TY - JOUR
T1 - High-throughput computational pipeline for 3-D structure preparation and in silico protein surface property screening
T2 - A case study on HBcAg dimer structures
AU - Klijn, Marieke E.
AU - Vormittag, Philipp
AU - Bluthardt, Nicolai
AU - Hubbuch, Jürgen
PY - 2019
Y1 - 2019
N2 - Knowledge-based experimental design can aid biopharmaceutical high-throughput screening (HTS) experiments needed to identify critical manufacturability parameters. Prior knowledge can be obtained via computational methods such as protein property extraction from 3-D protein structures. This study presents a high-throughput 3-D structure preparation and refinement pipeline that supports structure screenings with an automated and data-dependent workflow. As a case study, three chimeric virus-like particle (VLP) building blocks, hepatitis B core antigen (HBcAg) dimers, were constructed. Molecular dynamics (MD) refinement quality, speed, stability, and correlation to zeta potential data was evaluated using different MD simulation settings. Settings included 2 force fields (YASARA2 and AMBER03) and 2 pKa computation methods (YASARA and H++). MD simulations contained a data-dependent termination via identification of a 2 ns Window of Stability, which was also used for robust descriptor extraction. MD simulation with YASARA2, independent of pKa computation method, was found to be most stable and computationally efficient. These settings resulted in a fast refinement (6.6–37.5 h), a good structure quality (−1.17–−1.13) and a strong linear dependence between dimer surface charge and complete chimeric HBcAg VLP zeta potential. These results indicate the computational pipeline's applicability for early-stage candidate assessment and design optimization of HTS manufacturability or formulability experiments.
AB - Knowledge-based experimental design can aid biopharmaceutical high-throughput screening (HTS) experiments needed to identify critical manufacturability parameters. Prior knowledge can be obtained via computational methods such as protein property extraction from 3-D protein structures. This study presents a high-throughput 3-D structure preparation and refinement pipeline that supports structure screenings with an automated and data-dependent workflow. As a case study, three chimeric virus-like particle (VLP) building blocks, hepatitis B core antigen (HBcAg) dimers, were constructed. Molecular dynamics (MD) refinement quality, speed, stability, and correlation to zeta potential data was evaluated using different MD simulation settings. Settings included 2 force fields (YASARA2 and AMBER03) and 2 pKa computation methods (YASARA and H++). MD simulations contained a data-dependent termination via identification of a 2 ns Window of Stability, which was also used for robust descriptor extraction. MD simulation with YASARA2, independent of pKa computation method, was found to be most stable and computationally efficient. These settings resulted in a fast refinement (6.6–37.5 h), a good structure quality (−1.17–−1.13) and a strong linear dependence between dimer surface charge and complete chimeric HBcAg VLP zeta potential. These results indicate the computational pipeline's applicability for early-stage candidate assessment and design optimization of HTS manufacturability or formulability experiments.
KW - 3-D structure preparation
KW - Computational pipeline
KW - HBcAg
KW - High-throughput screening
KW - MD
KW - Surface charge
KW - VLP
UR - http://www.scopus.com/inward/record.url?scp=85064170551&partnerID=8YFLogxK
U2 - 10.1016/j.ijpharm.2019.03.057
DO - 10.1016/j.ijpharm.2019.03.057
M3 - Article
C2 - 30935914
AN - SCOPUS:85064170551
SN - 0378-5173
VL - 563
SP - 337
EP - 346
JO - International Journal of Pharmaceutics
JF - International Journal of Pharmaceutics
ER -