• Genomics & Informatics
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• v.21 no.1
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• pp.9.1-9.13
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• 2023

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer's disease, autoimmune diseases, cardiovascular diseases, and dental caries. Therefore, MMP-9 inhibition is recommended as a therapeutic strategy for combating various diseases. Cinnamic acid derivatives have shown therapeutic effects in different cancers, Alzheimer's disease, cardiovascular diseases, and dental caries. A computational drug discovery approach was performed to evaluate the binding affinity of selected cinnamic acid derivatives to the MMP-9 active site. The stability of docked poses for top-ranked compounds was also examined. Twelve herbal cinnamic acid derivatives were tested for possible MMP-9 inhibition using the AutoDock 4.0 tool. The stability of the docked poses for the most potent MMP-9 inhibitors was assessed by molecular dynamics (MD) in 10 nanosecond simulations. Interactions between the best MMP-9 inhibitors in this study and residues incorporated in the MMP-9 active site were studied before and after MD simulations. Cynarin, chlorogenic acid, and rosmarinic acid revealed a considerable binding affinity to the MMP-9 catalytic domain (ΔG_binding < -10 kcal/ mol). The inhibition constant value for cynarin and chlorogenic acid were calculated at the picomolar scale and assigned as the most potent MMP-9 inhibitor from the cinnamic acid derivatives. The root-mean-square deviations for cynarin and chlorogenic acid were below 2 Å in the 10 ns simulation. Cynarin, chlorogenic acid, and rosmarinic acid might be considered drug candidates for MMP-9 inhibition.

• Current Optics and Photonics
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• v.1 no.4
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• pp.278-283
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• 2017

We theoretically study the dynamics of water tetramer in intense femtosecond laser pulses with different frequencies. The simulations are carried out by incorporating the molecular dynamics method non-adiabatically into the time-dependent local-density approximation (TDLDA-MD). Three typical scenarios of water tetramer including the normal vibration with enlarged OH bonds, free OH bonds breaking and the pure Coulomb explosion are presented by investigating the electronic and ionic dynamics. The result indicates that the ionization is enhanced and the corresponding fragmentation effect as well as the damping of the dipole moment are found more notably when increasing the laser frequency especially when the frequency falls in the resonant region of the absorption spectra. The study of the level depletion reveals that the ratio of the emission amount from different levels can be controlled by changing the laser frequency referring to the Keldysh parameter.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2008.06a
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• pp.379-380
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• 2008

Molecular Dynamics (MD) simulations have been used to model the dynamics of the charge-compensating sodium ions in the non-stoichiometric hollandite Nax$(Ti_{8-x}Cr_x)O_{16}$. These interstitial ions reside in 'tunnels' in the crystal structure and move under the forces of both the ions making up the cage structure and the many body interactions of the other sodium ions in the tunnel. The Velocity Autocorrelation Function (VAF) of the sodium ions is calculated for a range of temperature from 250K to 1000K and converted into the linear ac-conductivity and ac-susceptibility response via Fourier transformation. A peak is found in the conductivity around $6\times10^{12}$ Hz that has some of the character of a Poley absorption. Here it is shown to be due to an harmonically coupled site vibrations of the sodium atoms, which extend only over a limited range. At frequencies below the peak the conductivity tends towards a constant i.e. dc value corresponding to a constant flow of ions through the simulation cell. At high temperatures the conductivity due to this ion transport process behaves like a metal with an insulator to metal transition occurring around a specific temperature.

• BMB Reports
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• v.49 no.8
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• pp.431-436
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• 2016

Human papillomavirus (HPV) is the major cause of cervical cancer, a deadly threat to millions of females. The early oncogene product (E7) of the high-risk HPV16 is the primary agent associated with HPV-related cervical cancers. In order to understand how E7 contributes to the transforming activity, we investigated the structural features of the flexible N-terminal region (46 residues) of E7 by carrying out N-15 heteronuclear NMR experiments and replica exchange molecular dynamics simulations. Several NMR parameters as well as simulation ensemble structures indicate that this intrinsically disordered region of E7 contains two transient (10-20% populated) helical pre-structured motifs that overlap with important target binding moieties such as an E2F-mimic motif and a pRb-binding LXCXE segment. Presence of such target-binding motifs in HPV16 E7 provides a reasonable explanation for its promiscuous target-binding behavior associated with its transforming activity.

