scholarly journals The in Silico Study of Nutmeg Seeds (Myristica fragrans Houtt) as Peroxisome Proliferator Activated Receptor Gamma Activator Using 3D-QSAR Pharmacophore Modelling

2016 ◽  
pp. 048-053
Author(s):  
M. Muchtaridi ◽  
Karen Low ◽  
Keri Lestari
Keyword(s):  
In Silico ◽  
3D Qsar ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Pharmacophore Modelling ◽  
Myristica Fragrans ◽  
In Silico Study ◽  
Myristica Fragrans Houtt

scholarly journals In Silico Ligand-Based Methods Targeting Porcupine Receptor Inhibitors with Potential Anticancer Effect

Proceedings ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
Ana Borota ◽  
Luminita Crisan
Keyword(s):  
Wnt Signaling ◽  
In Silico ◽  
Pharmacophore Model ◽  
Correlation Coefficients ◽  
3D Qsar ◽  
Qsar Model ◽  
Hydrogen Bond Donor ◽  
Screening Process ◽  
Wnt Proteins ◽  
In Silico Study

Porcupine is a protein belonging to the O-acyltransferase family, involved in the catalyzing of palmitoylation of wingless-related integration (WNT) proteins. WNT signaling has significant roles in many physiological functions, e.g., hematopoiesis, homeostasis, neurogenesis, and apoptosis. Anomalous WNT signaling has been observed to be related to tumor generation, and metabolic and neurodegenerative disorders. Therefore, compounds that inhibit this pathway are of great interest for the development of therapeutic approaches. For a better understanding of the common traits of such compounds, we have undertaken an in silico study in order to develop a valid ligand-based pharmacophore model based on a series of porcupine inhibitors. The best pharmacophore hypothesis found after the 3D QSAR validation process is represented by the following features: one hydrogen bond donor (D), three rings (R) and one hydrophobic centroid (H). The 3D-QSAR model obtained using the DRRRH hypothesis shows statistically significant parameters: correlation coefficients for the training set: R2 of 0.90, and a predictive correlation coefficient for the test set, Q2 of 0.86. The assessment of the pharmacophore model was also done and provided very reliable metrics values (Receiver Operating Characteristic—ROC of 1; Robust Initial Enhancement—RIE of 17.97). Thereby, we obtained valuable results which can be further used in the virtual screening process for the discovery of new active compounds with potential anticancer activity.

In silico study on indole derivatives as anti HIV-1 agents: a combined docking, molecular dynamics and 3D-QSAR study

2013 ◽  
Vol 37 (8) ◽  
pp. 1001-1015 ◽  
Author(s):  
Anand Balupuri ◽  
Changdev G. Gadhe ◽  
Pavithra K. Balasubramanian ◽  
Gugan Kothandan ◽  
Seung Joo Cho
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
3D Qsar ◽  
Indole Derivatives ◽  
Qsar Study ◽  
In Silico Study ◽  
Anti Hiv ◽  
Hiv 1

scholarly journals 3D-PHARMACOPHORE MODELLING OF OMEGA-3 DERIVATIVES WITH PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA AS AN ANTI-OBESITY AGENT

2021 ◽  
pp. 167-170
Author(s):  
IDA MUSFIROH ◽  
GINNA MEGAWATI ◽  
DEWI MARHENI DIAH HERAWATI ◽  
AGUS RUSDIN
Keyword(s):  
Functional Groups ◽  
Complex Structure ◽  
Pharmacophore Model ◽  
Docosapentaenoic Acid ◽  
Peroxisome Proliferator ◽  
Omega 3 ◽  
Peroxisome Proliferator Activated Receptor ◽  
Pharmacophore Modelling ◽  
Ppar Γ ◽  
3D Pharmacophore

Objective: The aim of this work was to study the pharmacophore model of omega-3 derivatives with the PPAR-γ receptor using LigandScout 4.4.3 to investigate the important chemical interactions of complex structure. Methods: The methods consisted of structure preparation of nine chemical compounds derived from omega-3 fatty acids, database preparation, creating 3D Pharmacophore modelling, validation pharmacophore, and screening test compounds. Results: The result of the research showed that the omega-3 derivatives docosahexaenoic acid (DHA), when eicosapentaenoic acid (HPA), and docosapentaenoic acid (DPA) have the best pharmacophore fit values of 36.59; 36.56; and 36.56, respectively. According to the results of the pharmacophore study, the carbonyl and hydroxyl of the carboxylate functional groups become the active functional groups that exhibit hydrogen bonding interactions. While the alkyl chain (Ethyl and methyl groups) was the portion that can be modified to increase its activity. Conclusion: Omega-3 derivatives could be used as a lead drug for the powerful PPAR-γ receptor in the prevention and treatment of obesity.

