Journal Article

Exploring the most promising anti ‐ Depressant drug targeting Microtubule Affinity Receptor Kinase 4 involved in Alzheimer’s Disease through molecular docking and molecular dynamics simulation

Ahmad, S. Rehan, Khan, Mohammad Suhail, Dawria, Adam, Mohieldin, Ali, Ahmed, Faheem, Ali, Haroon, AlShahrani, Abdullah M., Muzammil, Khursheed, Altijani, Abdelrhman A. G., Zeyaullah, Md

2024

Overview

Alzheimer’s Disease (AD) is the prevailing type of neurodegenerative illness, characterised by the accumulation of amyloid beta plaques. The symptoms associated with AD are memory loss, emotional variability, and a decline in cognitive functioning. To date, the pharmaceuticals currently accessible in the marketplace are limited to symptom management. According to several research, antidepressants have demonstrated potential efficacy in the management of AD. In this particular investigation, a total of 24 anti-depressant medications were selected as ligands, while the Microtubule Affinity Receptor Kinase 4 (MARK4) protein was chosen as the focal point of our study. The selection of MARK4 was based on its known involvement in the advancement of AD and other types of malignancies, rendering it a highly prospective target for therapeutic interventions. The initial step involved doing ADMET analysis, which was subsequently followed by molecular docking of 24 drugs. This was succeeded by molecular dynamics simulation and molecular mechanics generalised Born surface area (MMGBSA) calculations. Upon conducting molecular docking experiments, it has been determined that the binding affinities observed fall within the range of -5.5 kcal/mol to -9.0 kcal/mol. In this study, we selected six anti-depressant compounds (CID ID ‐ 4184, 2771, 4205, 5533, 4543, and 2160) based on their binding affinities, which were determined to be -9.0, -8.7, -8.4, -8.3, -8.2, and -8.2, respectively. Molecular dynamics simulations were conducted for all six drugs, with donepezil serving as the control drug. Various analyses were performed, including basic analysis and post-trajectory analysis such as free energy landscape (FEL), polarizable continuum model (PCM), and MMGBSA calculations. Based on the findings from molecular dynamics simulations and the MMGBSA analysis, it can be inferred that citalopram and mirtazapine exhibit considerable potential as anti-depressant agents. Consequently, these compounds warrant further investigation through in vitro and in vivo investigations in the context of treating AD.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Advertising executives / Affinity / Alzheimer Disease - drug therapy / Alzheimer Disease - metabolism / Alzheimer's disease / Analysis / Antidepressants / Antidepressive Agents - chemistry / Antidepressive Agents - pharmacology / Binding / Biology and Life Sciences / Citalopram / Cognitive ability / Continuum modeling / Diseases / Donepezil / Drugs / Free energy / Humans / In vivo methods and tests / Kinases / Ligands / Malignancy / Medicine and Health Sciences / Mental depression / Molecular docking / Molecular Docking Simulation / Molecular dynamics / Molecular Dynamics Simulation / Neurodegeneration / Neurodegenerative diseases / Pharmacokinetics / Physical Sciences / Physiology / Protein Binding / Protein Serine-Threonine Kinases - antagonists & inhibitors / Protein Serine-Threonine Kinases - chemistry / Protein Serine-Threonine Kinases - metabolism / Proteins / Receptors / Research and Analysis Methods / Senile plaques / Serotonin / Signs and symptoms / Simulation / Simulation methods / Symptom management / Therapeutic applications / Trajectory analysis / Trajectory control