• Advances in nano research
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• v.11 no.6
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• pp.607-620
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• 2021

In this paper, the vibrations of boron nitride nanotubes (BNNTs) are investigated by considering the electric field. To consider the size effect at nanoscale dimensions, the surface elasticity theory is exploited. The equations of motion of the BNNTs are obtained by applying Hamilton's principle, and the clamped-guided boundary conditions are also considered. The governing equations and boundary conditions are discretized using the differential quadrature method (DQM), and the natural frequency is obtained by using the eigenvalue problem solution. The results are compared with the molecular dynamic simulation in order to validate the accurate values of the surface effects. In the molecular dynamics (MD) simulation, the potential between boron and nitride atoms is considered as the Tersoff type. The Timoshenko beam model is adopted to model BNNT. The vibrations of two types of zigzag and armchair BNNTs are considered. In the result section, the effects of chirality, surface elasticity modulus, surface residual tension, surface density, electric field, length, and thickness of BNNT on natural frequency are investigated. According to the results, it should be noted that, as an efficient non-classical continuum mechanic approach, the surface elasticity theory can be used in scrutinizing the dynamic behavior of BNNTs.

• Genomics & Informatics
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• v.20 no.3
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Journal of the Korean Ceramic Society
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• v.34 no.7
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• pp.713-721
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• 1997

Molecular dynamic (MD) simulations with new interatomic potential function including the covalent bond were performed on the phase transition of $\alpha$-quartz-type GeO2 under high pressure. The optimized crystal structure and the pressure dependence of the lattice constant showed higher reproducibility than the previous models and were in very good agreement with the experimental data. A phase transition of $\alpha$-quartz and $\alpha$-quartz-type GeO2 by simulation was found approximately 24 GPa and 6-7 GPa, respectively. This phase transition involved an abrupt volume shrinkage and showed 4-6 coordination mixed structure with the increasing in the coordination number of cation.

• Journal of Integrative Natural Science
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• v.6 no.1
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• pp.8-11
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• 2013

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.

• Bulletin of the Korean Chemical Society
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• v.20 no.8
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• pp.948-952
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• 1999

Electrophilic substitutions on β-position of 2,5-dimethyl pyrrole have been investigated theoretically. The electron donating methyl groups enrich electron densities on C-3, C-4 positions and π* interactions with methyl groups substituted on C-2 and C-5 positions pushed up the HOMO level of the pyrroles consequently induce rapid substitutions on C-3, C-4 sites. Substitution of phenylsulfonyl group on nitrogen stabilized LUMO levels through weak π bonding interactions. Unexpected deoxidation reaction underwent on the sulfonyl group substituted at C-3 position. The structures were solved by X-ray crystallography. Meanwhile, gas phase HF/6-31G* and density functional method (B3LYP/6-31G*) calculations gave favorable energies for 1-phenylsulfinyl pyrrole (6) over 3-phenylsulfinyl pyrrole (5) by 3.6-4.7 kcal/mol which is contrary to the experimental result. However the methods involve the effects of molecular polarizability and solvent, molecular dynamics (MD) and ab-initio self consistent reaction field (SCRF) calculations showed same trend as experiments. According to MD calculations, compound 5 is more stable than compound 6 by 4.15 kcal/mol and the SCRF, HF/6-31G* calculations gave more stable energy value for structure 5 than 6 by 0.03 kcal/mol.

• Membrane Journal
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• v.27 no.4
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• pp.358-366
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• 2017

The most important factor in the performances of polymer electrolyte membranes for fuel cells is how fast hydrogen ions can be transported along the water channel formed inside the electrolyte membrane. Since the morphology of the water channel and the diffusivity of the protons are very important factors for the proton transport behavior, various molecular dynamics simulation studies are being carried out to clarify this. The force-field is an important variable parameterizing the movement and interaction of each atom in molecular dynamics simulation. In this study, proton diffusivities of the 3D models of polymer electrolyte membranes were calculated in order to analyze the effects of various types of force-fields on the molecular simulation. It has been found that the charge value determining the non-bonding interaction plays a very important role in the formation of the water channel morphology, and the COMPASS force-field can calculate the accurate proton diffusion behavior. Accordingly, for molecular dynamics simulation of polymer electrolyte membranes, the proper selection of the force-field is very important due to its great effect on the proton diffusion as well as the final molecular structure.