Molecular docking analysis of UniProtKB nitrate reductase enzyme with known natural flavonoids

A, Shaik; Thumma, Vishnu; Ak, Kotha; S, Kramadhati; Pochampally, Jalapathi; Bandi, Seshagiri

doi:10.6026/97320630012425

Cited by 6 publications

(4 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The total number of run was set to 50, and the lowest binding energy conformation was selected for UCSF Chimera analysis. The hydrogen bonds formed between C-9-H with the active site of PKS protein were analyzed …”

Section: Materials and Methodsmentioning

confidence: 99%

See 1 more Smart Citation

cis-9-Hexadecenal, a Natural Compound Targeting Cell Wall Organization, Critical Growth Factor, and Virulence of Aspergillus fumigatus

et al. 2020

View full text Add to dashboard Cite

Aspergillus fumigatus causes several nosocomial pulmonary infections and accounts for high morbidity and mortality rate globally. Among various virulence factors, 1,8-dihydroxynaphthalene-melanin plays an important role in the survival during unfavorable conditions both in vivo and in vitro, masks various molecular patterns associated with A. fumigatus, and protects it from the host immune system. In the present study, we aim to understand the potential of cis-9-hexadecenal as an antimelanogenic compound and its role in modulating other associated virulence factors in A. fumigatus. cis-9-Hexadecenal is a bioactive compound that belongs to C 16 mono-unsaturated fatty-aldehyde groups. Minimum effective concentration of cis-9-hexadecenal affecting A. fumigatus melanin biosynthesis was determined using broth microdilution method. The spectrophotometric analysis revealed reduced melanin content (91%) and hydrophobicity (59%) at 0.293 mM of cis-9-hexadecenal. Cell surface organizational changes using electron microscopy showed altered demelanized smooth A. fumigatus conidial surface without any protrusions after cis-9-hexadecenal treatment. The transcript analysis of polyketide synthase (PKS) pksP/alb1 gene was quantified through qRT-PCR which revealed an upregulated expression. Total proteome profiling conducted through LC-MS-MS showed upregulated PKS enzyme but other downstream proteins involved in the 1,8-dihydroxynaphthalene-melanin biosynthesis pathway were absent. The homology modeling of PKS using Expasy's web server predicted that PKS is stable at varied conditions and is hydrophilic in nature. The Ramachandran plot by PROCHECK confirmed the 3-D structure of PKS to be reliable. Docking analysis using AutoDock-4.2.6 predicted the binding of cis-9-hexadecenal and PKS at Thr-264 and Ser-171 residue via hydrogen bonding at a low binding energy of −4.95 kcal/mol.

show abstract

Section: Materials and Methodsmentioning

confidence: 99%

“…The hydrogen bonds formed between C-9-H with the active site of PKS protein were analyzed. 52 4.10. Statistical Analysis.…”

Section: Procurement Of Fungal Strains and The Naturalmentioning

confidence: 99%

cis-9-Hexadecenal, a Natural Compound Targeting Cell Wall Organization, Critical Growth Factor, and Virulence of Aspergillus fumigatus

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The Molegro virtual Docker [MVD] was used to dock the various metal complexes into the active site of the PTP-1B [39]. MVD has a higher accuracy than other stock softwares such as Glide, FlexX and Sor ex [40,41]. The structure of a protein loaded onto an MVD platform for the purpose of identifying potential active sites or cavities [42].…”

Section: Type Of Inhibition Exerted On Ptp-1b By Inhibitormentioning

confidence: 99%

Enzyme PTP-1B Inhibition Studies by Vanadium Metal Complexes: a Kinetic Approach

Shaik

Kondaparthy²,

Begum

et al. 2023

Biol Trace Elem Res

Self Cite

View full text Add to dashboard Cite

The medical eld now needs more novel drugs to treat obesity and type-2 diabetes mellitus (T2D) than ever before. Obesity and T2D are both characterized by resistance to the hormones leptin and insulin. PTP-1B is a promising target for drug growth as strong genetic, pharmacological and biochemical evidence points to the possibility of treating diabetes and obesity by blocking the PTP-1B enzyme.Studies have also found that PTP-1B is over expressed in patients with diabetes and obesity, suggesting that inhibiting PTP-1B may be a useful technique in their care. There aren't any clinically used PTP-1B inhibitors, despite the fact that numerous naturally occurring PTP-1B inhibitors demonstrated great therapeutic promise. This is most likely because of their low activity or lack of selectivity. It is still important to look for more effective and focused PTP-1B inhibitors. A few organo vanadium metal complexes were synthesized, characterized, and binding studies on vanadium complexes with PTP-B were also performed using Fluorescence Emission Spectroscopy. Additionally, we theoretically (molecular modeling) and experimentally (enzyme kinetics) examined the PTP-1B inhibitory effects of these vanadium metal complexes and found that they have excellent PTP-1B inhibitory properties.

show abstract

“…Because the retrieved targets may have irregular names or contain proteins or genes from different species, the target information needs to be standardized after each step of target collection. The specific methods are as follows: use uniprotkb search function in UniProt database, input protein name and define the species as human (Homo sapiens), correct all the retrieved proteins to their official names (official symbols) and extract the standard gene names, and obtain the correct target information through database retrieval and transformation (Shaik et al 2016).…”

Section: Protein and Gene Information Correctionmentioning

confidence: 99%

Extraction of Oleic Acid from Animals Oil and Its Anti-inflammatory Effect on Network Pharmacology

Wang

Ding

et al. 2021

Iran J Sci Technol Trans Sci

View full text Add to dashboard Cite

The purpose of this paper is to explore the possible mechanisms of anti-inflammatory and scar repair by Mongolian horse oil. We used TCM database and literature mining to collect active compounds of horse oil and used Swiss TargetPrediction and SuperPred server to find targets of compounds. Anti-inflammatory drug targets were collected through the CTD database. Go annotation of targets and KEGG pathway were enriched and analyzed through Metascape database platform. Molecular docking between active ingredients and targets was verified by AutoDock software. Metascape analysis revealed that the key candidate targets were significantly enriched in a number of pathways associated with inflammatory pathology. The results of molecular docking showed that oleic acid, a major component of animals oil, could influence the regulatory functions of TNF, NGF, IL6, IL1B, Jun, and CDK1. This suggests that animals oil can regulate the development of inflammation through its active ingredient, oleic acid, and can influence the expression of multiple signaling pathways, with theoretical endogenous interactions with TNF, NGF, IL6, IL1B, JUN, and CDK1 proteins.

show abstract

Molecular docking analysis of UniProtKB nitrate reductase enzyme with known natural flavonoids

Cited by 6 publications

References 15 publications

cis-9-Hexadecenal, a Natural Compound Targeting Cell Wall Organization, Critical Growth Factor, and Virulence of Aspergillus fumigatus

cis-9-Hexadecenal, a Natural Compound Targeting Cell Wall Organization, Critical Growth Factor, and Virulence of Aspergillus fumigatus

Enzyme PTP-1B Inhibition Studies by Vanadium Metal Complexes: a Kinetic Approach

Extraction of Oleic Acid from Animals Oil and Its Anti-inflammatory Effect on Network Pharmacology

Contact Info

Product

Resources

About