scholarly journals Dynamics of an amorphous pharmacologically active compound – diazepam: a QENS study combined with molecular dynamics simulations

RSC Advances ◽  
2017 ◽  
Vol 7 (56) ◽  
pp. 35504-35515 ◽  
Author(s):  
Aleksandra Pajzderska ◽  
Miguel A. Gonzalez ◽  
Jan P. Embs ◽  
Jadwiga Mielcarek ◽  
Jan W. Wąsicki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Compound ◽  
Methyl Groups ◽  
Theoretical Studies ◽  
Correlation Times ◽  
Dynamics Simulations ◽  
Pharmacologically Active ◽  
Experimental And Theoretical Studies

Understanding the origin of the distribution of correlation times of methyl groups reorientation by experimental and theoretical studies.

scholarly journals Proton Transport Mechanism and Pathways in the Superprotonic Phase of M3H(AO4)2 Solid Acids from Ab Initio Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Boris Merinov ◽  
Sergey Morozov
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Dynamics Simulations ◽  
Experimental And Theoretical Studies ◽  
Superprotonic Phase

The proton transport mechanism in superprotonic phases of solid acids is a subject of experimental and theoretical studies for a number of years. Despite this, details of the mechanism still...

scholarly journals Interface Characteristics of Neat Melts and Binary Mixtures of Polyethylenes from Atomistic Molecular Dynamics Simulations

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1059
Author(s):  
Sanghun Lee ◽  
Curtis W. Frank ◽  
Do Y. Yoon
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulations ◽  
Binary Mixtures ◽  
Surface Segregation ◽  
Surface Region ◽  
Polymer Chains ◽  
Methyl Groups ◽  
Free Standing ◽  
Dynamics Simulations

Molecular dynamics simulations of free-standing thin films of neat melts of polyethylene (PE) chains up to C150H302 and their binary mixtures with n-C13H28 are performed employing a united atom model. We estimate the surface tension values of PE melts from the atomic virial tensor over a range of temperatures, which are in good agreement with experimental results. Compared with short n-alkane systems, there is an enhanced surface segregation of methyl chain ends in longer PE chains. Moreover, the methyl groups become more segregated in the surface region with decreasing temperature, leading to the conclusion that the surface-segregation of methyl chain ends mainly arises from the enthalpic origin attributed to the lower cohesive energy density of terminal methyl groups. In the mixtures of two different chain lengths, the shorter chains are more likely to be found in the surface region, and this molecular segregation in moderately asymmetric mixtures in the chain length (C13H28 + C44H90) is dominated by the enthalpic effect of methyl chain ends. Such molecular segregation is further enhanced and dominated by the entropic effect of conformational constraints in the surface for the highly asymmetric mixtures containing long polymer chains (C13H28 + C150H3020). The estimated surface tension values of the mixtures are consistent with the observed molecular segregation characteristics. Despite this molecular segregation, the normalized density of methyl chain ends of the longer chain is more strongly enhanced, as compared with the all-segment density of the longer chain itself, in the surface region of melt mixtures. In addition, the molecular segregation results in higher order parameter of the shorter-chain segments at the surface and deeper persistence of surface-induced segmental order into the film for the longer chains, as compared with those in neat melt films.

Theoretical studies on FGFR isoform selectivity of FGFR1/FGFR4 inhibitors by molecular dynamics simulations and free energy calculations

2017 ◽  
Vol 19 (5) ◽  
pp. 3649-3659 ◽  
Author(s):  
Weitao Fu ◽  
Lingfeng Chen ◽  
Zhe Wang ◽  
Yanting Kang ◽  
Chao Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Free Energy Calculations ◽  
Theoretical Studies ◽  
Energy Calculations ◽  
Isoform Selectivity ◽  
Dynamics Simulations

Revealing the FGFR isoform selectivity of FGFR1/FGFR4 inhibitorsviamolecular dynamics simulations.

Evaluating Phenyl Propanoids Isolated from Citrus medica as Potential Inhibitors for Mitotic kinesin Eg5

2020 ◽  
Vol 17 (11) ◽  
pp. 1355-1363
Author(s):  
Himesh Makala ◽  
Venkatasubramanian Ulaganathan ◽  
Aravind Sivasubramanian ◽  
Narendran Rajendran ◽  
Shankar Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulations ◽  
Strong Basis ◽  
Citrus Medica ◽  
Kinesin Eg5 ◽  
Dynamics Simulations ◽  
Pharmacologically Active ◽  
Mitotic Kinesin Eg5

Background: Human mitotic kinesins play an essential role in mitotic cell division. Targeting the spindle separation phase of mitosis has gained much attention in cancer chemotherapy. Spindle segregation is carried out mainly by the kinesin, Eg5. Many Eg5 inhibitors are in different phases of clinical trials as cancer drugs. This enzyme has two allosteric binding sites to which the inhibitors can bind. The first site is formed by loop L5, helix α2 and helix α3 and all the current drug candidates bind un-competitively to this site with ATP/ADP. The second site, formed by helix α4 and helix α6, which has gained attention recently, has not been explored well. Some inhibitors that bind to this site are competitive, while others are uncompetitive to ATP/ADP. Phenylpropanoids are pharmacologically active secondary metabolites. Methods: In this study, we have evaluated fourteen phenyl propanoids extracted from Citrus medica for inhibitory activity against human mitotic kinesin Eg5 in vitro steady-state ATPase assay. Ther interactions and stability using molecular docking and molecular dynamics simulations. Results and Discussions: Of the fourteen compounds tested, naringin and quercetin showed good activity with IC50 values in the micromolar range. Molecular docking studies of these complexes showed that both the molecules interact with the key residues of the active site predominantly thorough hydrophobic & aromatic π–π interactions consistent with the known inhibitors. Besides, these molecules also form hydrogen bonding interactions stabilizing the complexes. Molecular dynamics simulations of these complexes confirm the stability of these interactions. Conclusion: These results can be used as a strong basis for further modification of these compounds to design new inhibitors with higher potency using structure-based drug design.

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