity maturation we aimed at finding the important amino acids of the m396 antibody. These amino acids were then replaced by other amino acids to improve antibody-binding affinity to receptor-binding domain (RBD) of the SARS-COV-2 spike protein. Finally, we measured the binding affinity of antibody variants to the antigen.
Result: Our findings disclosed that several variant mutations could successfully improve the characteristics of the antibody binding compared to the normal antibodies.
Conclusion: the antibodies developed may be possible candidates for stronger affinity binding to antigens.
Keywords:
- Coronavirus
- SARS-COV-2
- Bioinformatics
- Affinity Maturation
How to Cite
Sefid, F., Payandeh, Z., Azamirad, G. ., & Rasooli, I. (2021). Antibody Engineering Towards Enhancement of Spike Protein SARS-COV-2 -m396 Binding Affinity. Regeneration, Reconstruction & Restoration (Triple R), 5, e24. https://doi.org/10.22037/rrr.v5i.32838
References
References:
1. Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Advances in virus research. 100: Elsevier; 2018. p. 163-88.
2. Donoghue M, Hsieh F, Baronas E, Godbout K, Gosselin M, Stagliano N, et al. A novel angiotensin-converting enzyme–related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circulation research. 2000;87(5):e1-e9.
3. Zhang H, Kang Z, Gong H, Xu D, Wang J, Li Z, et al. The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes. BioRxiv. 2020.
4. Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov. BioRxiv. 2020.
5. Crackower MA, Sarao R, Oudit GY, Yagil C, Kozieradzki I, Scanga SE, et al. Angiotensin-converting enzyme 2 is an essential regulator of heart function. Nature. 2002;417(6891):822-8.
6. Shang J, Wan Y, Luo C, Ye G, Geng Q, Auerbach A, et al. Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences. 2020;117(21):11727-34.
7. Boehm M, Nabel EG. Angiotensin-converting enzyme 2—a new cardiac regulator. New England Journal of Medicine. 2002;347(22):1795-7.
8. Ge X-Y, Li J-L, Yang X-L, Chmura AA, Zhu G, Epstein JH, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503(7477):535-8.
9. ter Meulen J, Bakker AB, van den Brink EN, Weverling GJ, Martina BE, Haagmans BL, et al. Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets. The Lancet. 2004;363(9427):2139-41.
10. Ter Meulen J, Van Den Brink EN, Poon LL, Marissen WE, Leung CS, Cox F, et al. Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants. PLoS medicine. 2006;3(7).
11. Zhu Z, Chakraborti S, He Y, Roberts A, Sheahan T, Xiao X, et al. Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceedings of the National Academy of Sciences. 2007;104(29):12123-8.
12. Ying T, Prabakaran P, Du L, Shi W, Feng Y, Wang Y, et al. Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody. Nature communications. 2015;6(1):1-10.
13. Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, et al. Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerging Microbes & Infections. 2020;9(1):382-5.
14. Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS microbiology letters. 1999;174(2):247-50.
15. Albà MM, Castresana J. On homology searches by protein Blast and the characterization of the age of genes. BMC evolutionary biology. 2007;7(1):53.
16. Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, et al. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallographica Section D: Biological Crystallography. 1998;54(6):1078-84.
17. Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Current topics in medicinal chemistry. 2008;8(18):1555-72.
18. Prabakaran P, Gan J, Feng Y, Zhu Z, Choudhry V, Xiao X, et al. Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody. Journal of Biological Chemistry. 2006;281(23):15829-36.
19. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature protocols. 2009;4(7):1073.
20. Dunbar J, Krawczyk K, Leem J, Marks C, Nowak J, Regep C, et al. SAbPred: a structure-based antibody prediction server. Nucleic acids research. 2016;44(W1):W474-W8.
21. De Vries SJ, Van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nature protocols. 2010;5(5):883.
22. Chen W-H, Strych U, Hotez PJ, Bottazzi ME. The SARS-CoV-2 Vaccine Pipeline: an Overview. Current Tropical Medicine Reports. 2020:1-4.
23. Prompetchara E, Ketloy C, Palaga T. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol. 2020.
24. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020;395(10224):565-74.
25. Rockx B, Donaldson E, Frieman M, Sheahan T, Corti D, Lanzavecchia A, et al. Escape from human monoclonal antibody neutralization affects in vitro and in vivo fitness of severe acute respiratory syndrome coronavirus. The Journal of infectious diseases. 2010;201(6):946-55.
26. Tang X, Li G, Vasilakis N, Zhang Y, Shi Z, Zhong Y, et al. Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC evolutionary biology. 2009;9(1):52.
27. Holmes EC, Rambaut A. Viral evolution and the emergence of SARS coronavirus. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences. 2004;359(1447):1059-65.
