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Integrative Ligand-Based Pharmacophore Modeling, Virtual Screening, and Molecular Docking Simulation Approaches
Mohammad Habibur Rahman Molla1,2, Mohammed Othman Aljahdali1, Md Afsar Ahmed Sumon3
1Department of Biological Sciences, Faculty of Science, King Abdul-Aziz University, Jeddah 21598, Saudi Arabia.
Abstract:
Pancreatic cancer is a very deadly disease with a 5-year survival rate, making it one of the leading causes of cancer-related deaths globally. Focal adhesion kinase 1 (FAK1) is a ubiquitously expressed protein in pancreatic cancer. FAK, a tyrosine kinase that is overexpressed in cancer cells, is crucial for the development of tumors into malignant phenotypes. FAK functions in response to extracellular signals by triggering transmembrane receptor signaling, which enhances focal adhesion turnover, cell adhesion, cell migration, and gene expression. The ligand-based drug design approach was used to identify potential compounds against the target protein, which included molecular docking: ADME (absorption, distribution, metabolism, and excretion), toxicity, molecular dynamics (MD) simulation, and molecular mechanics generalized born surface area (MM-GBSA). Following the retrieval of twenty hits, four compounds were selected for further evaluation based on a molecular docking approach. Three newly discovered compounds, including PubChem CID24601203, CID1893370, and CID16355541, with binding scores of -10.4, -10.1, and -9.7 kcal/mol, respectively, may serve as lead compounds for the treatment of pancreatic cancer associated with FAK1. The ADME (absorption, distribution, metabolism, and excretion) and toxicity analyses demonstrated that the compounds were effective and nontoxic. However, further wet laboratory investigations are required to evaluate the activity of the drugs against the cancer.
Insights
Researchers identified potential new drugs targeting Focal Adhesion Kinase 1 (FAK1) to treat pancreatic cancer. Computational methods suggest three compounds show promise as effective and non-toxic treatments, pending further laboratory validation.
Area of Science:
- Oncology
- Computational Chemistry
- Drug Discovery
Background:
- Pancreatic cancer has a low survival rate, contributing significantly to global cancer deaths.
- Focal Adhesion Kinase 1 (FAK1), a tyrosine kinase, is overexpressed in pancreatic tumors and drives malignant progression.
- FAK1 plays a critical role in cell signaling, adhesion, migration, and gene expression, making it a key therapeutic target.
Purpose of the Study:
- To identify novel therapeutic compounds targeting FAK1 for pancreatic cancer treatment using a ligand-based drug design approach.
- To evaluate the efficacy and safety of potential drug candidates through computational methods.
Main Methods:
- Utilized a ligand-based drug design strategy.
- Performed molecular docking, ADME/toxicity prediction, molecular dynamics (MD) simulations, and MM-GBSA calculations.
- Screened and selected compounds based on binding affinity and drug-likeness properties.
Main Results:
- Identified three promising compounds (PubChem CID24601203, CID1893370, CID16355541) with strong binding scores (-10.4, -10.1, -9.7 kcal/mol) against FAK1.
- Computational analyses indicated these compounds possess favorable ADME properties and low toxicity.
- These compounds emerged as potential lead candidates for pancreatic cancer therapy.
Conclusions:
- The identified compounds represent potential novel therapeutic agents for pancreatic cancer targeting FAK1.
- Computational drug design successfully identified promising candidates with favorable predicted properties.
- Further experimental validation in wet laboratory settings is essential to confirm the therapeutic potential of these compounds.
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