TITLE: MORGAN FINGERPRINT–BASED SCREENING AND DOCKING IDENTIFY CALCIFEDIOL, A SECOSTEROIDAL VITAMIN D ANALOG, AS A PROMISING FARNESOID X RECEPTOR MODULATOR IN CHOLESTATIC LIVER DISEASE
AUTHOR(S): Nikita G. Tuppekar*, Vaishnavi S. Tuppekar, Kadambari V. Pawar, Sneha M. Kale, Rajani R. Pasale, Ashlesha S. Navale, Ishwari A. Nimbalkar, Tejaswini M. Biraje.
Abstract:
Cholestatic liver disease (CLD) encompasses a spectrum of hepatobiliary disorders characterized by impaired bile formation and accumulation of toxic bile acids, leading to hepatic injury, fibrosis, and progressive liver dysfunction. The Farnesoid X Receptor (FXR), a bile acid–activated nuclear receptor, serves as a crucial regulator of bile acid homeostasis, lipid metabolism, and inflammation. Pharmacological modulation of FXR has emerged as a promising therapeutic approach; however, existing agonists such as Obeticholic acid exhibit dose-limiting adverse effects.
In this study, Morgan fingerprint–based virtual screening was conducted using Obeticholic acid as the lead molecule to identify structurally similar analogs from the DrugBank database. The shortlisted candidates were subjected to molecular docking against FXR (PDB ID: 5Y1J) to evaluate their binding affinities and interaction profiles. Among 20 screened compounds, Calcifediol (25-hydroxyvitamin D₃) demonstrated the most favorable docking energy (–8.7 kcal/mol), surpassing the reference compound Obeticholic acid (–7.6 kcal/mol). Validation of the FXR model through PDB-REDO refinement confirmed enhanced stereochemical quality, with improved R-free values, Ramachandran plot normality, and bond geometry metrics.
Physicochemical and pharmacokinetic evaluation revealed that Calcifediol possesses a balanced lipophilic–hydrophilic profile, high gastrointestinal absorption, blood–brain barrier permeability, and compliance with major drug-likeness filters, indicating excellent pharmacological potential.
Overall, the computational findings highlight Calcifediol as a promising secosteroidal Vitamin D analog capable of modulating FXR activity. The results suggest a novel therapeutic avenue linking vitamin D metabolism with bile acid regulation, warranting further in vitro and in vivo validation for its potential use in cholestatic liver disease management.
Keywords:
Farnesoid X Receptor (FXR),Cholestatic Liver Disease, Calcifediol, Morgan Fingerprint Screening, Molecular Docking
Introduction:
Cholestatic liver disease (CLD) represents a diverse group of hepatobiliary disorders characterized by impaired bile formation and flow, resulting in accumulation of toxic bile acids, hepatocellular injury, and progressive fibrosis leading to cirrhosis or liver failure1. The condition can be intrahepatic, as seen in primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), or extrahepatic, involving bile duct obstruction2. Chronic cholestasis disrupts bile acid homeostasis, induces oxidative stress, and triggers inflammatory and fibrotic cascades that compromise hepatic architecture and function3.
Despite notable advances in hepatology, current therapeutic options remain limited. Ursodeoxycholic acid (UDCA) remains the first-line therapy for PBC; however, many patients exhibit incomplete biochemical or clinical response4. Obeticholic acid (OCA), a semi-synthetic bile acid derivative and potent Farnesoid X Receptor (FXR) agonist, represents a significant milestone as a second-line agent. Yet, its long-term administration is often associated with pruritus, dyslipidemia, and potential hepatotoxicity, emphasizing the need for safer and more effective FXR modulators5.
The Farnesoid X Receptor (FXR) (PDB ID: 5Y1J), a ligand-activated nuclear receptor, is predominantly expressed in the liver, intestine, and kidneys, where it plays a central role in bile acid synthesis, lipid metabolism, glucose regulation, and inflammation control 6. Activation of FXR induces expression of small heterodimer partner (SHP) and suppresses CYP7A1, the rate-limiting enzyme in bile acid synthesis, thereby maintaining bile acid homeostasis. Dysregulation of FXR signaling has been directly implicated in cholestasis, steatosis, and hepatic inflammation, making it a promising therapeutic target for restoring metabolic balance and reducing hepatocellular damage7.
In this context, computational drug repurposing represents an efficient strategy for discovering new FXR modulators from existing drug libraries, thereby reducing cost, time, and toxicity risks associated with traditional drug discovery. Modern cheminformatics techniques, such as Morgan fingerprinting, allow identification of structural analogs with potential pharmacophoric similarity to known active compounds.
In the present study, Morgan fingerprint–based virtual screening was performed using Obeticholic acid as the lead molecule against the DrugBank database, followed by molecular docking analysis of the shortlisted candidates against the FXR receptor. Among the screened compounds, Calcifediol (25-hydroxyvitamin D₃), a hydroxylated secosteroidal analog of Vitamin D, displayed the most favorable binding energy (–8.7 kcal/mol), outperforming Obeticholic acid (–7.6 kcal/mol). Owing to its known immunomodulatory, anti-inflammatory, and metabolic-regulatory effects, Calcifediol emerges as a promising repurposed candidate for FXR modulation in cholestatic liver disease.
This investigation highlights the potential of Vitamin D derivatives as novel nuclear receptor modulators, suggesting an unexplored mechanistic link between vitamin D metabolism and hepatic bile acid regulation. Such findings pave the way for future in vitro and in vivo validation to substantiate Calcifediol’s therapeutic role in managing cholestatic liver disorders.
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