Molecular dynamics simulations, docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors

Rico, Mia I.; Lebedenko, Charlotta G.; Mitchell, Saige M.; Banerjee, Ipsita A.

doi:10.1007/s11030-021-10354-9

Cited by 11 publications

(5 citation statements)

References 73 publications

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“…Finally, 100 ns of production MD runs were carried out, allowing all molecules to move in all directions using a Newtonian leap-frog MD integrator. The time steps for the simulations were 2fs, and the coordinates were saved every 10 ps [43]. Several studies, like root mean square deviation (RMSD), root mean square uctuation (RMSF), hydrogen bond and solvent accessible surface area (SASA), have been analyzed using the MD simulation trajectories for each protein-ligand complex system.…”

Section: Docking and Molecular Dynamics Simulation Of Nal Hitsmentioning

confidence: 99%

WITHDRAWN: In-silico discovery of novel microtubule inhibitors targeting colchicine binding site; A combined Group-based QSAR approach

Sahu

Ojha

2022

Preprint

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Microtubules are a potential target for the design and development of novel anti-mitotic drugs for cancer therapy Focusing on their mechanisms of action, Microtubuletargeting agents are classified into stabilizers and destabilizers, among them destabilizers binding to colchicine binding site domain is an important source of research in recent years. A number of molecules containing indole scaffold have been described as tubulin polymerization inhibitors with the potential to interact with the colchicine binding site. The research is focused on the search for new indole-based colchicine binding site inhibitors, for that fragment-based QSAR utilized for the important interacting site for potent fragment attachment and the designed fragment library screened for the finding of the potent molecule and finally, three molecules screened and validated for their reactivity using DFT and stability using Molecular dynamics simulation, among them m16 showing the potential result with high interaction energy, high molecular reactivity and confirms high stability as compared to others.

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Section: Docking and Molecular Dynamics Simulation Of Nal Hitsmentioning

confidence: 99%

WITHDRAWN: In-silico discovery of novel microtubule inhibitors targeting colchicine binding site; A combined Group-based QSAR approach

Sahu

Ojha

2022

Preprint

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“…CD22 is a transmembrane glycoprotein with seven immunoglobulin (Ig)-like domains (d1–d7). 56 , 57 , 58 , 59 Ereño-Orbea et al. 9 solved the full-length extracellular domain structure of CD22 (d2–d3 region).…”

Section: Resultsmentioning

confidence: 99%

Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia

Ruiz-Ciancio,

Lin,

Veeramani

et al. 2023

Molecular Therapy - Nucleic Acids

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“…The calculated binding free energy for Compound 6 and the reference ligand is not signi cantly different. Based on the energies of the individual components of binding free energies, vander waals forces, and lipophilic energies in uence binding free energies higher than the other individual energy components [34].…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the MMGBSA for the series of simulated trajectory complexes of lanosterol 14-α demethylase bound Compound 6 and uconazole was calculated using MM GBSA method [34] and [35].…”

Section: Mmgbsa Of Simulated Trajectoriesmentioning

confidence: 99%

Elucidation of furanone as ergosterol pathway inhibitor in Cryptococcus neoformans

Sathiyamoorthy

Rathore

Mohan

et al. 2023

Journal of Biomolecular Structure and Dynamics

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In the era of antiretroviral therapy, the prevalence of Cryptococcal infection among HIV patients in developed countries has decreased considerably. However, C. neoformans ranks top among the critical priority pathogen that affects a wide range of immunocompromised individuals. The threat of C. neoformans is because of its incredibly multifaceted intracellular survival capabilities. Cell membrane sterols especially ergosterol and enzymes of its biosynthetic pathway are considered fascinating drug targets because of their structural stability. In this study, the ergosterol biosynthetic enzymes were modeled and docked with furanone derivatives. Among the tested ligands Compound 6 has shown a potential interaction with Lanosterol 14 α-demethylase. This best docked protein-ligand complex was taken further to molecular dynamics simulation. In addition, an in vitro study was conducted to quantify the ergosterol in Compound 6 treated cells. Altogether the computational and in vitro study demonstrates that Compound 6 has anticryptococcal activity by targeting the biosynthetic pathway of ergosterol.

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Molecular dynamics simulations, docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors

Cited by 11 publications

References 73 publications

WITHDRAWN: In-silico discovery of novel microtubule inhibitors targeting colchicine binding site; A combined Group-based QSAR approach

WITHDRAWN: In-silico discovery of novel microtubule inhibitors targeting colchicine binding site; A combined Group-based QSAR approach

Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia

Elucidation of furanone as ergosterol pathway inhibitor in Cryptococcus neoformans

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