Ligand Binding Induces Agonistic-Like Conformational Adaptations in Helix 12 of Progesterone Receptor Ligand Binding Domain

Identification of Novel Progesterone Receptor (PR) Inhibitors (Homo sapiens) from Metabolites of Biotransformation Fungal: A Bioinformatics Approach

Background/Objectives: Steroids have demonstrated selective cytotoxic properties against tumor cells. The pro-gesterone receptor (PR) plays a vital role in the proliferation, cell differentiation, and maintenance of female reproductive tissue, and its malfunction can lead to breast cancer. The use of the biocatalytic method by filamentous fungi has sparked interest in the obtained of steroids due to the advantages of the process. Methods: Pharmacokinetic and toxicological properties (rat and mouse), molecular docking simulation studies, and prediction of the spectrum of biological activity were performed to select molecules with the potential for PR inhibition, from 155 biotransformed products of the progesterone. Subsequently, the chemical structures were subjected to an evaluation of their pharmacokinetic and toxicological properties and, with the application of ADMET filters. Results: Androstenedione, 17α-hydroxyprogesterone, and dihydrotestosterone, obtained by the process of biotransformation of PR by different filamentous fungi, showed good pharmacokinetic profiles and low toxicity compared to the control groups. The in-silico data associated with molecular docking studies revealed the best binding affinity and similarity in the interactions of these molecules against the human progesterone receptor target. Thus, the results of biological activity spectrum prediction highlight the great potential to investigate the role of molecular descriptors in the attribution of anti-cancer activities. Conclusions: The biocatalytic process, by filamentous fungi, can provide important molecules as a product of progesterone biotransformation, such as androstenedione, 17α-hydroxyprogesterone, and dihydrotestosterone. In this study we showed that these molecules have good pharmacokinetic profiles and low toxicity for antineoplastic activity (breast cancer).

Ancient and modern mechanisms compete in progesterone receptor activation

The progesterone receptor (PR) belongs to the steroid receptor family of ligand-regulated transcription factors, controlling genes important for development, metabolism, and reproduction. Understanding how diverse ligands bind and modulate PR activity will illuminate the design of ligands that control PR-driven signaling pathways. Here, we use molecular dynamics simulations to investigate how PR dynamics are altered by functionally diverse ligands. Using a library of 33 steroidal ligands that range from inactive to EC50 < 0.1 nM, we reveal an unexpected evolutionary basis for the wide gamut of activation. While other oxosteroid receptors employ an evolutionarily conserved mechanism dependent on a hydrogen bond between the receptor and ligand, extant PR has evolved a preference for activation that is not reliant on this polar interaction. We demonstrate that potent ligands utilize the modern PR mechanism while weaker ligands coopt the defunct ancestral mechanism by forming hydrogen bonds with Asn719. Based on their structures and dynamic signatures, ligands partition into four classes (inactive, weak, moderate and high potency) that interact distinctly with the PR binding pocket. Further, we use luciferase reporter assays and PR mutants to probe the roles of pocket residues in mediating distinct PR mechanisms. This combination of MD simulations and in vitro studies provide insight into how the evolutionary history of PR shapes its response to diverse ligands.

How nuclear receptors transition between active and inactive forms: An energetic perspective

Nuclear receptors regulate transcriptional programs in response to the binding of natural and synthetic ligands. These ligands modulate the receptor by inducing dynamic changes in the ligand binding domain that shift the C-terminal helix (H12) between active and inactive conformations. Despite decades of study, many questions persist regarding the nature of the inactive state and how ligands shift receptors between different states. Here, we use molecular dynamics (MD) simulations to investigate the timescale and energetic landscape of the conformational transition between inactive and active forms of progesterone receptor (PR) bound to a partial agonist. We observe that the microsecond timescale is insufficient to observe any transitions; only at millisecond timescales achieved via accelerated MD simulations do we find the inactive PR switches to the active state. Energetic analysis reveals that both active and inactive PR states represent energy minima separated by a barrier that can be traversed. In contrast, little or no transition is observed between active and inactive states when an agonist or antagonist is bound, confirming that ligand identity plays a key role in defining the energy landscape of nuclear receptor conformations.

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

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.

Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity

Progesterone receptor (PR) transcriptional activity is a key factor in the differentiation of the uterine endometrium. By consequence, progestin has been identified as an important treatment modality for endometrial cancer. PR transcriptional activity is controlled by extracellular-signal-regulated kinase (ERK) mediated phosphorylation, downstream of growth factor receptors such as EGFR. However, phosphorylation of PR also targets it for ubiquitination and destruction in the proteasome. Quantitative studies of these opposing roles are much needed toward validation of potential new progestin-based therapeutics. In this work, we propose a spatial stochastic model to study the effects of the opposing roles for PR phosphorylation on the levels of active transcription factor. Our numerical simulations confirm earlier in vitro experiments in endometrial cancer cell lines, identifying clustering as a mechanism that amplifies the ability of progesterone receptors to influence gene transcription. We additionally show the usefulness of a statistical method we developed to quantify and control variations in stochastic simulations in general biochemical systems, assisting modelers in defining minimal but meaningful numbers of simulations while guaranteeing outputs remain within a pre-defined confidence level.

Identification of steroidal saponins from Tribulus terrestris and their in silico docking studies

Tribulus terrestris is known to possess many pharmacological properties, most notably its anticancer activities, owing to its rich steroidal saponin contents. Even though many reports are available elucidating the anticancer potential of the herb, we, for the very first time have attempted to isolate and identified the active compound present in seed crude saponin extract and confers its in silico docking ability with various cellular targets proteins. High performance thin layer chromatography confirms the presence of active saponins in leaf and seed saponin extracts which were further fractionated by silica gel column chromatography. Fractions collected were assessed for cytotoxicity on human breast cancer cells. High resolution liquid chromatography and mass spectroscopy was employ to identify the active components present in fraction with highest cytotoxicity. Intriguingly, Nautigenin type of steriodal saponin was identified to present in the active fraction of seed extract (SF11) and the identified compound was further analyzed for its in silico docking interaction using PyRx AutodockVina. Docking studies revealed the high binding affinity of Nuatigenin at significant sites with apoptotic proteins Bcl-2, Bax, caspase-3, caspase-8, p53 and apoptosis inducing factor along with cell surface receptors estrogen receptor, projesterone receptor, epidermal growth factor receptor, and human epidermal growth factor receptor-2. Thus, the conclusions were drawn that saponin fraction of Tribulus terrestis possesses active compounds having anticancer property and specifically, Nuatigenin saponin can be considered as an important therapeutic drug for the breast cancer treatment.

Rational Drug Design of Axl Tyrosine Kinase Type I Inhibitors as Promising Candidates Against Cancer

The high level of Axl tyrosine kinase expression in various cancer cell lines makes it an attractive target for the development of anti-cancer drugs. In this study, we carried out several sets of in silico screening for the ATP-competitive Axl kinase inhibitors based on different molecular docking protocols. The best drug-like candidates were identified, after parental structure modifications, by their highest affinity to the target protein. We found that our newly designed compound R5, a derivative of the R428 patented analog, is the most promising inhibitor of the Axl kinase according to the three molecular docking algorithms applied in the study. The molecular docking results are in agreement with the molecular dynamics simulations using the MM-PBSA/GBSA implicit solvation models, which confirm the high affinity of R5 toward the protein receptor. Additionally, the selectivity test against other kinases also reveals a high affinity of R5 toward ABL1 and Tyro3 kinases, emphasizing its promising potential for the treatment of malignant tumors.