Visn. Nac. Akad. Nauk Ukr. 2019. (2):69-85 
https://doi.org/10.15407/visn2019.02.069

S.I. Romanyuk, S.V. Komisarenko
Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kyiv

MOLECULAR BIOLOGY AND IMMUNOLOGY REVOLUTIONIZE CHEMISTRY, OR HOW TO GUIDE THE EVOLUTION OF PROTEINS FOR THE BENEFIT OF HUMANITY
Nobel Prize in Chemistry for 2018

The Nobel Prize in Chemistry for 2018 was shared by three scientists. Half the prize went to the American researcher Frances H. Arnold “for the guided evolution of enzymes”, the other half was shared between the American George P. Smith and Briton Sir Gregory P. Winter “for the phage display of peptides and antibodies.” The methods developed by Nobel laureates will promote the development of more environmentally friendly production of chemical products, new materials, pharmaceuticals, biofuels, etc.

Language of article: ukrainian

 

REFERENCES

1.     The 2018 Clarivate Citation Laureates. https://web.ornl.gov/sci/first/ClarivateAnalyticsCitationLaureates.pdf

2.     The Nobel Prize in Chemistry 2018. Press Release. https://www.nobelprize.org/prizes/chemistry/2018/press-release/

3.     Nobel prize in literature 2018 cancelled after sexual assault scandal. https://www.theguardian.com/books/2018/may/04/nobel-prize-for-literature-2018-cancelled-after-sexual-assault-scandal/

4.     Frances Arnold. Wikipedia. https://en.wikipedia.org/wiki/Frances_Arnold

5.     George Smith. Wikipedia. https://en.wikipedia.org/wiki/George_Smith_(chemist)

6.     Greg Winter. Wikipedia. https://en.wikipedia.org/wiki/Greg_Winter

7.     Spiegelman S., Haruna I., Holland I.B., Beaudreau G., Mills D. The Synthesis of a Self-propagating and Infectious Nucleic Acid with a Purified Enzyme. Proc. Natl. Acad. Sci. USA. 1965. 54(3): 919. http://dx.doi.org/10.1073/pnas.54.3.919

8.     Eigen M., Gardiner W. Evolutionary molecular engineering based on RNA replication. Pure Appl. Chem. 1984. 56(8): 967. http://dx.doi.org/10.1351/pac198456080967

9.     Chen K., Arnold F.H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. USA. 1993. 90(12): 5618. http://dx.doi.org/10.1073/pnas.90.12.5618

10. Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 1994. 370(6488): 389. http://dx.doi.org/10.1038/370389a0

11. Crameri A., Dawes G., Rodriguez E. Jr., Silver S., Stemmer W.P. Molecular evolution of an arsenate detoxification pathway by DNA shuffling. Nat. Biotechnol. 1997. 15(5): 436. http://dx.doi.org/10.1038/nbt0597-436

12. Zhang J.H., Dawes G., Stemmer W.P. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc. Natl. Acad. Sci. USA. 1997. 94(9): 4504. http://dx.doi.org/10.1073/pnas.94.9.4504

13. Crameri A., Whitehorn E.A., Tate E., Stemmer W.P. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 1996. 14(3): 315. http://dx.doi.org/10.1038/nbt0396-315

14. Zhao H., Giver L., Shao Z., Affholter J.A., Arnold F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 1998. 16(3): 258. http://dx.doi.org/10.1038/nbt0398-258

15. Arnold F. The nature of chemical innovation: new enzymes by evolution. Q. Rev. Biophys. 2015. 48(4): 404. http://dx.doi.org/10.1017/S003358351500013X

16. Chen K., Huang X., Kan S.B.J., Zhang R.K., Arnold F.H. Enzymatic construction of highly strained carbocycles. Science. 2018. 360(6384): 71. http://dx.doi.org/10.1126/science.aar4239

17. Schmidt-Dannert C., Umeno D., Arnold F.H. Molecular breeding of carotenoid biosynthetic pathways. Nat. Biotechnol. 2000. 18(7): 750. http://dx.doi.org/10.1038/77319

