Molecular modelling studies of tricyclic triazinone analogues as potential PKC-θ inhibitors through combined QSAR, molecular docking and molecular dynamics simulations techniques

2018 ◽  
Vol 91 ◽  
pp. 155-175 ◽  
Author(s):  
Lingwei Meng ◽  
Kairui Feng ◽  
Yujie Ren
MedChemComm ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 101-115 ◽  
Author(s):  
Shanshan Huang ◽  
Kairui Feng ◽  
Yujie Ren

Reliable QSAR models for quinazolinones were constructed and eight novel MMP-13 inhibitors with higher predictive activity were identified.


2015 ◽  
Vol 11 (3) ◽  
pp. 723-733 ◽  
Author(s):  
Yu-Chung Chuang ◽  
Ching-Hsun Chang ◽  
Jen-Tai Lin ◽  
Chia-Ning Yang

In this work, a CoMFA model and molecular dynamics simulations provide guidelines for drug development of SIRT2 inhibitors.


Author(s):  
Mahendera Kumar Meena ◽  
Durgesh Kumar ◽  
Kamlesh Kumari ◽  
Nagendra Kumar Kaushik ◽  
Rammapa Venkatesh Kumar ◽  
...  

2004 ◽  
Vol 382 (1) ◽  
pp. 293-305 ◽  
Author(s):  
Roman G. EFREMOV ◽  
Yuri A. KOSINSKY ◽  
Dmitry E. NOLDE ◽  
Ruslan TSIVKOVSKII ◽  
Alexander S. ARSENIEV ◽  
...  

WNDP (Wilson's disease protein) is a copper-transporting ATPase that plays an essential role in human physiology. Mutations in WNDP result in copper accumulation in tissues and cause a severe hepato-neurological disorder known as Wilson's disease. Several mutations were surmised to affect the nucleotide binding and hydrolysis by WNDP; however, how the nucleotides bind to normal and mutated WNDP remains unknown. To aid such studies, we performed the molecular modelling of the spatial structure and dynamics of the ATP-binding domain of WNDP and its interactions with ATP. The three-dimensional models of this domain in two conformations were built using the X-ray structures of the Ca2+-ATPase in the E1 and E2 states. To study the functional aspects of the models, they were subjected to long-term molecular dynamics simulations in an explicit solvent; similar calculations were performed for the ATP-binding domain of Ca2+-ATPase. In both cases, we found large-scale motions that lead to significant changes of distances between several functionally important residues. The ATP docking revealed two possible modes of ATP binding: via adenosine buried in the cleft near residues H1069, R1151 and D1164, and via phosphate moiety ‘anchored’ by H-bonds with residues in the vicinity of catalytic D1027. Furthermore, interaction of ATP with both sites occurs if they are spatially close to each other. This may be achieved after relative domain motions of the ‘closure’ type observed in molecular dynamics simulations. The results provide a framework for analysis of disease mutations and for future mutagenesis studies.


2020 ◽  
Author(s):  
Md. Chayan Ali ◽  
Yeasmin Akter Munni ◽  
Raju Das ◽  
Marium sultana ◽  
Nasrin Akter ◽  
...  

AbstractCurcuma amada or Mango ginger, a member of the Zingiberaceae family, has been revealed as a beneficiary medicinal plant having diverse pharmacological activities against a wide range of diseases. Due to having neuromodulation properties of this plant, the present study characterized the secondary metabolites of Curcuma amada for their drug-likeness properties, identified potent hits by targeting Acetylcholinesterase (AChE) and revealed neuromodulatory potentiality by network pharmacology approaches. Here in silico ADMET analysis was performed for chemical profiling, and molecular docking and molecular dynamics simulations were used to hit selection and binding characterizations. Accordingly, ADMET prediction showed that around 87.59% of compounds processed drug-likeness activity, where four compounds have been screened out by molecular docking. Guided from induced-fit docking, molecular dynamics simulations revealed phytosterol and curcumin derivatives as the most favorable AChE inhibitors with the highest binding energy, as resulted from MM-PBSA analysis. Furthermore, all of the four hits were appeared to modulate several signaling molecules and intrinsic cellular pathways in network pharmacology analysis, which are associated with neuronal growth survival, inflammation, and immune response, supporting their capacity to revert the condition of neuro-pathobiology. Together, the present in silico based characterization and system pharmacology based findings demonstrate Curcuma amada, as a great source of neuromodulating compounds, which brings about new development for complementary and alternative medicine for the prevention and treatment of neurodegenerative disorders.


Sign in / Sign up

Export Citation Format

Share Document