Screening of commercial cyclic peptide conjugated to HIV-1 Tat peptide as inhibitor of N-terminal heptad repeat glycoprotein-2 ectodomain Ebola virus through in silico analysis

Tambunan, Usman Sumo Friend; Alkaff, Ahmad Husein; Nasution, Mochammad Arfin Fardiansyah; Parikesit, Arli Aditya; Kerami, Djati

doi:10.1016/j.jmgm.2017.04.001

Cited by 23 publications

(17 citation statements)

References 30 publications

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“…This step generated the pharmacophore model around the binding site of EBOV VP35 after we performed the protonating process of EBOV VP35 through "LigX" feature of MOE 2014.09 software. Later on, we conducted molecular docking simulation using the modification of our current approach [71,72]. Instead of using "Triangle Matcher" and "London dG," we used "Pharmacophore" and "Affinity dG" for "Placement" and "Rescoring 1" parameters to accommodate the pharmacophore model that created in an earlier phase, while the rest of parameters were set according to the default setup.…”

Section: Our In Silico Methodsmentioning

confidence: 99%

Bioinformatics Approach to Screening and Developing Drug against Ebola

Tambunan¹,

Alkaff²,

Nasution³

2018

Advances in Ebola Control

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Ebola is an acute disease causing hemorrhagic fever marked with high mortality rate. The patients who suffer from Ebola only receive palliative care because there is no available drug which can consistently cure this disease. To date, no cure has been found to treat this disease. Bioinformatics and computer-aided drug discovery and development (CADDD) are employed to utilize the readily available genomic and proteomic data and enhance the hit rate of the novel and repurposed drug for Ebola therapy. Additionally, the time and cost of wet laboratory experiments can be drastically reduced by the support of bioinformatics approach. Our laboratory has succeeded not only in creating the bioinformatics research pipeline but also screening and developing the drug candidate to cure Ebola. Through pharmacophore-based virtual screening and molecular docking simulations, we discovered that about three Indonesian natural product compounds have noteworthy molecular interactions against EBOV VP35 protein, which are responsible for the RNA synthesis of the Ebola. These compounds can be reevaluated further through advances in in silico simulation and in vitro experiments.

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Section: Our In Silico Methodsmentioning

confidence: 99%

Bioinformatics Approach to Screening and Developing Drug against Ebola

Tambunan¹,

Alkaff²,

Nasution³

2018

Advances in Ebola Control

Self Cite

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“…Its potential also can be determined through the score computed by software. As a result, through years, molecular docking simulation as part of computational drug delivery has developed significantly and become a crucial part of a new compound as a potential drug [13,19]. However, the molecular docking simulation may lead to false results as the rigid receptor docking employed in molecular docking simulation is not resembling the real characteristic of the receptor.…”

Section: Molecular Docking Simulations Of Ligandmentioning

confidence: 99%

Discovery of GPX4 inhibitor by molecular docking simulation as a potential ferroptosis inducer

Fatonah

Tambunan²,

Pamungkas

et al. 2020

Biointerface Res Appl Chem

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As one of the most complex diseases in the world, cancer continues as one of the significant public health problems. It was recorded by 2014 that cancer caused 1,551,000 death in Indonesia. One type of programmed cell death (PCD) that played a role in cancer cell treatment is Ferroptosis. Ferroptosis is PCD on iron and characterized by the inactivation of glutathione-dependent peroxidase (GPx4). In this research, a new therapeutic strategy for cancer was developed through the computational approach on synthetic compounds to discover its potential as an inhibitor of GPx4. About 688 compounds derivative from mercaptosuccinic acid acquired from the Zinc15 database. These compounds screened through the Lipinski’s Rule of Three and pharmacological prediction to eliminate ligands with undesired molecular properties. After that, the ligands underwent both rigid and flexible molecular docking simulations to predict their inhibition activity toward GPx4. From molecular docking simulation, (2S)-2-[(Z)-3-phenylprop-2-enyl]sulfanylbutanedioic acid show favorable characteristics as a drug candidate.

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“…M. tuberculosis is known to have more than millions of base pairs and approximately around thousands genes (Méndez-Samperio, 2016). To make sure the protein we choose is right we will run the protein against the retrieved antigen using automated BLASTP (Altschul et al, 1997;Tambunan et al, 2017). To improve the predictions of protein from FASTA secreted by Type II secretion pathway by SignalPor PAPROC-1, we will use VaxiJen, NetMHCIIpan, MHCpred or Propred (Dyrløv Bendtsen et al, 2004;Tambunan et al, 2016).…”

Section: Immunoinformatic Approach In Designing New Vaccinementioning

confidence: 99%

Strategies of Tuberculosis–HIV Vaccines Design using Immunoinformatic Approach

Fatonah

Wicaksono

Tambunan³

2019

OnLine Journal of Biological Sciences

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Tuberculosis is amongst the highest cause death worldwide. According to WHO, an estimated of more than a million people fell ill with Tuberculosis (TB) in 2016. The resistances of the M. tuberculosis (MTb) bacteria make drugs, not that useful in battle with TB. Vaccination is a better choice to avoid the worst cases of TB. The resistance possessed by MTb bacteria with some of the drugs reported creates its challenge to reduce the high rate of TB related death. One of the concerns is the high mortality rate due to TB associated with HIV. However, there's still no effective vaccine for Tuberculosis-Human Immunodeficiency Virus (TB-HIV). Vaccines for Tuberculosis-HIV even on the way of progress to get the demanding the mutation of the bacteria and challenging scientists to get the right vaccines for this disease. Immunoinformatic is one of the approaches that can speed up the making of the vaccine.

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Screening of commercial cyclic peptide conjugated to HIV-1 Tat peptide as inhibitor of N-terminal heptad repeat glycoprotein-2 ectodomain Ebola virus through in silico analysis

Cited by 23 publications

References 30 publications

Bioinformatics Approach to Screening and Developing Drug against Ebola

Bioinformatics Approach to Screening and Developing Drug against Ebola

Discovery of GPX4 inhibitor by molecular docking simulation as a potential ferroptosis inducer

Strategies of Tuberculosis–HIV Vaccines Design using Immunoinformatic Approach

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