Fab fragment of V H H-based antibody netakimab: Crystal structure and modeling interaction with cytokine Il-17A

Crystals

Volumn 9, Issue 3, 2019, Pages

  Kostareva, Olga ^a   Kolyadenko, Ilya ^a   Ulitin, Andrey ^b   Ekimova, Victoria ^b   Evdokimov, Stanislav ^b   Garber, Maria ^a   Tishchenko, Svetlana ^a   Gabdulkhakov, Azat ^a  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^b Department of Infectious Diseases   (Russian Federation)

Author keywords

Complementarity determining regions; Crystal structure; Fab fragment; Interleukin 17A; Netakimab; V H H domain

Indexed keywords

EID: 85064659977     PISSN: None     EISSN: 20734352     Source Type: Journal    
DOI: 10.3390/cryst9030177     Document Type: Article

References (42)

1. Cypowyj, S.; Picard, C.; Maródi, L.; Casanova, J.-L.; Puel, A. Immunity to Infection in IL-17-Deficient Mice and Humans. Eur. J. Immunol. 2012, 42, 2246–2254. [CrossRef]
2. Beringer, A.; Noack, M.; Miossec, P. IL-17 in Chronic Inflammation: From Discovery to Targeting. Trends Mol. Med. 2016, 22, 230–241. [CrossRef]
3. Paek, S.Y.; Frieder, J.; Kivelevitch, D.; Menter, M.A. IL-17 Inhibitors for Psoriasis. Semin. Cutan. Med. Surg. 2018, 37, 148–157. [CrossRef]
4. Wolfson, W. Ablynx Makes Nanobodies from Llama Bodies. Chem. Biol. 2006, 13, 1243–1244. [CrossRef] [PubMed]
5. Muyldermans, S. Single domain camel antibodies: Current status. J. Biotechnol. 2001, 74, 277–302. [CrossRef]
6. Schmitz, K.R.; Bagchi, A.; Roovers, R.C.; van Bergen en Henegouwen, P.M.P.; Ferguson, K.M. Structural Evaluation of EGFR Inhibition Mechanisms for nanobodies/VHH Domains. Structure 2013, 21, 1214–1224. [CrossRef]
7. Cortez-Retamozo, V. Efficient Cancer Therapy with a Nanobody-Based Conjugate. Cancer Res. 2004, 64, 2853–2857. [CrossRef]
8. Cortez-Retamozo, V.; Lauwereys, M.; Hassanzadeh, G.; Gobert, M.; Conrath, K.; Muyldermans, S.; De Baetselier, P.; Revets, H. Efficient Tumor Targeting by Single-Domain Antibody Fragments of Camels. Int. J. Cancer 2002, 98, 456–462. [CrossRef]
9. Harmsen, M.M.; Van Solt, C.B.; Fijten, H.P.D.; Van Setten, M.C. Prolonged in Vivo Residence Times of Llama Single-Domain Antibody Fragments in Pigs by Binding to Porcine Immunoglobulins. Vaccine 2005, 23, 4926–4934. [CrossRef] [PubMed]
10. Richard, G.; Meyers, A.J.; McLean, M.D.; Arbabi-Ghahroudi, M.; MacKenzie, R.; Hall, J.C. In Vivo Neutralization of α-Cobratoxin with High-Affinity Llama Single-Domain Antibodies (VHHs) and a VHH-Fc Antibody. PLoS ONE 2013, 8, e69495. [CrossRef] [PubMed]
11. Kontermann, R.E. Strategies to Extend Plasma Half-Lives of Recombinant Antibodies. BioDrugs 2009, 23, 93–109. [CrossRef] [PubMed]
12. Hoefman, S.; Ottevaere, I.; Baumeister, J.; Sargentini-Maier, M. Pre-Clinical Intravenous Serum Pharmacokinetics of Albumin Binding and Non-Half-Life Extended Nanobodies®. Antibodies 2015, 4, 141–156. [CrossRef]
13. Ulitin, A.; Evdokimov, S.; Soloviev, V.; Chernyh, Y.; Goncharova, O.; Korzhavin, D.; Chernovskaya, T.; Nemankin, T.; Ivanov, R.; Morozov, D., et al. High Affinity and Aggregatively Stable Antibodies on the Basis of Variable Domains vl and a Derivative vhh. U.S. Patent 2016048188A1, 31 March 2016.
14. International Nonproprietary Names for Pharmaceutical Substances (INN). INN: List 80; WHO Drug Information; WHO: Geneva, Switzerland, 2018; Volume 32, pp. 425–508.
15. Samtsov, A.V.; Khairutdinov, V.R.; Bakulev, A.L.; Kubanov, A.A.; Karamova, A.E.; Artem’eva, A.V.; Korotaeva, T.V. Efficacy and Safety of BCD-085, a Novel Interleukin-17 Inhibitor. Results of Phase II Clinical Trial in Patients with Moderate-to-Severe Plaque Psoriasis. Vestn. Dermatol. Venerol. 2017, 5, 52–63. [CrossRef]
16. Nurizzo, D.; Mairs, T.; Guijarro, M.; Rey, V.; Meyer, J.; Fajardo, P.; Chavanne, J.; Biasci, J.C.; McSweeney, S.; Mitchell, E. The ID23-1 Structural Biology Beamline at the ESRF. J. Synchrotron Radiat. 2006, 13 Pt 3, 227–238. [CrossRef]
17. Gabadinho, J.; Beteva, A.; Guijarro, M.; Rey-Bakaikoa, V.; Spruce, D.; Bowler, M.W.; Brockhauser, S.; Flot, D.; Gordon, E.J.; Hall, D.R.; et al. MxCuBE: A Synchrotron Beamline Control Environment Customized for Macromolecular Crystallography Experiments. J. Synchrotron Radiat. 2010, 17, 700–707. [CrossRef]
