Identification of Protein-Excipient Interaction Hotspots Using Computational Approaches.
Protein formulation development relies on the selection of excipients that inhibit protein-protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein-excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein-protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations.
EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies, University College London, Biochemical Engineering Department, Bernard Katz Building, Gordon Street, London WC1H 0AH, UK. t.barata@ucl.ac.uk.|UCL School of Pharmacy, Department of Pharmaceutics, 29-39 Brunswick Square, London WC1N 1AX, UK. t.barata@ucl.ac.uk.
Teresa S
TS
Barata
EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies, University College London, Biochemical Engineering Department, Bernard Katz Building, Gordon Street, London WC1H 0AH, UK. c.zhang.11@ucl.ac.uk.
Cheng
C
Zhang
EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies, University College London, Biochemical Engineering Department, Bernard Katz Building, Gordon Street, London WC1H 0AH, UK. p.dalby@ucl.ac.uk.
Paul A
PA
Dalby
EPSRC Centre for Innovative Manufacturing in Emergent Macromolecular Therapies, University College London, Biochemical Engineering Department, Bernard Katz Building, Gordon Street, London WC1H 0AH, UK. ucnvsbr@ucl.ac.uk.|UCL School of Pharmacy, Department of Pharmaceutics, 29-39 Brunswick Square, London WC1N 1AX, UK. ucnvsbr@ucl.ac.uk.
Steve
S
Brocchini
Department of Pharmacy, Pharmacology and Postgraduate Medicine, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK. m.zloh@herts.ac.uk.
Mire
M
Zloh
D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D005079:Excipients / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results; D013329:Structure-Activity Relationship
D000596:Amino Acids; D005079:Excipients; D011506:Proteins
Fab formulation; molecular docking; molecular dynamics; protein stability; protein–excipient interactions