18. May O., Nguyen P.T., Arnold F.H. Inverting enantioselectivity by directed evolution of hydantoinase for improved production of L-methionine. Nat. Biotechnol. 2000. 18(3): 317. https://doi.org/10.1038/73773

19. Wintrode P.L., Miyasaki K., Arnold F.H. Patterns of adaptation in a laboratory evolved thermophilic enzyme. BBA Protein Struct. Mol. Evol. 2001. 1549(1): 1. http://dx.doi.org/10.1016/S0167-4838(01)00226-6

20. Bastian S., Liu X., Meyerowitz J.T., Snow C.D., Chen M.M.Y., Arnold F.H. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab. Eng. 2011. 13(3): 345. https://doi.org/10.1016/j.ymben.2011.02.004

21. McIntosh J.A., Coelho P.S., Farwell C.C., Wang Z.J., Lewis J.C., Brown T.R., Arnold F.H. Enantioselective intramolecular C-H amination catalyzed by engineered cytochrome P450 enzymes in vitro and in vivo. Angew. Chem. Int. Ed. Engl. 2013. 52(35): 9309. http://dx.doi.org/10.1002/anie.201304401

22. Kan S.B.J., Huang X., Gumulya Y., Chen K., Arnold F.H. Genetically programmed chiral organoborane synthesis. Nature. 2017. 552(7683): 132. http://dx.doi.org/10.1038/nature24996

23. Kan S.B., Lewis R.D., Chen K., Arnold F.H. Directed evolution of cytochrome c for carbon-silicon bond formation: Bringing silicon to life. Science. 2016. 354(6315): 1048. http://dx.doi.org/10.1126/science.aah6219

24. Smith G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 1985. 228(4705): 1315. http://dx.doi.org/10.1126/science.4001944

25. Parmley S.F., Smith G.P. Antibody-selectable filamentous fd phage vectors: affinity purification of target genes. Gene. 1988. 73(2): 305. http://dx.doi.org/10.1016/0378-1119(88)90495-7

26. de la Cruz V.F., Lal A.A., McCutchan T.F. Immunogenicity and epitope mapping of foreign sequences via genetically engineered filamentous phage. J. Biol. Chem. 1988. 263(9): 4318.

27. Devlin J.J., Panganiban L.C., Devlin P.E. Random peptide libraries: a source of specific protein-binding molecules. Science. 1990. 249(4967): 404. http://dx.doi.org/10.1126/science.2143033

28. Scott J.K., Smith G.P. Searching for peptide ligands with an epitope library. Science. 1990. 249(4967): 386. http://dx.doi.org/10.1126/science.1696028

29. McCafferty J., Griffiths A.D., Winter G., Chiswell D.J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature. 1990. 348(6301): 552. http://dx.doi.org/10.1038/348552a0

30. Kang A.S., Barbas C.F., Janda K.D., Benkovic S.J., Lerner R.A. Linkage of recognition and replication functions by assembling combinatorial antibody Fab libraries along phage surfaces. Proc. Nat. Acad. Sci. USA. 1991. 88(10): 4363. http://dx.doi.org/10.1073/pnas.88.10.4363

31. Hoogenboom H.R., Griffiths A.D., Johnson K.S., Chiswell D.J., Hudson P., Winter G. Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucl. Acid. Res. 1991. 19(15): 4133. http://dx.doi.org/10.1093/nar/19.15.4133

32. Clackson T., Hoogenboom H.R., Bonnert T.P., McCafferty J., Griffiths A.D., Winter G. Making antibody fragments using phage display libraries. Nature. 1991. 352(6336): 624. http://dx.doi.org/10.1038/352624a0

33. Burton D.R., Barbas C.F. 3rd, Persson M.A., Koenig S., Chanock R.M., Lerner R.A. A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals. Proc. Nat. Acad. Sci. USA. 1991. 88(22): 10134. http://dx.doi.org/10.1073/pnas.88.22.10134

34. Kovalenko O.V., Olland A., Piché-Nicholas N.J. Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis. Biol. Chem. 2013. 288(24): 17408. http://dx.doi.org/10.1074/jbc.M112.435289

35. Siontorou C.G. Nanobodies as novel agents for disease diagnosis and therapy. Int. J. Nanomedicine. 2013. (8): 4215. http://dx.doi.org/10.2147/IJN.S39428

36. Holt L.J., Herring Ch., Jespers L.S. et al. Domain antibodies: proteins for therapy. Trends Biotechnol. 2003. 21(11): 484. http://dx.doi.org/10.1016/j.tibtech.2003.08.007

37. Guo J., Cai M. New type recombinant antibody fragment scFv multimer and cancer targeting. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2003. 20(2): 361.

