Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants

Patel, Rushika; Chudasama, Rajesh K; Solanki, Rutujaben; Patel, Paresh V.; Parmar, Krupali; Munshi, Nasreen S.

doi:10.1080/10934529.2019.1672457

Cited by 12 publications

(6 citation statements)

References 53 publications

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“…It also forms Pi-alkyl interactions with HIS 96, ILE 94, VAL 381, and PRO95 which is important for conformational stability of the compound and also for recognition of ligand by protein. 56 It also displayed a number of hydrophobic contacts with 10 amino acid residues HIS 96 (3.30 Å), VAL 381 (3.56 Å), ILE 382 (3.60 Å), ILE 94 (2.94 Å), ILE 382 (2.31 Å), HIS 96 (5.29 Å), TYR 232 (2.69 Å), PRO 95, LEU 92, GLY 93. The naphthalene moiety could be responsible for these hydrophobic contacts.…”

Section: Resultsmentioning

confidence: 99%

“…It also forms Pi-alkyl bond with VAL 381, PRO 95 and ILE 382, these interactions are playing a crucial role in the recognition of ligand by protein. 56 …”

Section: Resultsmentioning

confidence: 99%

“…) is a crotofolane-type diterpenoid isolated from leaves of C. dichogamus. 55 The compound has a very good docking pose with the reverse transcriptase enzyme (PDB: 1REV) with a binding energy of -7.73 kcal/mol and inhibitory constant 56 The furan ring is responsible for formation of the hydrogen bonding with HIS 96 and for the formation of Pi-Alkyl bond with ILE 382, PRO 95 and VAL382. The hydroxyl group at position 12 is responsible for the formation of hydrogen bonding with LEU 92 and ILE 94 (Table S1 in Supplementary).…”

Section: Interaction Of Crotoxide a (L135) And Crotoxide B (L136) Cro...mentioning

confidence: 99%

Section: Interaction Of Crothalimene a (L292) And Crothalimene B (L29...mentioning

confidence: 99%

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Molecular Docking, Validation, Dynamics Simulations, and Pharmacokinetic Prediction of Phytochemicals Isolated From Croton dichogamus Against the HIV-1 Reverse Transcriptase

Terefe

Ghosh

2022

Bioinform Biol Insights

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The human immunodeficiency virus (HIV) infection and the associated acquired immune deficiency syndrome (AIDS) remain global challenges even after decades of successful treatment, with eastern and southern Africa still bearing the highest burden of disease. Following a thorough computational study, we report top 10 phytochemicals isolated from Croton dichogamus as potent reverse transcriptase inhibitors. The pentacyclic triterpenoid, aleuritolic acid (L12) has displayed best docking pose with binding energy of -8.48 kcal/mol and Ki of 0.61 μM making it superior in binding efficiency when compared to all docked compounds including the FDA-approved drugs. Other phytochemicals such as crotoxide A, crothalimene A, crotodichogamoin B and crotonolide E have also displayed strong binding energies. These compounds could further be investigated as potential antiretroviral medication.

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Section: Resultsmentioning

confidence: 99%

“…It also forms Pi-alkyl bond with VAL 381, PRO 95 and ILE 382, these interactions are playing a crucial role in the recognition of ligand by protein. 56 …”

Section: Resultsmentioning

confidence: 99%

Section: Interaction Of Crotoxide a (L135) And Crotoxide B (L136) Cro...mentioning

confidence: 99%

Section: Interaction Of Crothalimene a (L292) And Crothalimene B (L29...mentioning

confidence: 99%

See 2 more Smart Citations

Molecular Docking, Validation, Dynamics Simulations, and Pharmacokinetic Prediction of Phytochemicals Isolated From Croton dichogamus Against the HIV-1 Reverse Transcriptase

Terefe

Ghosh

2022

Bioinform Biol Insights

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“…Biosensors have been used in wearable medical monitoring, health diagnosis, and environmental monitoring. − Natural evolution of receptors have led to microbes’ ability to detect and respond to known human health hazards, such as phenanthrene, lead, copper, and organophosphate pesticides. , These molecular components provide a basis for sensor engineering in living systems. One environmental pollutant for which there is currently no zero-power monitoring technology is the fungicide, 2-phenylphenol (2-PP).…”

mentioning

confidence: 99%

Engineered Biosensors in an Encapsulated and Deployable System for Environmental Chemical Detection

et al. 2022

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The long-term exposure of low levels of the fungicide, 2-phenylphenol (2-PP), to the environment presents a hazard to human and aquatic health. The cost and difficulty in large-scale production limit the use of existing sensors to detect 2-PP for applications such as personal protection and persistent environmental monitoring of large areas. While advances have been made in using whole cells as biosensors for specific chemical detection, a whole-cell biosensor system with robust biocontainment for field deployment and a strong visual reporter for readouts in the deployed environment has yet to be realized. Here, engineered biosensors in an encapsulated and deployable system (eBEADS) were created to demonstrate a portable, no-power living sensor for detection of 2-PP in the environment. A whole-cell living sensor to detect 2-PP was developed in Escherichia coli by utilizing the 2-PP degradation pathway with an agenetic amplification circuit to produce a visual colorimetric output. To enable field deployment, a physical biocontainment system comprising polyacrylamide alginate beads was designed to encapsulate sensor strains, support long-term viability without supplemental nutrients, and allow permeability of the target analyte. Integration of materials and sensing strains has led to the development of a potential deployable end-to-end living sensor that, with the addition of an amplification circuit, has up to a 66-fold increase in β-galactosidase reporter output over non-amplified strains, responding to as little as 1 μM 2-PP while unencapsulated and 10 μM 2-PP while encapsulated. eBEADS enable sensitive and specific in-field detection of environmental perturbations and chemical threats without electronics.

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Evaluation of self-amplifying mRNA platform for protein expression and genetic stability: Implication for mRNA therapies

Deo,

Desai,

Patare

et al. 2023

Biochemical and Biophysical Research Communications

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Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants

Cited by 12 publications

References 53 publications

Molecular Docking, Validation, Dynamics Simulations, and Pharmacokinetic Prediction of Phytochemicals Isolated From Croton dichogamus Against the HIV-1 Reverse Transcriptase

Molecular Docking, Validation, Dynamics Simulations, and Pharmacokinetic Prediction of Phytochemicals Isolated From Croton dichogamus Against the HIV-1 Reverse Transcriptase

Engineered Biosensors in an Encapsulated and Deployable System for Environmental Chemical Detection

Evaluation of self-amplifying mRNA platform for protein expression and genetic stability: Implication for mRNA therapies

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