scholarly journals The Potential of Acetylfuran and Furfural from Tamarindus indica as Lipoxygenase Inhibitor: In Silico Study

2021 ◽  
Vol 8 (2) ◽  
pp. 139
Author(s):  
Apriani Herni Rophi ◽  
Yohanes Bare ◽  
Dewi Ratih Tirto Sari
Keyword(s):  
Arachidonic Acid ◽  
Amino Acid ◽  
Protein Interactions ◽  
Amino Acid Residues ◽  
Tamarindus Indica ◽  
Lipoxygenase Inhibitor ◽  
Discovery Studio ◽  
Pubchem Database ◽  
In Silico Study ◽  
Action Methods

Background: Tamarindus indica is a type of plant sub-family Caesalpinioideae, which is predicted to have anti-inflammatory properties. When inflammation occurs, arachidonic acid will undergo metabolism, the LOX pathway will release 5-lipoxygenase (5-LOX). Objective: This study aimed to analyze the potential of acetylfuran and furfural compounds on LOX action. Methods: The compound Acetylfuran (CID 14505), Furfural (CID 7362) were downloaded from the PubChem database. The 5-LOX protein was obtained from PDB (6N2W), preparation by removing ligands and molecules that bind to Discovery Studio V19.1.0.18287. Compound and protein interactions have interacted with the Vina autodock software integrated into the PyRX software and analyzed by Discovery Studio V19.1.0.18287. Results: The results showed that the content of Acetylfuran and Furfural compounds in Tamarindus indica is predicted to have the potential as an inhibitor of the LOX gene on different amino acid residues, namely 3 amino acid residues and 4 amino acid residues, respectively and produce binding energy. In addition, van der Waals forces, hydrogen and hydrophobic bonds were found, giving the strength of the bonds formed. Conclusion:  Bioactive acetylfuran and furfural have the potential as a drug to curve inflammation in the human body.

scholarly journals In silico study: Potential prediction of Curcuma longa and Cymbopogon citratus essential oil as Lipoxygenase inhibitor

JSMARTech ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 075-080
Author(s):  
Yohanes Bare ◽  
◽  
Lilin Indahsari ◽  
Dewi Sari ◽  
Theopilus Watuguly ◽  
...  
Keyword(s):  
Essential Oil ◽  
Curcuma Longa ◽  
Chemical Compounds ◽  
Amino Acid Residues ◽  
Cymbopogon Citratus ◽  
Lipoxygenase Inhibitor ◽  
Discovery Studio ◽  
Pubchem Database ◽  
In Silico Study ◽  
Body Response

Abstract: Inflammation is the human body response by the injure as a results the inflammation will release LOX. To curve the conditions we use the bioactive from the nature are essential oil from Curcuma longa and Cymbopogon citratus because has a potential has pharmacologist activity. The purpose of this research to investigate the role essential oil from Curcuma longa and Cymbopogon citratus through LOX gene. Several chemical substances, including 3,7-dimethyl-1,3,6-octatriene, camphor, eugenol, curzerene and isoborneol were retrivied from PubChem database. The PyRx 0.8 was used to minimize and convert the sdf file to pdb format file of ligands. Those compounds were predicted their interaction using STITCH online server. Ligands and protein were docked by HEX Cuda 8.0.0 program, 3D and 2D views were evaluated using Discovery studio ver.19.0.0 and LigPlot+ ver 2.2, respectively. We found fourteen amino acid residues from LOX which bound the chemical compounds. Those interaction was supported by hydrogen bond with variety energy binding. To sum up, the essential oil from Curcuma longa and Cymbopogon citratus has a potential function as inhibitor LOX by inhibiting fourteen active side of the LOX gene.

scholarly journals In silico study: Potential prediction of Curcuma longa and Cymbopogon citratus essential oil as Lipoxygenase inhibitor

JSMARTech ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 081-086
Author(s):  
Yohanes Bare ◽  
◽  
Lilin Indahsari ◽  
Dewi Sari ◽  
Theopilus Watuguly ◽  
...  
Keyword(s):  
Essential Oil ◽  
Curcuma Longa ◽  
Chemical Compounds ◽  
Amino Acid Residues ◽  
Cymbopogon Citratus ◽  
Lipoxygenase Inhibitor ◽  
Discovery Studio ◽  
Pubchem Database ◽  
In Silico Study ◽  
Body Response

