Bioinformatics-led design of single-chain antibody molecules targeting DNA sequences for retinoblastoma

International Journal of Ophthalmology

Volumn 4, Issue 1, 2011, Pages 8-13

  Shang, Guo Gang ^a   Zhang, Jian Hua ^b   Lü, Yong Gang ^c   Yun, Jun ^c  

^a ZHENGZHOU PEOPLE S HOSPITAL   (China)

^b ZHENGZHOU UNIVERSITY   (China)

^c FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Bioinformatics; Retinoblastoma; Single chain antibody; Structure activity relationship

Indexed keywords

EID: 84894590598     PISSN: 22223959     EISSN: 22274898     Source Type: Journal    
DOI: 10.3980/j.issn.2222-3959.2011.01.02     Document Type: Article

References (56)

1. Zhong XF, Li Y P, Huang SQ. Cloning variable region gene of light chain of monoclonal antibody against human retinoblastoma. Chin Int J Med. 2002;2(3):211-214.
2. Ohshima M, Tadakuma T, Hayashi H, Inoue K, Itoh K. Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'- deoxcytidine. J Biochem. 2010;147(1):135-141.
3. Kamphausen S, Höltge N, Wirsching F, Morys-Wortmann C, Riester D, Goetz R, Thürk M, Schwienhorst A. Genetic algorithm for the design of molecules with desired properties. J Comput Aided Mol Des. 2002;16(8-9):551-567.
4. Hajduk PJ, Huth JR, Tse C. Predicting protein druggability. Drug Discov Today. 2005;10(23-24):1675-1682.
5. Jiang Z, Zhou Y . Using bioinformatics f or drug target identification from the genome. Am J Pharmacogenomics. 2005;5(6):387-396.
6. Wei LH, Olafsen T, Radu C, Hildebrandt IJ, McCoy MR, Phelps ME, Meares C, Wu AM, Czernin J, Weber WA. Engineered antibody fragments with infinite affinity as reporter genes f or PET imaging. J Nucl Med. 2008;49(11):1828-1835.
7. Zdobnova TA, Dorofeev SG, Tananaev PN, Vasiliev RB, Balandin TG, Edelweiss EF, Stremovskiy OA, Balalaeva IV, Turchin IV, Lebedenko EN, Zlomanov VP, Deyev SM. Fluorescent immunolabeling of cancer cells by quantum dots and antibody scFv fragment. J Biomed Opt. 2009;14(2):021004.
8. v on zur Muhlen C, Peter K, Ali ZA, Schneider JE, McAteer MA, Neubauer S, Channon KM, Bode C, Choudhury RP. Visualization of activated platelets by targeted magnetic resonance imaging utilizing conformation-specific antibodies against glycoprotein IIb/IIIa. J Vasc Res. 2009;46(1):6-14.
9. Johnson TS, Mahnke K, Storn V, Schönfeld K, Ring S, Nettelbeck DM, Haisma HJ, Le Gall F, Kontermann RE, Enk AH. Inhibition of melanoma growth by targeting of antigen to dendritic cells via an anti-DEC-205 single-chain fragment variable molecule. Clin Cancer Res. 2008;14(24):8169-8177.
10. Nam CH, Lobato MN, Appert A, Drynan LF, Tanaka T, Rabbitts TH. An antibody inhibitor of the LMO2-protein complex blocks its normal and tumorigenic functions. Oncogene. 2008;27(36):4962-4968.
11. Zhu H, Y ang B, Yang X, Wang L, Xu J, Liao C, Feng Q, Tang H, Hu L, Chen Z, Li Y. A novel antibody fragment targeting HAb18G/CD147 with cytotoxicity and decreased immunogenicity. Cancer Biol Ther. 2009;8(11):1035-1044.
12. Le Gall F, Reusch U, Little M, Kipriyanov SM. Effect of linker sequences between the antibody variable domains on the formation, stability and biological activity of a bispecific tandem diabody. Protein Eng Des Sel. 2004;17(4):357-66.
