scholarly journals In Silico Inhibition Studies of Jun-Fos-DNA Complex Formation by Curcumin Derivatives

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Anil Kumar ◽  
Utpal Bora
Keyword(s):  
Complex Formation ◽  
In Silico ◽  
Activator Protein 1 ◽  
Amino Acid Residues ◽  
Lung Cancers ◽  
Cellular Processes ◽  
Curcumin Derivatives ◽  
In Silico Study ◽  
Responsive Element ◽  
Dna Complex

Activator protein-1 (AP1) is a transcription factor that consists of the Jun and Fos family proteins. It regulates gene expression in response to a variety of stimuli and controls cellular processes including proliferation, transformation, inflammation, and innate immune responses. AP1 binds specifically to 12-O-tetradecanoylphorbol-13-acetate (TPA) responsive element 5′-TGAG/CTCA-3′ (AP1 site). It has been found constitutively active in breast, ovarian, cervical, and lung cancers. Numerous studies have shown that inhibition of AP1 could be a promising strategy for cancer therapeutic applications. The present in silico study provides insights into the inhibition of Jun-Fos-DNA complex formation by curcumin derivatives. These derivatives interact with the amino acid residues like Arg155 and Arg158 which play a key role in binding of Jun-Fos complex to DNA (AP1 site). Ala151, Ala275, Leu283, and Ile286 were the residues present at binding site which could contribute to hydrophobic contacts with inhibitor molecules. Curcumin sulphate was predicted to be the most potent inhibitor amongst all the natural curcumin derivatives docked.

scholarly journals In Silico Investigation of Luminol, Its Analogues and Mechanism of Chemiluminescence for Blood Identification Beyond Forensics

2020 ◽  
Vol 14 (2) ◽  
pp. 117-127
Author(s):  
Toluwase H. Fatoki
Keyword(s):  
Rattus Norvegicus ◽  
In Silico ◽  
Homo Sapiens ◽  
Canis Familiaris ◽  
Amino Acid Residues ◽  
Molecular Binding ◽  
Binding Score ◽  
In Silico Study ◽  
Fluorescent Products ◽  
New Methodologies

Objective: This study aimed at discovering chemiluminescent analogues of luminol, predict their molecular binding to hemoglobin of bloodstains in household crime, and expound the mechanism of chemiluminescence of luminol. Materials and Methods: Similarity and clustering analyses of luminol analogues were conducted, and molecular docking was carried out using hemoglobin from Homo sapiens and four domestic organisms namely Gallus gallus, Drosophila melanogaster, Rattus norvegicus, and Canis familiaris. Results: The results showed the order of overall binding score as D. melanogaster > H. sapiens > C. familiaris > R. norvegicus > G. gallus. Seven compounds namely ZINC16958228, ZINC17023010, ZINC19915427, ZINC34928954, ZINC19915369, ZINC19915444, and ZINC82294978, were found to be consistently stable in binding with diverse hemoglobin and possibly have chemiluminescence than luminol in this in silico study. The interaction of human hemoglobin with luminol and its analogues, showed that amino acid residues His45, Lys61, Asn68, Val73, Met76, Pro77, Ala79, Ala82, Leu83, Pro95, Phe98, Lys99, Ser102, Ser133, Ala134, and Thr134, were possibly significant in the mechanism of action of presumptive test compounds. It was hypothesized that the improved mechanism of chemiluminescent for the identification of blood was based on peroxidase-like reaction, that produces nitric oxide which binds to hemoglobin (Hb) and inhibits Hb degradation without yielding fluorescent products. The compound 2,3-benzodioxine-1,4,5(6H)-trione was formed, which possibly emits light. Conclusion: This study provides novel insight on the luminol and its expanded mechanism for broader possible applications with careful development of new methodologies.

In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

2013 ◽  
Vol 13 (10) ◽  
pp. 1407-1414 ◽  
Author(s):  
L. Fabian ◽  
V. Sulsen ◽  
F. Frank ◽  
S. Cazorla ◽  
E. Malchiodi ◽  
...  
Keyword(s):  
In Silico ◽  
Sesquiterpene Lactones ◽  
Trypanocidal Activity ◽  
In Silico Study

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

In Silico Study of Ethylene Biosynthesis: Seeking New Effectors of ACC Synthase and ACC Oxidase

2016 ◽  
Vol 11 (3) ◽  
pp. 346-356
Author(s):  
Nada Ayadi ◽  
Sarra Aloui ◽  
Rabeb Shaiek ◽  
Oussama Rokbani ◽  
Faten Raboud ◽  
...  
Keyword(s):  
In Silico ◽  
Acc Oxidase ◽  
Acc Synthase ◽  
Ethylene Biosynthesis ◽  
In Silico Study

In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA Dependent RNA polymerase (RdRp) and Essential Proteases

2020 ◽  
Vol 20 ◽  
Author(s):  
Trinath Chowdhury ◽  
Gourisankar Roymahapatra ◽  
Santi M. Mandal
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
In Silico ◽  
Rna Dependent Rna Polymerase ◽  
Replication Complex ◽  
In Silico Study ◽  
Life Threatening ◽  
In Vivo Analysis ◽  
3Cl Protease

Background: COVID-19 is a life threatening novel corona viral infection to our civilization and spreading rapidly. Terrific efforts are generous by the researchers to search for a drug to control SARS-CoV-2. Methods: Here, a series of arsenical derivatives were optimized and analyzed with in silico study to search the inhibitor of RNA dependent RNA polymerase (RdRp), the major replication factor of SARS-CoV-2. All the optimized derivatives were blindly docked with RdRp of SARS-CoV-2 using iGEMDOCK v2.1. Results: Based on the lower idock score in the catalytic pocket of RdRp, darinaparsin (-82.52 kcal/mol) revealed most effective among them. Darinaparsin strongly binds with both Nsp9 replicase protein (-8.77 kcal/mol) and Nsp15 endoribonuclease (-8.3 kcal/mol) of SARS-CoV-2 as confirmed from the AutoDock analysis. During infection, the ssRNA of SARS-CoV2 is translated into large polyproteins forming viral replication complex by specific proteases like 3CL protease and papain protease. This is also another target to control the virus infection where darinaparsin also perform the inhibitory role to proteases of 3CL protease (-7.69 kcal/mol) and papain protease (-8.43 kcal/mol). Conclusion: In host cell, the furin protease serves as a gateway to the viral entry and darinaparsin docked with furin protease which revealed a strong binding affinity. Thus, screening of potential arsenic drugs would help in providing the fast invitro to in-vivo analysis towards development of therapeutics against SARS-CoV-2.

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