Analysis of Binding Affinities for Celecoxib Analogues with COX-1 and COX-2 from Combined Docking and Monte Carlo Simulations and Insight into the COX-2/COX-1 Selectivity

2000 ◽  
Vol 122 (39) ◽  
pp. 9455-9466 ◽  
Author(s):  
Melissa L. Plount Price ◽  
William L. Jorgensen
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Binding Affinities ◽  
Cox 2 ◽  
Insight Into ◽  
Cox 1

scholarly journals Synthesis of Novel Diclofenac Hydrazones: Molecular Docking, Anti-Inflammatory, Analgesic, and Ulcerogenic Activity

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Nawaf A. Alsaif ◽  
Mashooq A. Bhat ◽  
Mohamed A. Al-Omar ◽  
Hanaa M. Al-Tuwajiri ◽  
Ahmed M. Naglah ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Analgesic Activity ◽  
Binding Affinities ◽  
Standard Drug ◽  
Reference Drug ◽  
Ulcerogenic Activity ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Sparing Effect ◽  
Cox 1

This study was aimed to design novel diclofenac hydrazones having anti-inflammatory and analgesic activity with gastric sparing effect. A new series of 2-[2-(2,6-dichloroanilino)phenyl]-N’-[(substituted phenyl) methylidene] acetohydrazide derivatives (1−14) were synthesized and evaluated for their anti-inflammatory, analgesic, and ulcerogenic activity. The compounds were identified and confirmed by elemental analysis and spectral data. During anti-inflammatory activity by carrageenan-induced paw edema method, compounds (2, 3, 7, 8, 11, and 13) were found to be most promising. Compounds 3, 8, and 13 have been found to have significant analgesic activity compared to the reference drug diclofenac in analgesic activity by both the hot plate method and acetic acid-induced writhing method. The compounds which presented highly significant anti-inflammatory and analgesic activity were further tested for their ulcerogenic activity. Compounds 3 and 8 showed maximum ulcerogenic reduction activities. Compound 8 was found to have LD50 of 168 mg/kg. Compound 8 with 3,5-dimethoxy-4-hydroxyphenyl substitution was found to be the most promising anti-inflammatory and analgesic agent with gastric sparing activity. Molecular docking of compounds was performed for COX−1/COX−2 binding site. Lead compound 8 showed better binding affinities of −9.4 kJ/mol with both COX-1 and COX-2 as compared to the standard drug, diclofenac with binding affinities of −6.6 kJ/mol and −8.1 kJ/mol for COX−1 and COX−2, respectively.

Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

1998 ◽  
Vol 41 (26) ◽  
pp. 5272-5286 ◽  
Author(s):  
Richard H. Smith, ◽  
William L. Jorgensen ◽  
Julian Tirado-Rives ◽  
Michelle L. Lamb ◽  
Paul A. J. Janssen ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Reverse Transcriptase ◽  
Monte Carlo Simulations ◽  
Linear Response ◽  
Binding Affinities ◽  
Response Method ◽  
Hiv 1

scholarly journals Chemical Profiles and Pharmacological Properties with in Silico Studies on Elatostema papillosum Wedd

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 809 ◽  
Author(s):  
Md. Zia Uddin ◽  
Arkajyoti Paul ◽  
Ahmed Rakib ◽  
Saad Ahmed Sami ◽  
Shafi Mahmud ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Serotonin Receptor ◽  
Computational Study ◽  
Biological Activities ◽  
Binding Affinities ◽  
In Silico Studies ◽  
Cox 2 ◽  
Cox 1

The current study attempted, for the first time, to qualitatively and quantitatively determine the phytochemical components of Elatostema papillosum methanol extract and their biological activities. The present study represents an effort to correlate our previously reported biological activities with a computational study, including molecular docking, and ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analyses, to identify the phytochemicals that are potentially responsible for the antioxidant, antidepressant, anxiolytic, analgesic, and anti-inflammatory activities of this plant. In the gas chromatography-mass spectroscopy analysis, a total of 24 compounds were identified, seven of which were documented as being bioactive based on their binding affinities. These seven were subjected to molecular docking studies that were correlated with the pharmacological outcomes. Additionally, the ADME/T properties of these compounds were evaluated to determine their drug-like properties and toxicity levels. The seven selected, isolated compounds displayed favorable binding affinities to potassium channels, human serotonin receptor, cyclooxygenase-1 (COX-1), COX-2, nuclear factor (NF)-κB, and human peroxiredoxin 5 receptor proteins. Phytol acetate, and terpene compounds identified in E. papillosum displayed strong predictive binding affinities towards the human serotonin receptor. Furthermore, 3-trifluoroacetoxypentadecane showed a significant binding affinity for the KcsA potassium channel. Eicosanal showed the highest predicted binding affinity towards the human peroxiredoxin 5 receptor. All of these findings support the observed in vivo antidepressant and anxiolytic effects and the in vitro antioxidant effects observed for this extract. The identified compounds from E. papillosum showed the lowest binding affinities towards COX-1, COX-2, and NF-κB receptors, which indicated the inconsequential impacts of this extract against the activities of these three proteins. Overall, E. papillosum appears to be bioactive and could represent a potential source for the development of alternative medicines; however, further analytical experiments remain necessary.

Insight into the adsorption mechanism of benzene in HY zeolites: the effect of loading

RSC Advances ◽  
2016 ◽  
Vol 6 (41) ◽  
pp. 34175-34187 ◽  
Author(s):  
Huimin Zheng ◽  
Liang Zhao ◽  
Qing Yang ◽  
Shanqing Dang ◽  
Yuxian Wang ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Inflection Point ◽  
Adsorption Mechanism ◽  
Two Stage ◽  
Hy Zeolites ◽  
Insight Into

An interesting two-stage adsorption mechanism, defined as “ideal adsorption” and “insertion adsorption”, was first proposed for the benzene/HY system by Metropolic Monte Carlo simulations at loadings below and above an “inflection point”.

scholarly journals Monte Carlo Simulations for Proteins:  Binding Affinities for Trypsin−Benzamidine Complexes via Free-Energy Perturbations

1997 ◽  
Vol 101 (46) ◽  
pp. 9663-9669 ◽  
Author(s):  
Jonathan W. Essex ◽  
Daniel L. Severance ◽  
Julian Tirado-Rives ◽  
William L. Jorgensen
Keyword(s):  
Monte Carlo ◽  
Free Energy ◽  
Monte Carlo Simulations ◽  
Binding Affinities ◽  
Free Energy Perturbations
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