13. Geng SS, Feng J, Li Y, Sun Y, Gu X, Huang Y, Wang Y, Kang X, Chang H, Shen B. Binding activity difference of anti-CD20 scFv-Fc fusion protein derived from variable domain exchange. Cell Mol Immunol. 2006;3(6):439-43.
14. Wang Y, Li X, Chen W. Construction, structure prediction and phylogenetic analysis of murine scFv gene against human cervical cancer. Xibao Yu Fenzi Mianyi Xue Zazhi. 2005;21(6):723-726.
15. Arcangeli C, Cantale C, Galeffi P, Rosato V. Structure and dynamics of the anti-AMCV scFv(F8): effects of selected mutations on the antigen combining site. J Struct Biol. 2008;164(1):119-133.
16. Messerschmidt SK, Kolbe A, Müller D, Knoll M, Pleiss J, Kontermann RE. Novel single-chain Fv' formats for the generation of immunoliposomes by site-directed coupling. Bioconjug Chem. 2008;19(1):362-369.
17. Kumada Y, Hamasaki K, Shiritani Y, Nakagawa A, Kuroki D, Ohse T, Choi DH, Katakura Y, Kishimoto M. Direct immobilization of functional single-chain variable fragment antibodies (scFvs) onto a polystyrene plate by genetic fusion of a polystyrene-binding peptide (PS-tag) Anal Bioanal Chem. 2009;395(3):759-765.
18. Zh u J, Rong Z, Jiang B, Liu J. Characterization and analysis of the aggregation of a single-chain chimeric anti-ErbB2 antibody. Shengwu Gongcheng Xuebao. 2008;24(11):1918-1923.
19. Kubetzko S, Balic E, Waibel R, Zangemeister-Wittke U, Plückthun A. PEGylation and multimerization of the anti-p185HER-2 single chain Fv fragment 4D5: effects on tumor targeting. J Biol Chem. 2006;281(46):35186-35201.
20. Kaontermann RE. Recombinant bispecific antibodies for cancer therapy. Acta Pharmacologica Sinica. 2005;26(1):1-9.
21. Chang L, Zhou C, Xu M, Liu J. Interactions between anti-ErbB2 antibody A21 and the ErbB2 extracellular domain provide a basis for improving A21 affinity. J Comput Aided Mol Des. 2010;24(1):37-47.
22. Xu J, Song J, Yan F, Ch u H, Luo J, Zhao Y, Cheng X, Luo G, Zheng Q, Wei J. Improving GPX activity of selenium-containing human single-chain Fv antibody by site-directed mutation based on the structural analysis. J Mol Recognit. 2009;22(4):293-300.
23. Tiwari A, Khanna N, Acharya SK, Sinha S. Humanization of high affinity anti-HBs antibody by using human consensus sequence and modification of selected minimal positional template and packing residues. Vaccine. 2009;27(17):2356- 2366.
24. Ye G, Y ang DH, Tang SH, Zhou M, Ding SH, Luo JL. Molecular simulation of a single chain Fv against hepatocellular carcinoma. Chin J Pathophysilol. 2007;23(6):1246-1248.
25. Tang ZJ, Liao WJ, Yu B, Zhong JX, Zhu HF, Ye Q, Cheng X, Li WH, Shen GX. Modeling of scFv of human antibody against liver cancer. A CTA Biophysica Sinica. 2005;21(3):195-199.
26. Wang Y, Li X, Chen W. Expression, structure prediction and functional analysis of murine single-chain fragment variable antibody against human cervical cancer. Nanfang Yike Daxue Xuebao. 2006;26(1):16-21.
27. Yan LY, Chen JH, Zhang XG. Research Progress in the Linker of Fusion Protein. Biotechnology. 2008;18(3):92-94.
