Active and allosteric site binding MM-QM studies of Methylidene tetracyclo derivative in PCSK9 protein intended to make a safe antilipidemic agent

Irfan, N.; Vaithyanathan, Prakash; Anandaram, Harishchander; Mohammed Zaidh, S.; Priya Varshini, S.; Puratchikody, A.

doi:10.1080/07391102.2023.2239928

Cited by 7 publications

(2 citation statements)

References 33 publications

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“…Prior to simulation, the model was relaxed. [19,22,23] The analysis of dynamic interactions for the 100 ns simulations was done by plotting the relevant graphs involving pressure, temperature and volume.…”

Section: System Builder and Dynamic Simulation Set Upmentioning

confidence: 99%

Insilco analysis of an interaction between an endogenous peptide fragment of NUR77 receptor from human cells and USAG1 protein - may induce teeth regeneration

VAITHYANATHAN

2024

Preprint

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BMP-7 and WNT signaling are responsible for the development of teeth. USAG-1 (uterine sensitization associated gene-1) inhibits bone morphogenetic protein-7 protein (BMP-7) as well as WNT receptors leading to suppression of tooth development and growth. The inhibition of USAG-1 using an antibody has been shown to induce tooth regeneration in mice. Hence, USAG-1 is a drug target that is promising enough for teeth generation. In this paper, for the first time, it has been proposed that an endogenous peptide that is part of the NUR-77 receptor in human cells may inhibit USAG-1 protein to induce tooth regeneration when injected locally. The peptide FSRSLHSL of the NUR-77 receptor interacts with the usag-1 protein through enough hydrogen bonds as shown by the docking studies. BCL-2 expression determines the mineralogical composition of enamel crystals of tooth structure. The peptide FSRSLHSL doesn’t convert the character of BCL-2 to proapoptotic although the addition of an extra amino acid “L” to derive FSRSLHSLL leads to an orthogonal behavior.

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Section: System Builder and Dynamic Simulation Set Upmentioning

confidence: 99%

Insilco analysis of an interaction between an endogenous peptide fragment of NUR77 receptor from human cells and USAG1 protein - may induce teeth regeneration

VAITHYANATHAN

2024

Preprint

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“…To identi ed the best novel compound and also predicted the toxicity studies using the protein-based Fragment development drug discovery. [21][22][23][24][25] In this work Molecular docking and dynamic simulation stability studies inside the binding site was performed and also to predict toxicity of the newly identi ed lead is related to the structure toxicity relationships was performed and an evaluation was also performed to analyzed actions of molecules inside the binding cavity of the TNF-α receptor.…”

Section: Introductionmentioning

confidence: 99%

Tumor necrosis factor- α Inhibition analysis by chemotherapy agent through QM/MM studies

Navabshan,

2023

Preprint

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TNF (Tumor Necrosis Factor) is a multifunctional cytokine with a strong pro-inflammatory action and it is a proven therapeutic target receptor for a variety of autoimmune and inflammation-related illnesses. The current investigation is looking for a new chemotherapy small lead molecule that can directly bind to TNF receptors and modify the conformation. The TNF-α fold was docked with the 56 AI-designed molecules by a three-step algorithm in the Schrodinger Maestro interface. The interaction analysis results revealed that the best-hit molecule with a binding capacity score of -6.987 Kcal/mol and the MMGBSA value was found to be -52.42 Kcal/mol with the TNF receptor. Interaction map illustrates that 29 active amino acid of TNF receptor networked through 3 hydrogen bond, hydrophobic, 2 Salt bridges and negative charges type interactions with ring system such as piperazine and azetidine od the best hit molecule. Further, the environment solvent stability was confirmed using MD simulation in Desmund interface and analyzed the trajectory at 100 ns scale level, and it concludes that the formed bonds are 40–99% strong enough to modify the secondary structure of the TNF-α. Which leads target specific inhibition and safe chemotherapy agent for Tumor necrosis factor (TNF-α)

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Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin

Radhakrishnan,

Dani,

Navabshan

et al. 2023

Protein J

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Active and allosteric site binding MM-QM studies of Methylidene tetracyclo derivative in PCSK9 protein intended to make a safe antilipidemic agent

Cited by 7 publications

References 33 publications

Insilco analysis of an interaction between an endogenous peptide fragment of NUR77 receptor from human cells and USAG1 protein - may induce teeth regeneration

Insilco analysis of an interaction between an endogenous peptide fragment of NUR77 receptor from human cells and USAG1 protein - may induce teeth regeneration

Tumor necrosis factor- α Inhibition analysis by chemotherapy agent through QM/MM studies

Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin

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