In silico design of fragment-based drug targeting host processing α-glucosidase i for dengue fever

Toepak, Erwin Prasetya; Tambunan, Usman Sumo Friend

doi:10.1088/1757-899x/172/1/012017

Cited by 14 publications

(5 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This research was performed using the in silico drug design research pipeline by employing Molecular Operating Environment (MOE) 2014.09, DataWarrior 4.2.2, SwissADME, and pkCSM software [7]. The three dimensional (3D) structure of HER2 tyrosine kinase protein was obtained from Research Collaborators for Structural Bioinformatics Protein Data Bank (RCSB-PDB).…”

Section: Methodsmentioning

confidence: 99%

Utilization of Flavonoid Compounds as HER2 Tyrosine Kinase Inhibitor in Breast Cancer Using Fragment-Based Drug Design

Fleming

Saragih

Tambunan

2020

KEM

View full text Add to dashboard Cite

Breast cancer has become one of the leading cause of women’s death around the world. Breast cancer can be caused by genetic or environmental factors. Human epidermal growth factor receptor 2 (HER2) is one of the main causes of breast cancer. The HER2 tyrosine kinase plays a significant role in the dimerization reaction which causes auto-phosphorylation of tyrosine residues in the cytoplasmic domain that triggers growth of the cancer cells. Inhibition of HER2 protein activity can be a potential alternative for breast cancer treatment. Flavonoids have become an important scaffold in medicinal chemistry due to its bioactivity and availability. Therefore, flavonoids were used as the database on this in silico research. Fragment-based drug design was applied to determine novel drug candidates. Three potential candidates were obtained in this research. VC-962 was selected as the best inhibitor candidates for HER2 tyrosine kinase.

show abstract

Section: Methodsmentioning

confidence: 99%

Utilization of Flavonoid Compounds as HER2 Tyrosine Kinase Inhibitor in Breast Cancer Using Fragment-Based Drug Design

Fleming

Saragih

Tambunan

2020

KEM

View full text Add to dashboard Cite

show abstract

“…A virtual screening was performed taking into account the biological activity prediction model developed in the software KNIME Analytics Platform 3.6 [ 8 ] using the classifier "Random Forest" [ 9 ] and the predictor "Weka predictor 3.7" [ 10 ]. The active molecules were imported into the OSIRIS DataWarrior 4.7.3 [ 11 ] software to estimate the risks of cytotoxicity based on four parameters: mutagenicity, carcinogenicity, skin irritability and effect on the reproductive system. Of the active molecules that did not present any risk of cytotoxicity and only those that had good absorption rates (lower absorption rate among the controls used) were considered, so with the remaining molecules, molecular docking with proteins PDB ID 4DXD and 4WVG to obtain the ligand-receptor interaction energies and the amino acid residues involved in this interaction using software Molegro Virtual Docker 6.0 [ 12 , 13 , 14 ].…”

Section: Methodsmentioning

confidence: 99%

PROPOSITION IN SILICO OF BENZOIC ANALOGS AGAINST Staphylococcus aureus

Monteiro

Viana

Barros

et al. 2018

Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th Edition

View full text Add to dashboard Cite

The microorganism Staphylococcus aureus is a gram-positive spherical bacteria present in the healthy human body, commonly found in the nostrils and skin. It is responsible for a number of infections such as inflammation in the follicles, contribution to the onset of acne, inflammation in the meninges, cardiovascular inflammation, lung inflammation and others. This work aims to propose new benzoic in silico bioactives to combat Staphylococcus aureus. To a prediction model of biological activity developed in the KNIME Analytics Platform 3.6, where the molecules that showed activity in the model were imported into OSIRIS DataWarrior 4.7.3 to predict the risks of cytotoxicity, the calculation of the absorption rate (% ABS). For the molecules approved by the virtual screening already commented, the calculation of the energies of interaction between receptor and binder by molecular docking and the analysis of the interactions with the residues of amino acids were carried out, comparing with the interactions of the drugs used as control in this research. As conclusion of this work it was possible to propose bioactive molecules against S. aureus based on the obtained computational data.

show abstract

“…In this study, the ability of ligands to inhibit the activity of the target protein was predicted through the pKi value. A large, positive value for pKi indicates that the protein-ligand complex has a low dissociation rate 38 . Then, all ligands were screened based on their interaction with 4M0Q.…”

Section: Molecular Docking Simulationsmentioning

confidence: 99%

Screening of terpenoids as potential therapeutics against Zaire ebolavirus infection through pharmacophore-based drug design

Natalia

Tambunan

2019

F1000Res

View full text Add to dashboard Cite

Backgroud: Ebola virus disease (EVD) has spread to various countries in the world and has caused many deaths. Five different virus species can cause EVD, but the most virulent is Zaire ebolavirus (EBOV). The genome of EBOV includes seven genes that encode proteins playing essential roles in the virus lifecycle. Among these proteins, VP24 plays a vital role in the inhibition of the host cells’ immune system. Therefore, VP24 is a potential target for EVD therapy. In the present study, a potential inhibitor of EBOV VP24 activity was identified through pharmacophore-based drug design. Methods: This research was a in silico study, using pharmacophore based molecular docking simulation to obtain inhibitor candidates. Result: Terpenoids were used as VP24 inhibitor candidates. In particular, 55,979 terpenoids were obtained from the PubChem database. An initial screening based on the toxicity prediction test was performed with DataWarrior software: 3,353 ligands were shown to have a favorable toxicity profile, but only 1,375 among them had suitable pharmacophore features. These ligands were used for pharmacophore-based rigid and flexible molecular docking simulations with PDB ID: 4M0Q, chosen as the crystal structure of EBOV VP24. Six ligands predicted to have strong molecular interactions with EBOV VP24 underwent pharmacological property analysis through various software packages, including DataWarrior, SwissADME, admetSAR, pkCSM, and Toxtree. Conclusions: Taxumairol V was identified as the best candidate for EVD drug therapy via EBOV VP24 inhibition based on its molecular properties, predicted molecular interactions with the target molecule, and predicted pharmacological properties.

show abstract

In silico design of fragment-based drug targeting host processing α-glucosidase i for dengue fever

Cited by 14 publications

References 27 publications

Utilization of Flavonoid Compounds as HER2 Tyrosine Kinase Inhibitor in Breast Cancer Using Fragment-Based Drug Design

Utilization of Flavonoid Compounds as HER2 Tyrosine Kinase Inhibitor in Breast Cancer Using Fragment-Based Drug Design

<strong>PROPOSITION <em>IN SILICO</em> OF BENZOIC ANALOGS AGAINST <em>Staphylococcus aureus</em></strong>

Screening of terpenoids as potential therapeutics against Zaire ebolavirus infection through pharmacophore-based drug design

Contact Info

Product

Resources

About