28. Rea A M, Thurston V, Searle MS. Mechanism of ligand-induced folding of a natively unfolded helixless variant of rabbit I-BABP. Biochemistry. 2009;48(31):7556-7564.
29. Xi Y, Y uan Z, Zhang H, Guan H, Kong F, Liu N, Liang F, Cui J, Guo S, Sun Y, Xi C. Molecular construction and characterization of a novel exotoxin fusion protein that selectively blocks the B7:CD28 costimulatory signal system. J Immunother. 2006;29(6):586-595.
30. Xue F, Gu Z, Feng JA. LINKER: a web server to generate peptide sequences with extended conformation. Nucleic Acids Res. 2004;32(Web Server issue):W562-565.
31. Shibata K, Maruyama-Takahashi K, Yamasaki M, Hirayama N. G-CSF receptor-binding cyclic peptides designed with artificial amino-acid linkers. Biochem Biophys Res Commun. 2006;341(2):483-488.
32. Kim GB, Wang Z, Liu YY, Stavrou S, Mathias A, Goodwin KJ, Thomas JM, Neville DM. A fold-back single-chain diabody format enhances the bioactivity of an anti-monkey CD3 recombinant diphtheria toxin-based immunotoxin. Protein Eng Des Sel. 2007;20(9):425-432.
33. Theisen DM, Pongratz C, Wiegmann K, Rivero F, Krut O, Krönke M. Targeting of HIV-1 Tat traffic and function by transduction-competent single chain antibodies. Vaccine. 2006;24(16):3127-3136.
34. Liu ZG, Lin JB, Du Y, Yu WY. Anti-proteolysis study of recombinant Hn-UK fusion protein in CHO cell. Shengwu Huaxue Y u Shengwu Wuli Jinzhan. 2005;2(6):544-550.
35. Y ang LJ, Hou Y C, Bai Y J, Y ao LB, Su CZ. Analysis of primary structure and modeling of spatial structure of single-chain variable region of antibody against human gastric cancer. Shijie Huaren Xiaohua Zazhi. 2008;16(21):2333- 2336.
36. Arcangeli C, Cantale C, Galeffi P, Gianese G, Paparcone R, Rosato V. Understanding structural/functional properties of immunoconjugates for cancer therapy by computational approaches. J Biomol Struct Dyn. 2008;26(1):35-48.
37. Feng J, Xie Z, Gu o N, Shen B. Design and assembly of anti-CD16 ScFv antibody with two different linker peptides. J Immunol Methods. 2003;282(1-2):33-43.
38. Shan D, Press OW, Tsu TT, Hayden MS, Ledbetter JA . Characterization of scFv-Ig constructs generated from the anti-CD20 mAb 1F5 using linker peptides of varying lengths. J Immunol. 1999;162(11):6589-6595.
39. Kim GB, Wang Z, Liu YY, Stavrou S, Mathias A, Goodwin KJ, Thomas JM, Neville DM. A fold-back single-chain diabody format enhances the bioactivity of an anti-monkey CD3 recombinant diphtheria toxin-based immunotoxin. Protein Eng Des Sel. 2007;20(9):425-432.
40. Wajanarogana S, Prasomrothanakul T, Udomsangpetch R, Tungpradabkul S. Construction of a human functional single-chain variable fragment (scFv) antibody recognizing the malaria parasite Plasmodium falciparum. Biotechnol Appl Biochem. 2006;44(Pt 1):55-61.
41. Wang SH, Zhang JB, Zhang ZP, Zhou Y F, Yang RF, Chen J, Guo Y C, Y ou F, Zhang XE. Construction of single chain variable fragment (ScFv) and BiscFv-alkaline phosphatase fusion protein for detection of Bacillus anthracis. Anal Chem. 2006;78(4):997-1004.