18. Bourenkov, G.P.; Popov, A.N. Optimization of Data Collection Taking Radiation Damage into Account. Acta Crystallogr. D Biol. Crystallogr. 2010, 66 Pt 4, 409–419. [CrossRef]
19. Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 2010, 66 Pt 2, 125–132. [CrossRef]
20. McCoy, A.J.; Grosse-Kunstleve, R.W.; Adams, P.D.; Winn, M.D.; Storoni, L.C.; Read, R.J. Phaser Crystallographic Software. J. Appl. Crystallogr. 2007, 40 Pt 4, 658–674. [CrossRef]
21. Murshudov, G.N.; Skubák, P.; Lebedev, A.A.; Pannu, N.S.; Steiner, R.A.; Nicholls, R.A.; Winn, M.D.; Long, F.; Vagin, A.A. REFMAC5 for the Refinement of Macromolecular Crystal Structures. Acta Crystallogr. D Biol. Crystallogr. 2011, 67 Pt 4, 355–367. [CrossRef]
22. Emsley, P.; Lohkamp, B.; Scott, W.G.; Cowtan, K. Features and Development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010, 66 Pt 4, 486–501. [CrossRef]
23. The PyMOL Molecular Graphics System. Available online: https://pymol.org/2/(accessed on 1 March 2019).
24. Yan, Y.; Zhang, D.; Zhou, P.; Li, B.; Huang, S. HDOCK: A web server for protein—Protein and protein—DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res. 2017, 45, 365–373. [CrossRef] [PubMed]
25. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008, 4, 435–447. [CrossRef] [PubMed]
26. MacKerell, A.D.; Bashford, D.; Bellott, M.; Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; et al. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586–3616. [CrossRef]
27. Mackerell, A.D., Jr.; Feig, M.; Brooks, C.L., 3rd. Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations. J. Comput. Chem. 2004, 25, 1400–1415. [CrossRef] [PubMed]
28. Hess, B.; Bekker, H.; Berendsen, H.; Johannes, G. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18, 1463–1472. [CrossRef]
29. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089–10092. [CrossRef]
30. Essmann, U.; Perera, L.; Berkowitz, M.L.; Darden, T.; Lee, H.; Pedersen, L.G. A Smooth Particle Mesh Ewald Method. J. Chem. Phys. 1995, 103, 8577–8593. [CrossRef]
31. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; DiNola, A.; Haak, J.R. Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81, 3684–3690. [CrossRef]
32. PDBePISA (Proteins, Interfaces, Structures and Assemblies). Available online: http://www.ebi.ac.uk/pdbe/prot_int/pistart.html (accessed on 1 March 2019).
33. Krissinel, E.; Henrick, K. Inference of Macromolecular Assemblies from Crystalline State. J. Mol. Biol. 2007, 372, 774–797. [CrossRef]
34. Liu, S.; Song, X.; Chrunyk, B.A.; Shanker, S.; Hoth, L.R.; Marr, E.S.; Griffor, M.C. Crystal Structures of Interleukin 17A and Its Complex with IL-17 Receptor A. Nat. Commun. 2013, 4, 1888. [CrossRef]
35. Hassanzadeh-Ghassabeh, G.; Devooght, N.; Pauw, P.; Vincke, C.; Muyldermans, S. Nanobodies and their potential applications. Nanomedicine 2013, 8, 1013–1026. [CrossRef] [PubMed]
36. North, B.; Lehmann, A.; Dunbrack, R.L., Jr. A New Clustering of Antibody CDR Loop Conformations. J. Mol. Biol. 2011, 406, 228–256. [CrossRef]
37. Martin, A.C.; Thornton, J.M. Structural Families in Loops of Homologous Proteins: Automatic Classification, Modelling and Application to Antibodies. J. Mol. Biol. 1996, 263, 800–815. [CrossRef] [PubMed]
38. Stanfield, R.L.; Zemla, A.; Wilson, I.A.; Rupp, B. Antibody Elbow Angles Are Influenced by Their Light Chain Class. J. Mol. Biol. 2006, 357, 1566–1574. [CrossRef]
39. Bailey, L.J.; Sheehy, K.M.; Dominik, P.K.; Liang, W.G.; Rui, H.; Clark, M.; Jaskolowski, M.; Kim, Y.; Deneka, D.; Tang, W.-J.; et al. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J. Mol. Biol. 2018, 430, 337–347. [CrossRef] [PubMed]
40. Gerhardt, S.; Abbott, W.M.; Hargreaves, D.; Pauptit, R.A.; Davies, R.A.; Needham, M.R.C.; Langham, C.; Barker, W.; Aziz, A.; Snow, M.J.; et al. Structure of IL-17A in Complex with a Potent, Fully Human Neutralizing Antibody. J. Mol. Biol. 2009, 394, 905–921. [CrossRef]
41. Ekimova, V.; Ulitin, A.; Evdokimov, S.; Sofronova, E.; Nemankin, T.; Solovyev, V.; Ustugov, I.; Nedorubov, A.; Chernykh, Y.; Goncharova, O.; et al. High Affinity Anti-Il-17a Monoclonal Antibody. In Proceedings of the Conference: PEGS, Boston, MA, USA, 4–8 May 2015.
42. Padova, D.; Gram, H.; Hofstetter, H.; Jeschke, M.; Rondeau, J.; Van Den Berg, W. IL-17 Antagonistic Antibodies. U.S. Patent 7,807,155 B2, 5 October 2010.