Inflammation is the human body response by the injure as a results the inflammation will release LOX. To curve the conditions we use the bioactive from the nature are essential oil from Curcuma longa and Cymbopogon citratus because has a potential has pharmacologist activity. The purpose of this research to investigate the role essential oil from Curcuma longa and Cymbopogon citratus through LOX gene. Several chemical substances, including 3,7-dimethyl-1,3,6-octatriene, camphor, eugenol, curzerene and isoborneol were retrivied from PubChem database. The PyRx 0.8 was used to minimize and convert the sdf file to pdb format file of ligands. Those compounds were predicted their interaction using STITCH online server. Ligands and protein were docked by HEX Cuda 8.0.0 program, 3D and 2D views were evaluated using Discovery studio ver.19.0.0 and LigPlot+ ver 2.2, respectively. We found fourteen amino acid residues from LOX which bound the chemical compounds. Those interaction was supported by hydrogen bond with variety energy binding. To sum up, the essential oil from Curcuma longa and Cymbopogon citratus has a potential function as inhibitor LOX by inhibiting fourteen active side of the LOX gene.

scholarly journals Peptide recognition and dephosphorylation by the vaccinia VH1 phosphatase

2020 ◽  
Author(s):  
Bryan M. Zhao ◽  
Megan Hogan ◽  
Michael S Lee ◽  
Beverly K. Dyas ◽  
Robert G. Ulrich
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Catalytic Site ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Protein Protein Interactions ◽  
Host Cell Proteins ◽  
Enzyme Substrate ◽  
Dual Specificity ◽  
Contact Residues

ABSTRACTThe VH1 protein encoded by the highly conserved H1 locus of orthopoxviruses is a dual-specificity phosphatase (DUSPs) that hydrolyzes phosphate groups from phosphorylated tyrosine, serine, and threonine residues of viral and host cell proteins. Because the DUSP activities are required for virus replication, VH1 is a prime target for the development of therapeutic inhibitors. However, the presentation of a shallow catalytic site has thwarted all drug development efforts. As an alternative to direct targeting of catalytic pockets, we describe surface contacts between VH1 and substrates that are essential for full activity and provide a new pathway for developing inhibitors of protein-protein interactions. Critical amino acid residues were manipulated by site-directed mutagenesis of VH1, and perturbation of peptide substrate interactions based on these mutations were assessed by high-throughput assays that employed surface plasmon resonance and phosphatase activities. Two positively-charged residues (Lys-20 and Lys-22) and the hydrophobic side chain of Met-60 appear to orient the polarity of the pTyr peptide on the VH1 surface, while additional amino acid residues that flank the catalytic site contribute to substrate recognition and productive dephosphorylation. We propose that the enzyme-substrate contact residues described here may serve as molecular targets for the development of inhibitors that specifically block VH1 catalytic activity and thus poxvirus replication.

scholarly journals Insights on cross-species transmission of SARS-CoV-2 from structural modeling

2020 ◽  
Author(s):  
João PGLM Rodrigues ◽  
Susana Barrera-Vilarmau ◽  
João MC Teixeira ◽  
Elizabeth Seckel ◽  
Panagiotis Kastritis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Protein Interactions ◽  
Animal Species ◽  
Host Protein ◽  
Spike Protein ◽  
Computational Studies ◽  
Wild Animals ◽  
Amino Acid Residues ◽  
Global Pandemic

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global pandemic that has infected more than 14 million people in more than 180 countries worldwide. Like other coronaviruses, SARS-CoV-2 is thought to have been transmitted to humans from wild animals. Given the scale and widespread geographical distribution of the current pandemic, the question emerges whether human-to-animal transmission is possible and if so, which animal species are most at risk. Here, we investigated the structural properties of several ACE2 orthologs bound to the SARS-CoV-2 spike protein. We found that species known not to be susceptible to SARS-CoV-2 infection have non-conservative mutations in several ACE2 amino acid residues that disrupt key polar and charged contacts with the viral spike protein. Our models also predict affinity-enhancing mutations that could be used to design ACE2 variants for therapeutic purposes. Finally, our study provides a blueprint for modeling viral-host protein interactions and highlights several important considerations when designing these computational studies and analyzing their results.

