AutoDock

In present scenario there are different terminologies which are used for categorizing the branches of computer aided drug designing like molecular modeling, theoretical chemistry, bioinformatics, computational chemistry, chemo informatics, computational biology, etc fundamental scientific developments in this field has shaped up even before computational sciences emerged as a prominent field in engineering. Alzheimer disease is the most widespread origin of mental turn off, or dementia. But dementia too has various additional causes. The description of this disease for the first time was given by German psychiatrist as well as neuropathologist named Alois Alzheimer in year 1906 and so it was named after him.Rapid memory loss is familiar in public older than 60. The depositions of amyloid are known to be as 'plaques' and it causes the brain cells to shrivel up and form 'tangles', which will lead to changes in the brain structure and causes the brain cells to die. Treating medical circumstances which may contribute to perplexity or physical decline eg: anemia or lung disease, cheering social interface to help put off feelings of seclusion and depression, for tumbling misunderstanding normal habitual must be optimistic. Acetylcholinesterase (AChE) plays an significant function in Alzheimer's disease (AD).The extreme action of acetylcholinesterase causes a variety of neuronal troubles predominantly dementia as well as neuronal cell deaths.The tools and methodology which are used in this project are FASTA ,BLAST, Phyre2, Easy Modeller, AutoDock and ADMET. The main tools used are AutoDock for the docking of specific protein and ligands whereas ADMET is used for the toxicity check.The conclusion for this project is that ß amyloid and abnormal tau protein is responsible for this disease and acetyl cholinesterase is a key inhibitor which is used for the treatment of this disease. The drugs used in this project may compensate for the death of cholinergic neurons and offer symptomatic relief by inhibiting acetylcholine turnover as it directly interact with amyloid ß in a manner that increases the deposition of this peptide into insoluble plaques. After homology modeling we will get the final structure of our protein. The docking will be carried out with the best ligand. This drug will be helpful in the treatment of Alzheimer's disease. Anjali Tripathi | Harshita Nigam | Noopur Khare"The Discovery of Potential Acetyl Cholinesterase Inhibitors: A Combination of Virtual Screening and Molecular Docking Studies" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-2 | Issue-4 , June 2018, URL: http://www.ijtsrd.com/papers/ijtsrd14389.pdf

Purpose of the Study Breast cancer is a severe malignancy responsible for significant mortality in women globally. This has attracted a wider attention of the scientific community in order to find an effective therapeutic solution by the development of novel, potent antagonistic bioavailable ligands to be used as future anticancer drugs. Mechanistic target of rapamycin (mTOR), being a protein kinase, has been implicated in variety of activities regulating cell growth, survival, metabolism, and immunity. mTOR activation has been associated with tumor growth and metastasis as well. Since chromones and flavonoids are an important class of natural products having numerous biological properties, the aim of our study was to explore these molecules for the development of a potential bioavailable inhibitor against mTOR using computer-aided drug designing (CADD). Recent Findings Results indicated that the best designed ligand displayed maximum binding affinity (ΔG − 4.91 kcal/mol) around the binding cleft along with lower RMSD value, exhibiting safety and efficacy features as well. Further molecular docking studies based on PEM, equilibrated NVT-NPT, radius of gyration, and RMSF revealed the stability of the complex as well. Summary The substrate recruiting triad of mTOR protein was targeted, for which a library of molecules was developed and after extensive screening, a final ligand molecule (lig34) was identified as the most promising candidate having enough binding energy and fits best with biosafety parameters. Ligand (lig34) was adjudged best upon the bioavailability parameters, displaying inhibitory characteristics with lower toxicity levels.

Over expression of Protein kinase (CK2) suppresses apoptosis induced by a variety of agents, whereas down-regulation of CK2 sensitizes cells to induction of apoptosis. In this study, we have built quantitative structure activity relationship (QSAR) models, which were trained and tested on experimentally verified 38 enzyme׳s inhibitors having inhibitory value IC50 in µM. These inhibitors were docked at the active site of CK2 (PDB id: 2ZJW) using AutoDock software, which resulted in energy-based descriptors such as binding energy, intermol energy, torsional energy, internal energy and docking energy. For QSAR modeling, Multiple Linear Regression (MLR) model was engendered using energy-based descriptors yielding correlation coefficient r(2) of 0.4645. To assess the predictive performance of QSAR models, different cross-validation procedures were adopted. Our results suggests that ligand-receptor binding interactions for CK2 employing QSAR modeling seems to be a promising approach for p...