QSAR, Molecular Docking, MD Simulation and MMGBSA Calculations Approaches to Recognize Concealed Pharmacophoric Features Requisite for the Optimization of ALK Tyrosine Kinase Inhibitors as Anticancer Leads

• Published in: Molecules (Basel, Switzerland) Switzerland), 2022-08, Vol.27 (15), p.4951
• Main Authors: Jawarkar, Rahul D, Sharma, Praveen, Jain, Neetesh, Gandhi, Ajaykumar, Mukerjee, Nobendu, Al-Mutairi, Aamal A, Zaki, Magdi E A, Al-Hussain, Sami A, Samad, Abdul, Masand, Vijay H, Ghosh, Arabinda, Bakal, Ravindra L
• Format: Article
• Language: English
• Subjects: ALK tyrosine kinase inhibitors; Anaplastic Lymphoma Kinase; anticancer; Antitumor activity; Biological activity; Chemical bonds; Chemists; Datasets; Drug development; Drug resistance; Enzyme inhibitors; Fluorine; Gene amplification; Genetic algorithms; Kinases; Lipophilic; Lung cancer; Lymphoma; Mathematical models; MD simulation; MMGBSA; Molecular docking; Molecular Docking Simulation; Molecular Dynamics Simulation; Nitrogen; Optimization; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Protein-tyrosine kinase; Proteins; QSAR; Quantitative Structure-Activity Relationship; Signal transduction; Simulation; Solvents; Statistical analysis; Structure-activity relationships; Tyrosine
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules27154951

ALK tyrosine kinase ALK TK is an important target in the development of anticancer drugs. In the present work, we have performed a QSAR analysis on a dataset of 224 molecules in order to quickly predict anticancer activity on query compounds. Double cross validation assigns an upward plunge to the genetic algorithm−multi linear regression (GA-MLR) based on robust univariate and multivariate QSAR models with high statistical performance reflected in various parameters like, fitting parameters; R2 = 0.69−0.87, F = 403.46−292.11, etc., internal validation parameters; Q2LOO = 0.69−0.86, Q2LMO = 0.69−0.86, CCCcv = 0.82−0.93, etc., or external validation parameters Q2F1 = 0.64−0.82, Q2F2 = 0.63−0.82, Q2F3 = 0.65−0.81, R2ext = 0.65−0.83 including RMSEtr < RMSEcv. The present QSAR evaluation successfully identified certain distinct structural features responsible for ALK TK inhibitory potency, such as planar Nitrogen within four bonds from the Nitrogen atom, Fluorine atom within five bonds beside the non-ring Oxygen atom, lipophilic atoms within two bonds from the ring Carbon atoms. Molecular docking, MD simulation, and MMGBSA computation results are in consensus with and complementary to the QSAR evaluations. As a result, the current study assists medicinal chemists in prioritizing compounds for experimental detection of anticancer activity, as well as their optimization towards more potent ALK tyrosine kinase inhibitor.