Structural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators

Abstract

Uterine fibroids (UF) are benign smooth muscle neoplasm of uterus that have a significant impact on a woman’s quality of life as they perturb hormonal homeostasis resulting in heavy menstrual bleeding, impaired fertility, pregnancy complications and loss. UF can be surgically removed through invasive procedures, but their recurrence rate is often high. Progesterone receptor (PR) has an imperative role in UF management. Mifepristone, ulipristal acetate (UPA) and asoprisnil (ASO) are some selective progesterone receptor modulators (SPRMs), acts on PR, but due to their side effects in long term use, they were withdrawn from the market. Hence, there is a dire need for novel, highly efficient with least side effects, therapeutics for the treatment of UF. To contribute toward the drug discovery for UF, we made an extensive structural comparison of reported PR crystal structures, also elucidated the binding modes of four existing SPRMs against human PR through ensemble docking approach. Our studies revealed the presence of 5 highly repeating water molecules that has an important role in ligand binding and structural stability. Our ensemble docking and MD simulation revealed that studied ligands have preferential selectivity toward the specific conformation of PR. It is anticipated that our study will be a useful resource to all the drug discovery scientists who are engaged in the identification of lead molecules against UF.

Communicated by Ramaswamy H. Sarma

Keywords:

• Uterine fibroids
• progesterone receptor
• SPRM
• antagonists
• ensemble docking
• molecular dynamics

Acknowledgement

The authors are thankful for the computational facilities at Laboratory for Structural Biology, RIKEN, Japan.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

The financial assistance from Department of Health Research, Govt. of India (Project number R.12015/01/2021-HR/E-Office:8116780) is gratefully acknowledged.