The Role of Cyclodextrins against Interface-Induced Denaturation in Pharmaceutical Formulations: A Molecular Dynamics Approach

Abstract

Protein-based pharmaceutical products are subject to a variety of environmental stressors, during both production and shelf-life. In order to preserve their structure, and, therefore, functionality, it is necessary to use excipients as stabilizing agents. Among the eligible stabilizers, cyclodextrins (CDs) have recently gained interest in the scientific community thanks to their properties. Here, a computational approach is proposed to clarify the role of β-cyclodextrin (βCD) and 2-hydroxypropyl-β-cyclodextrin (HPβCD) against granulocyte colony-stimulating (GCSF) factor denaturation at the air-water and ice-water interfaces, and also in bulk water at 300 or 260 K. Both traditional molecular dynamics (MD) simulations and enhanced sampling techniques (metadynamics, MetaD) are used to shed light on the underlying molecular mechanisms. Bulk simulations revealed that CDs were preferentially included within the surface hydration layer of GCSF, and even included some peptide residues in their hydrophobic cavity. HPβCD was able to stabilize the protein against surface-induced denaturation in proximity of the air-water interface, while βCD had a destabilizing effect. No remarkable conformational changes of GCSF, or noticeable effect of the CDs, were instead observed at the ice surface. GCSF seemed less stable at low temperature (260 K), which may be attributed to cold-denaturation effects. In this case, CDs did not significantly improve conformational stability. In general, the conformationally altered regions of GCSF seemed not to depend on the presence of excipients that only modulated the extent of destabilization with either a positive or a negative effect.

Keywords: cyclodextrins; denaturation; interface; molecular dynamics; protein stability.

Figure 1

Snapshots of (a) β-cyclodextrin and (b) 2-hydroxypropyl-β-cyclodextrin. The red surface encompasses the primary rim, while the light-blue one delimitates the secondary rim. (c) Granulocyte-colony stimulating factor. The different colors identify different secondary structures. Purple: α-helix, cyan: turn, white: coil.

Figure 2

Normalized density profiles for the GCSF formulations at the air–water interface. (a) Protein profiles (sims. 7, 8). (b) Density profiles for βCD and its rims (sim. 7). (c) Density profiles for HPβCD and its rims (sim. 7).

Figure 3

Normalized density profiles for the GCSF formulations at the ice–water interface. (a) Protein profiles (sims. 9, 10). (b) Density profiles for βCD and its rims (sim. 9). (c) Density profiles for HPβCD and its rims (sim. 9).

Figure 4

Probability distributions of the interface-GCSF distance. (a) Air–water systems (sims. 15 and 16 in Table 1). (b) Ice–water systems (sims. 17 and 18 in Table 1).

Figure 5

Probability distributions of R_g and dRMSD values for GCSF. (a, d) GCSF systems without excipients (sims. 12, 14, 16, and 18 in Table 1). (b, e) Systems in aqueous bulk at 300 K (sims. 11 and 12 in Table 1). (c, f) Systems at the air-water interface (sims. 15 and 16 in Table 1).

Figure 6

Probability distributions of R_g and dRMSD values for GCSF. (a, c) Systems in the aqueous bulk at 260 K (sims. 13 and 14 in Table 1). (b, d) Systems at the ice-water interface (sims. 17 and 18 in Table 1).

Figure 7

Probability distributions for GCSF residues (ranging from 7 to 174). (a) Residues with a Q_res lower than 0.5, distinguishing the type of excipient (sims. 11–18 in Table 1). (b) Residues with a Q_res lower than 0.5, averaging all the systems together (sims. 11–18 in Table 1). (c) Residues included by CD hydrophobic cavities (simulations 3, 5, 7, and 9 in Table 1).