Defining Amino Acid Residues Involved in DNA−Protein Interactions and Revelation of 3‘-Exonuclease Activity in Endonuclease V†

Biochemistry ◽  
2005 ◽  
Vol 44 (34) ◽  
pp. 11486-11495 ◽  
Author(s):  
Hong Feng ◽  
Liang Dong ◽  
Athena M. Klutz ◽  
Nima Aghaebrahim ◽  
Weiguo Cao
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Exonuclease Activity ◽  
Amino Acid Residues ◽  
Endonuclease V ◽  
Dna Protein Interactions

Molecular Cloning of TSARG6 Gene Related to Apoptosis in Human Spermatogenic Cells

2004 ◽  
Vol 36 (2) ◽  
pp. 93-98 ◽  
Author(s):  
Gang Liu ◽  
Guang-Xiu Lu ◽  
Xiao-Wei Xing
Keyword(s):  
Amino Acid ◽  
Protein Interactions ◽  
Critical Role ◽  
Human Testis ◽  
Amino Acid Residues ◽  
Spermatogenic Cells ◽  
Protein Protein Interactions ◽  
New Gene ◽  
Pcr Technology ◽  
Dnak Protein

Abstract Beginning from a mouse EST (GenBank accession No. BE644537) which was significantly up-regulated in cryptorchidism and represented a novel gene, we cloned a new gene (GenBank accession No. AY138810) which is related to apoptosis in human spermatogenic cells by means of GeneScan program and PCR technology. The gene whose full cDNA length is 1875 bp containing 8 exons and 7 introns is located in human chromosome 11q13.3. Its protein containing 316 amino acid residues is a new member of HSP40 protein family because the sequence contains the highly conserved J domain which is present in all DnaJ-like proteins and is considered to have a critical role in DnaJ-DnaK protein-protein interactions. TSARG6 protein displays a 45% identity in a 348-amino acid overlap with DJB5_HUMAN protein. The result of RT-PCR and Northern blot analysis showed that TSARG6 is specifically expressed in adult testis and the transcript is 1.8 kb. Based upon all these observations, it is considered that we cloned a new gene which probably inhibited human testis spermatogenesis apoptosis.

scholarly journals Analysis of molecular interactions of 8-gingerol compounds in Ginger (Zingiber officinale) as ACE Inhibitor

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (2) ◽  
pp. 183-187
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Aprianus Pani Pili ◽  
Maria Helvina
Keyword(s):  
Amino Acid ◽  
Hydrogen Bonds ◽  
Ace Inhibitor ◽  
Van Der Waals ◽  
Zingiber Officinale ◽  
Van Der Waals Forces ◽  
Amino Acid Residues ◽  
Protein Database ◽  
Discovery Studio ◽  
Software Analysis

Background: Hypertension is a disease with increasing characteristics of blood pressure. The ACE gene has a role in the conversion of ATI to ATII in hypertensive conditions. Healing is done by using the 8-gingerol content contained in ginger. The purpose of this study is to analyze the molecular interaction that occurs between 8-gingerol and ACE. Method: ACE model proteins (ID: 3bkk) were obtained from the Bank Data Protein database (PDB) through 8-gingerol ligands (CID: 168114) obtained from the PubChem database. ACE and 8-gingerol were docked by Discovery Study Client 4.1 software. Analysis of amino acid residues, binding energy, Van der Waals forces, and hydrogen bonds formed using Discovery Studio Client 4.1. Results: The interaction between 8-gingerol and ACE showed that there were seven amino acid residues that interacted with 8-gingerol, also found hydrogen bonds, hydrophobic and Van der Waals forces that strengthen and stabilize these bonds. Conclusion: the interaction of 8-ginger with the active side of ACE is determined as an ACE inhibitor, the inhibition is a significant effect on the obstruction of ACE conversion.

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