Pharmacophore-Based Virtual Screening and In Silico Investigations of Small Molecule Library for Discovery of Human Hepatic Ketohexokinase Inhibitors for the Treatment of Fructose Metabolic Disorders

Tilal Elsaman ^1* Magdi Awadalla Mohamed ^1* Abozer Y. Elderdery ² Abdullah Alsrhani ² Badr Alzahrani ² Heba Bassiony Ghanem ² Jeremy Mills ³ Musaed Rayzah ⁴ Nasser A. N. Alzerwi ⁴ Afnan Al-Sultan ⁵ Bandar Idrees ⁶ Fares Rayzah ⁷

• ¹ Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
• ² Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
• ³ School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
• ⁴ Department of Surgery, College of Medicine, Majmaah University, Al Majma'ah, Riyadh, Saudi Arabia
• ⁵ Department of surgery, King Saud Medical City,, Riyadh, Saudi Arabia
• ⁶ Department of Surgery, Prince Sultan Military Medical City, As Sulimaniyah, Saudi Arabia
• ⁷ Aseer Central Hospital, Abha, Saudi Arabia

Introduction:Excessive fructose consumption is a significant driver of metabolic disorders, including obesity, diabetes, non-alcoholic fatty liver disease (NAFLD), and non-alcoholic steatohepatitis (NASH), primarily by promoting insulin resistance and fat accumulation. Ketohexokinase C (KHK-C), a pivotal enzyme in fructose metabolism, catalyzes the phosphorylation of fructose to fructose-1-phosphate, initiating a cascade of downstream metabolic processes. In contrast to glucose metabolism, KHK-C lacks negative feedback regulation, allowing the continuous phosphorylation of fructose, which leads to heightened levels of glucose, glycogen, and triglycerides in the bloodstream and liver. While targeting KHK-C offers a promising therapeutic avenue, no drugs have yet been approved for clinical use. Pfizer’s PF-06835919 has progressed to phase II trials, demonstrating a reduction in liver fat and improved insulin sensitivity, while Eli Lilly’s LY-3522348 also shows significant potential. Nonetheless, there remains a critical need for the development of novel KHK-C inhibitors that offer improved pharmacokinetics, enhanced efficacy, and superior safety profiles.Methods: In the present study, a comprehensive computational strategy was employed to screen 460,000 compounds from the NCI library for potential KHK-C inhibitors. Initially, pharmacophore-based virtual screening was used to identify potential hits, followed by multi-level molecular docking, binding free energy estimation, pharmacokinetic analysis, and molecular dynamics (MD) simulations to further evaluate the compounds. This multi-step approach aimed to identify compounds with strong binding affinity, favorable pharmacokinetic profiles, and high potential for efficacy as KHK-C inhibitors.Results: Ten compounds exhibited docking scores ranging from ‒7.79 to ‒9.10 kcal/mol, surpassing those of the compounds currently undergoing clinical trials, PF-06835919 (‒7.768 kcal/mol) and LY-3522348 (‒6.54 kcal/mol). Their calculated binding free energies ranged from ‒57.06 to ‒70.69 kcal/mol, further demonstrating their superiority over PF-06835919 (‒56.71 kcal/mol) and LY-3522348 (‒45.15 kcal/mol). ADMET profiling refined the selection to five compounds (1, 2, and 4-6), and MD simulations identified compound 2 as the most stable and promising candidate compared to the clinical candidate PF-06835919. Conclusions: These findings highlight compound 2 as a potent KHK-C inhibitor with predicted pharmacokinetics and toxicity profiles supporting its potential for treating fructose-driven metabolic disorders, warranting further validation.