Comparative study of the binding mode between cytochrome P450 17A1 and prostate cancer drugs in the absence of haem iron

Abstract

According to the X-ray crystal structures of CYP17A1 (including its complexes with inhibitors), it is shown that a hydrogen bond exists between CYP17A1 and its inhibitors (such as abiraterone and TOK-001). Previous short MD simulations (50 ns) suggested that the binding of abiraterone to CYP17A1 is stronger than that of TOK-001. In this work, by carrying out long atomistic MD simulations (200 ns) of CYP17A1 and its complexes with abiraterone and TOK-001, we observed a binding mode between CYP17A1 and abiraterone, which is different from the binding mode between CYP17A1 and TOK-001. In the case of abiraterone binding, the unfilled volume in the active site cavity increases the freedom of movement of abiraterone within CYP17A1, leading to the collective motions of the helices G and B′ as well as the breaking of hydrogen bond existing between the 3β-OH group of abiraterone and N202 of CYP17A1. However, the unfilled volume in the active site cavity can be occupied by the benzimidazole ring of TOK-001, restraining the motion of TOK-001. By pulling the two inhibitors (abiraterone and TOK-001) out of the binding pocket in CYP17A1, we discovered that abiraterone and TOK-001 were moved from their binding sites to the surface of protein similarly through the channels formed by the helices G and B′. In addition, based on the free energy calculations, one can see that it is energetically favorable for the two inhibitors (abiraterone and TOK-001) to enter into the binding pocket in CYP17A1.

Keywords:

• Prostate cancer
• abiraterone
• cytochrome P450 17A1
• molecular dynamics simulation
• binding mode

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work is supported by the funds from Guizhou Provincial Administration of Traditional Chinese Medicine for Traditional Chinese Medicine program (No. QZYY-2018-063), the National Natural Science Foundation of China (No. 21863002), the Plan Project for Guizhou Provincial Science and Technology Department (No. QKHJC[2016]1109), the start-up fund from the Guizhou Education University and the construction project for Guizhou Provincial Key Disciplines (No. ZDXK[2015]10).