38. Hanes J., Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Nat. Acad. Sci. USA. 1997. 94(10): 4937.

39. Georgiou G., Staphopolous C., Daugherty P., Nayak A.R., Iverson B.L., Curtiss R. 3rd. Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nature Bioctech. 1997. 15(1): 29. http://dx.doi.org/10.1038/nbt0197-29

40. Boder E.T., Wittrup K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotech. 1997. 15(6): 553. http://dx.doi.org/10.1038/nbt0697-553

41. Jespers L.S., Roberts A., Mahler S.M., Winter G., Hoogenboom H.R. Guiding the selection of human antibodies from phage display repertoires to a single epitope of an antigen. Biotechnology (NY). 1994. 12(9): 899. http://dx.doi.org/10.1038/nbt0994-899

42. Cirino N.M., Sblattero D., Allen D., Peterson S.R., Marks J.D., Jackson P.J., Bradbury A., Lehnert B.E. Disruption of anthrax toxin binding with the use of human antibodies and competitive inhibitors. Infect. Immun. 1999. 67(6): 2957.

43. Brüggemann M., Spicer C., Buluwela L., Rosewell I., Barton S., Surani M.A., Rabbitts T.H. Human antibody production in transgenic mice: expression from 100 kb of the human IgH locus. Eur. J. Immunol. 1991. 21(5): 1323. http://dx.doi.org/10.1002/eji.1830210535

44. Moran N. Mouse platforms jostle for slice of humanized antibody market. Nat. Biotechnol. 2013. 31(4): 267. http://dx.doi.org/10.1038/nbt0413-267

45. Brüggemann M., Osborn M.J., Ma B., Hayre J., Avis S., Lundstrom B., Buelow R. Human antibody production in transgenic animals. Arch. Immunol. Ther. Exp. (Warsz). 2015. 63(2): 101. http://dx.doi.org/10.1007/s00005-014-0322-x

46. Wolchok J.D., Hodi F.S., Weber J.S., Allison J.P., Urba W.J., Robert C., O'Day S.J., Hoos A., Humphrey R., Berman D.M., Lonberg N., Korman A.J., Ann N.Y. Development of ipilimumab: a novel immunotherapeutic approach for the treatment of advanced melanoma. Acad. Sci. 2013. (1291): 1. http://dx.doi.org/10.1111/nyas.12180

47. Oyama H., Tanaka E., Kawanaka T. et al. Anti-idiotype scFv-enzyme fusion proteins: a clonable analyte-mimicking probe for standardized immunoassays targeting small biomarker. Anal. Chem. 2013. 85(23): 11553. http://dx.doi.org/10.1021/ac402868f

48. Kumada Y., Hamasaki K., Shiritani Y. et al. 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. http://dx.doi.org/10.1007/s00216-009-2999-y

49. Pavlova M.V., Nikolaev Iu.S., Irodov D.M., Okunev O.V., Kordium V.A., Gil'chuk P.V. Characterization of a panel of mouse single-chain antibodies against recombinant human interferon beta1b. Tsitol. Genet. 2008. 42(4): 3.

50. Oliinyk O.S., Kaberniuk A.A., Redchuk T.A., Korotkevich N.V., Labyntsev A.J., Romanyuk S.I., Kolibo D.V., Komisarenko S.V. Construction of immune library of murine immunoglobulin genes and screening of single-chain Fv-antibodies to diphtheria toxin b subunit. Ukr. Biochem. J. 2009. 81(2): 68.

51. Oliinyk O.S., Kaberniuk A.A., Burkaleva D.O., Romaniuk S.I., Kolibo D.V., Shepelyakovskaya A.O., Laman A.G., Komisarenko S.V. Obtaining of recombinant scFv-antibodies against diphtheria toxin using phage display system. Ukr. Biochem. J. 2007. 79(5): 91. 