The Design and Evaluation of a Novel Monoamine Oxidase B Inhibitor Through in Silico Approach

2019 ◽  
Vol 10 (02) ◽  
Author(s):  
Hasanain Abdulhameed Odhar ◽  
Safaa Muhsen Kareem ◽  
Mohammed Ridha A Alhaideri ◽  
Mohammed Abbas Hasan ◽  
Werner J Geldenhuys
Keyword(s):  
Monoamine Oxidase ◽  
In Silico ◽  
Neuroprotective Effect ◽  
Monoamine Oxidase B ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Mao B ◽  
Age Related ◽  
Novel Scaffold

Parkinson’s disease is an age related neurodegenerative disease. Pioglitazone is a Peroxisome proliferator-activated receptor gamma agonist that has been shown to display a neuroprotective effect in parkinsonian models (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine treated mice). This effect was partially attributed to the ability of thiazolidinedione (TZD) moiety in Pioglitazone to selectively inhibit monoamine oxidase B (MAO-B) enzyme. In the current study, we screened several thiazolidine containing compounds against MAO-B enzyme both in silico and in vitro. Based on the resulted data and information from previous literatures, we were able to design a novel scaffold for MAO-B inhibitors. This scaffold (compound 5482440) was able to inhibit MAO-B enzyme with IC50 value of 1.447 μM. Structure-based virtual analysis showed that this compound was able to participate in water-bridge formation and obtain an extended conformation within MAO-B active site.

STUDI IN SILICO DAN HUBUNGAN KUANTITATIF STRUKTUR TERHADAP AKTIVITAS TANAMAN MANGROVE (Avicennia marina (Forssk.) Vierh.) SEBAGAI ANTIDIABETES

2020 ◽  
Vol 2 (1) ◽  
pp. 112
Author(s):  
Arinil Hidayati ◽  
Siswandono Siswandono ◽  
Pramudita Riwanti
Keyword(s):  
Regression Analysis ◽  
In Silico ◽  
Avicennia Marina ◽  
Three Dimensions ◽  
Peroxisome Proliferator ◽  
Nonlinear Relationship ◽  
Peroxisome Proliferator Activated Receptor ◽  
Molegro Virtual Docker ◽  
Relationship Of

The research is applied to 20 compounds contained  into <em>Avicennia marina</em> which is : <em>4’,5-dihydroxy-3’,5’,7-trimethoxyflavone, isorhamnetin 3-O-rutinoside, quercetin, stenocarproquinone B, avicennone C, avicennone E, avicennone F, avicennone D,   4’,5-dihydroxy-3’,7-dimethoxyflavone, chrysoeriol 7-O-glucoside, naphta(1,2-b)furan-4,5-dione, 3-hydroxy-naphta(1,2-b)furan-4,5-dione, kaempferol, 5-hydroxy-4’,7-dimethoxyflavone, avicequinone C, 2-[2’-(2’-hydroxy)propyl]-naphta[1,2-b]furan-4,5-dione, 4’,5,7-trihydroxyflavone, luteolin 7-O-methylether, luteolin 7-O-methylether 3’-O-beta-D-glucoside, 5,7-dihydroxy-3’,4’,5’-trimethoxyflavone</em> which are expected  to have an  effect as antidiabetics agent. It is undertaken to find out the linier or nonlinier relationship of  the structure activty (QSAR), the physicochemical characters (lipophilic, electronic, dan steric) to the activity changing (<em>rerank score</em>). Moreover, it is also undertaken to find out which one of those 20 <em>Avicennia marina </em>compounds are predicted to possess the activity as the best antidiabetics agent by the comparison of pioglitazon. It is arranged through computerized methods or <em>in silico</em> not only for having  the structure of two and three dimensions but also knowing the physicochemical characters too; through some programs such as  <em>ChemBioDraw Ultra </em>12.0 and <em>ChemBio3D Ultra </em>12.0 from <em>CambridgeSoft. The docking </em>program is used to make prediction of  the activity  by using <em>Molegro Virtual  Docker </em>2011.5.0.0 from CLCBio<em>.</em> by using the <em>peroxisome proliferator-activated receptor-gamma </em>(PPAR𝛾) in code of PDB: 2XKW. The result of the regression analysis through IBM SPSS program shows nonlinear relationship among structures, <em>Avicennia marina</em> physicochemical characters of twenty compound contents dealing with the activity changing. The compound of  <em>isorhamnetin 3-O-rutinoside</em><em>, chrysoeriol 7-O-glucoside, </em>and <em>luteolin 7-O-methylether 3’-O-beta-D-glucoside </em>are predicted to have the best antidiabetics agent if it is compared with the comparing drug pioglitazon.

3D QSAR studies on peroxisome proliferator-activated receptor ? agonists using CoMFA and CoMSIA

2004 ◽  
Vol 10 (3) ◽  
pp. 165-177 ◽  
Author(s):  
Chenzhong Liao ◽  
Jiaju Zhou ◽  
Leming Shi ◽  
Zhibin Li ◽  
Xian-Ping Lu ◽  
...  
Keyword(s):  
3D Qsar ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Qsar Studies ◽  
Receptor Agonists
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