42. Zhang JH, Yun J, Shang ZG, Zhang XH, Pan BR. Design and optimization of a linker for fusion protein construction. Ziran Kexue Jinzhan. 2009;19(10):1197-1200.
43. Montgomery DL, Wang Y J, Hrin R, Luftig M, Su B, Miller MD, Wang F, Haytko P, Huang L, Vitelli S, Condra J, Liu X, Hampton R, Carfi A, Pessi A, Bianchi E, Joyce J, Lloyd C, Geleziunas R, Bramhill D, King VM, Finnefrock A C, Strohl W, An Z. Affinity maturation and characterization of a human monoclonal antibody against HIV-1 gp41. MAbs. 2009;1(5):462- 474.
44. Clark KR, Walsh ST. Crystal structure of a 3B3 variant-a broadly neutralizing HIV-1 scFv antibody. Protein Sci. 2009;18(12):2429-2441.
45. Koti M, Farrugia W, Nagy E, Ramsland PA, Kaushik AK. Construction of single-chain Fv with two possible CDR3H conformations but similar inter-molecular forces that neutralize bovine herpesvirus 1. Mol Immunol. 2010;47(5):953- 960.
46. Shen Z, Yan H, Zhang Y, Mernaugh RL, Zeng X. Engineering peptide linkers for scFv immunosensors. Anal Chem. 2008;80(6):1910-1917.
47. Sheng WJ, Miao QF, Zhen Y S. Construction and screening of phage antibody libraries against epidermal growth factor receptor and soluble expression of single chain Fv. Yao Xue Xue Bao. 2009;44(6):597-602.
48. Fisher A C, DeLisa MP. Efficient isolation of soluble intracellular single-chain antibodies using the twin-arginine translocation machinery. J Mol Biol. 2009;385(1):299-311.
49. Asano R, Ikoma K, Kawaguchi H, Ishiyama Y, Nakanishi T, Umetsu M, Hayashi H, Katayose Y, Unno M, Kudo T, Kumagai I. Application of the Fc fusion format to generate tag-free bi-specific diabodies. FEBS J. 2010;277(2):477-487.
50. Stork R, Zettlitz KA, Müller D, Rether M, Hanisch FG, Kontermann RE. N-glycosylation as novel strategy to improve pharmacokinetic properties of bispecific single-chain diabodies. J Biol Chem. 2008;283(12):7804-7812.
51. Gurkan C, Ellar DJ. Expression in Pichia pastoris and purification of a membrane-acting immunotoxin based on a synthetic gene coding for the Bacillus thuringiensis Cyt2Aa1 toxin. Protein Expr Purif. 2003;29(1):103-116.
52. Olafsen T, Sirk SJ, Betting DJ, Kenanova VE, Bauer KB, Ladno W, Raubitschek AA, Timmerman JM, Wu AM. ImmunoPET imaging of B-cell lymphoma using 124I-anti-CD20 scFv dimers (diabodies) Protein Eng Des Sel. 2010;23(4):243-249.
53. Schmiedl A, Zimmermann J, Scherberich JE, Fischer P, Dübel S. Recombinant variants of antibody 138H11 against human gamma-glutamyltransferase for targeting renal cell carcinoma. Hum Antibodies. 2006;15(3):81-94.
54. Szántai-Kis C, Kövesdi I, Eros D, Bánhegyi P, Ullrich A, Kéri G, Orfi L. Prediction oriented QSAR modelling of EGFR inhibition. Curr Med Chem. 2006;13(3):277-287.
55. Y an DD, Fang J, Song, JD Construction and expression of bivalent single-chain antibodies with different linker sequence against human colorectal carcinoma. Chin J Cell Biol. 2007;29(2):272-276.
56. Gu X, Jia X, Feng J, Shen B, Huang Y, Geng S, Sun Y, Wang Y, Li Y, Long M. Molecular modeling and affinity determination of ScFv antibody: proper linker peptide enhances its activity. Ann Biomed Eng. 2010;38(2):537-549.