52. Oliinyk O.S., Kaberniuk A.A., Kolibo D.V., Komisarenko S.V. Single chain variable fragments of antibodies against diphtheria toxin b-subunit isolated from phage display human antibody library. Biotechnologia Acta. 2014. 7(1): 54. http://dx.doi.org/10.15407/biotech7.01.054

53. Oliinyk O.S., Kaberniuk A.A., Redchuk T.A., Kolibo D.V., Komisarenko S.V. Construction of bifunctional molecules specific to antigen and antibody’s Fc-fragment by fusion of scFv-antibodies with staphylococcal protein A. Biopolym. Cell. 2009. 25(3): 245. http://dx.doi.org/10.7124/bc.0007E3

54. Oliinyk O.S., Labyntsev A.J., Korotkevich N.V., Kolibo D.V., Komisarenko S.V. Study on toxin-neutralization properties of recombinant single-chain variable antibody’s fragments against diphtheria toxin B subunit. Biopolym. Cell. 2009. 25(4): 315. http://dx.doi.org/10.7124/bc.0007EB

55. Oliinyk O.S., Kaberniuk A.A., Kolibo D.V., Komisarenko S.V. Isolation and characterisation of recombinant single chain variable fragment antibodies (scFv) against human heparinbinding EGF-like growth factor. Biotechnologia. 2012. 5(6): 61.

56. Oliinyk O.S., Labyntsev A.J., Manoylov K.Yu., Kolibo D.V., Komisarenko S.V. Immunoliposomes for the targeted delivery of biologically active compounds into tumor tissue cells. In: Nano-size systems and nanomaterials: research in Ukraine. (Kyiv: Akademperiodyka, 2014). 

57. Palyvoda K.O., Oliinyk O.S., Kolibo D.V., Komisarenko S.V. Obtaining and characterization of recombinant single-chain variable antibody fragments (scFv) against MRT63. Ukr. Biochem. J. 2014. 86(5): 121.  

58. Jacobs A.J., Mongkolsapaya J., Screaton G.R., McShane H., Wilkinson R.J. Antibodies and tuberculosis. Tuberculosis (Edinb). 2016. (101): 102. http://dx.doi.org/10.1016/j.tube.2016.08.001

59. Oliinyk O.S., Palyvoda K.O., Lugovskaya N.E., Kolibo D.V., Lugovskoy E.V., Komisarenko S.V. Recombinant single chain variable fragment antibodies (scFv) against Pro144–Leu155 fragment of human protein C. Ukr. Biochem. J. 2015. 87(2): 88. http://dx.doi.org/10.15407/ubj87.02.088

60. Koval L., Lykhmus O., Kalashnyk O. et al. The presence and origin of autoantibodies against α4 and α7 nicotinic acetylcholine receptors in the human blood: possible relevance to Alzheimer’s pathology. J. Alzheimer’s Dis. 2011. 25(4): 747. http://dx.doi.org/10.3233/JAD-2011-101845

61. Chen C., Constantinou A., Deonarain M. Modulating antibody pharmacokinetics using hydrophilic polymers. Expert Opin. Drug Deliv. 2011. 8(9): 1221. http://dx.doi.org/10.1517/17425247.2011.602399

62. Könning D., Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb. Cell Fact. 2018. 17(1): 32. http://dx.doi.org/10.1186/s12934-018-0881-3

63. Ye L., Yang C., Yu H. From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution. Appl. Microbiol. Biotechnol. 2018. 102(2): 559. http://dx.doi.org/10.1007/s00253-017-8568-y

64. Liu C.C., Mack A.V., Tsao M.L., Mills J.H., Lee H.S., Choe H., Farzan M., Schultz P.G., Smider V.V. Protein evolution with an expanded genetic code. Proc. Nat. Acad. Sci. USA. 2008. 105(46): 17688. http://dx.doi.org/10.1073/pnas.0809543105

65. Arnold F.H. Directed Evolution: Bringing New Chemistry to Life. Angew. Chem. Int. Ed. Engl. 2018. 57(16): 4143. http://dx.doi.org/10.1002/anie.201708408