28. Tipnis SR, Hooper NM, Hyde R, Karran E, Christie G, Turner AJ. A human homolog of angiotensin-converting enzyme cloning and functional expression as a captopril-insensitive carboxypeptidase. Journal of Biological Chemistry. 2000;275(43):33238-43.
29. Wong DW, Oudit GY, Reich H, Kassiri Z, Zhou J, Liu QC, et al. Loss of angiotensin-converting enzyme-2 (Ace2) accelerates diabetic kidney injury. The American journal of pathology. 2007;171(2):438-51.
30. Rentzsch B, Todiras M, Iliescu R, Popova E, Campos LA, Oliveira ML, et al. Transgenic angiotensin-converting enzyme 2 overexpression in vessels of SHRSP rats reduces blood pressure and improves endothelial function. Hypertension. 2008;52(5):967-73.
31. Der Sarkissian S, Grobe JL, Yuan L, Narielwala DR, Walter GA, Katovich MJ, et al. Cardiac overexpression of angiotensin converting enzyme 2 protects the heart from ischemia-induced pathophysiology. Hypertension. 2008;51(3):712-8.
32. Presta LG. Molecular engineering and design of therapeutic antibodies. Current opinion in immunology. 2008;20(4):460-70.
33. Igawa T, Tsunoda H, Tachibana T, Maeda A, Mimoto F, Moriyama C, et al. Reduced elimination of IgG antibodies by engineering the variable region. Protein Engineering, Design & Selection. 2010;23(5):385-92.
34. Frank SA. Specificity and cross-reactivity. Immunology and Evolution of Infectious Disease: Princeton University Press; 2002.
35. Renaut L, Monnet C, Dubreuil O, Zaki O, Crozet F, Bouayadi K, et al. Affinity maturation of antibodies: optimized methods to generate high-quality ScFv libraries and isolate IgG candidates by high-throughput screening. Antibody engineering: Springer; 2012. p. 451-61.
36. Payandeh Z, Rajabibazl M, Mortazavi Y, Rahimpour A, Taromchi AH. Ofatumumab monoclonal antibody affinity maturation through in silico modeling. Iranian biomedical journal. 2018;22(3):180.
37. Payandeh Z, Rajabibazl M, Mortazavi Y, Rahimpour A, Taromchi AH, Dastmalchi S. Affinity maturation and characterization of the ofatumumab monoclonal antibody. Journal of cellular biochemistry. 2019;120(1):940-50.
38. Floudas C, Fung H, McAllister S, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: A review. Chemical Engineering Science. 2006;61(3):966-88.
39. Prisant M, Richardson J, Richardson D. Structure validation by Calpha geometry: Phi, psi and Cbeta deviation. Proteins. 2003;50:437-50.
40. Benkert P, Künzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic acids research. 2009;37(suppl_2):W510-W4.
1. Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Advances in virus research. 100: Elsevier; 2018. p. 163-88.
2. Donoghue M, Hsieh F, Baronas E, Godbout K, Gosselin M, Stagliano N, et al. A novel angiotensin-converting enzyme–related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circulation research. 2000;87(5):e1-e9.
3. Zhang H, Kang Z, Gong H, Xu D, Wang J, Li Z, et al. The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes. BioRxiv. 2020.
4. Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov. BioRxiv. 2020.
5. Crackower MA, Sarao R, Oudit GY, Yagil C, Kozieradzki I, Scanga SE, et al. Angiotensin-converting enzyme 2 is an essential regulator of heart function. Nature. 2002;417(6891):822-8.
6. Shang J, Wan Y, Luo C, Ye G, Geng Q, Auerbach A, et al. Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences. 2020;117(21):11727-34.
7. Boehm M, Nabel EG. Angiotensin-converting enzyme 2—a new cardiac regulator. New England Journal of Medicine. 2002;347(22):1795-7.
8. Ge X-Y, Li J-L, Yang X-L, Chmura AA, Zhu G, Epstein JH, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503(7477):535-8.
9. ter Meulen J, Bakker AB, van den Brink EN, Weverling GJ, Martina BE, Haagmans BL, et al. Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets. The Lancet. 2004;363(9427):2139-41.
10. Ter Meulen J, Van Den Brink EN, Poon LL, Marissen WE, Leung CS, Cox F, et al. Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants. PLoS medicine. 2006;3(7).
11. Zhu Z, Chakraborti S, He Y, Roberts A, Sheahan T, Xiao X, et al. Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies. Proceedings of the National Academy of Sciences. 2007;104(29):12123-8.
12. Ying T, Prabakaran P, Du L, Shi W, Feng Y, Wang Y, et al. Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody. Nature communications. 2015;6(1):1-10.
13. Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, et al. Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerging Microbes & Infections. 2020;9(1):382-5.
14. Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS microbiology letters. 1999;174(2):247-50.
15. Albà MM, Castresana J. On homology searches by protein Blast and the characterization of the age of genes. BMC evolutionary biology. 2007;7(1):53.
16. Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, et al. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallographica Section D: Biological Crystallography. 1998;54(6):1078-84.
17. Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Current topics in medicinal chemistry. 2008;8(18):1555-72.
18. Prabakaran P, Gan J, Feng Y, Zhu Z, Choudhry V, Xiao X, et al. Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody. Journal of Biological Chemistry. 2006;281(23):15829-36.
19. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature protocols. 2009;4(7):1073.
20. Dunbar J, Krawczyk K, Leem J, Marks C, Nowak J, Regep C, et al. SAbPred: a structure-based antibody prediction server. Nucleic acids research. 2016;44(W1):W474-W8.
21. De Vries SJ, Van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nature protocols. 2010;5(5):883.
22. Chen W-H, Strych U, Hotez PJ, Bottazzi ME. The SARS-CoV-2 Vaccine Pipeline: an Overview. Current Tropical Medicine Reports. 2020:1-4.
23. Prompetchara E, Ketloy C, Palaga T. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol. 2020.
24. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet. 2020;395(10224):565-74.
25. Rockx B, Donaldson E, Frieman M, Sheahan T, Corti D, Lanzavecchia A, et al. Escape from human monoclonal antibody neutralization affects in vitro and in vivo fitness of severe acute respiratory syndrome coronavirus. The Journal of infectious diseases. 2010;201(6):946-55.
26. Tang X, Li G, Vasilakis N, Zhang Y, Shi Z, Zhong Y, et al. Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC evolutionary biology. 2009;9(1):52.
27. Holmes EC, Rambaut A. Viral evolution and the emergence of SARS coronavirus. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences. 2004;359(1447):1059-65.
28. Tipnis SR, Hooper NM, Hyde R, Karran E, Christie G, Turner AJ. A human homolog of angiotensin-converting enzyme cloning and functional expression as a captopril-insensitive carboxypeptidase. Journal of Biological Chemistry. 2000;275(43):33238-43.
29. Wong DW, Oudit GY, Reich H, Kassiri Z, Zhou J, Liu QC, et al. Loss of angiotensin-converting enzyme-2 (Ace2) accelerates diabetic kidney injury. The American journal of pathology. 2007;171(2):438-51.
30. Rentzsch B, Todiras M, Iliescu R, Popova E, Campos LA, Oliveira ML, et al. Transgenic angiotensin-converting enzyme 2 overexpression in vessels of SHRSP rats reduces blood pressure and improves endothelial function. Hypertension. 2008;52(5):967-73.
31. Der Sarkissian S, Grobe JL, Yuan L, Narielwala DR, Walter GA, Katovich MJ, et al. Cardiac overexpression of angiotensin converting enzyme 2 protects the heart from ischemia-induced pathophysiology. Hypertension. 2008;51(3):712-8.
32. Presta LG. Molecular engineering and design of therapeutic antibodies. Current opinion in immunology. 2008;20(4):460-70.
33. Igawa T, Tsunoda H, Tachibana T, Maeda A, Mimoto F, Moriyama C, et al. Reduced elimination of IgG antibodies by engineering the variable region. Protein Engineering, Design & Selection. 2010;23(5):385-92.
34. Frank SA. Specificity and cross-reactivity. Immunology and Evolution of Infectious Disease: Princeton University Press; 2002.
35. Renaut L, Monnet C, Dubreuil O, Zaki O, Crozet F, Bouayadi K, et al. Affinity maturation of antibodies: optimized methods to generate high-quality ScFv libraries and isolate IgG candidates by high-throughput screening. Antibody engineering: Springer; 2012. p. 451-61.
36. Payandeh Z, Rajabibazl M, Mortazavi Y, Rahimpour A, Taromchi AH. Ofatumumab monoclonal antibody affinity maturation through in silico modeling. Iranian biomedical journal. 2018;22(3):180.
37. Payandeh Z, Rajabibazl M, Mortazavi Y, Rahimpour A, Taromchi AH, Dastmalchi S. Affinity maturation and characterization of the ofatumumab monoclonal antibody. Journal of cellular biochemistry. 2019;120(1):940-50.
38. Floudas C, Fung H, McAllister S, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: A review. Chemical Engineering Science. 2006;61(3):966-88.
39. Prisant M, Richardson J, Richardson D. Structure validation by Calpha geometry: Phi, psi and Cbeta deviation. Proteins. 2003;50:437-50.
40. Benkert P, Künzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic acids research. 2009;37(suppl_2):W510-W4.
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