Role of molecular dynamics in optimising ligand discovery: Case study with novel inhibitor search for peptidyl t-RNA hydrolase

Dandekar, Bhupendra R.; Sinha, Suman; Mondal, Jagannath

doi:10.1016/j.chphi.2021.100048

Cited by 3 publications

(3 citation statements)

References 41 publications

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“…To develop a drug for SARS-CoV-2, the in silico screening followed by MD simulation was applied to many existing drugs, and then metadynamics was applied to remaining poses to select better drug candidates (Kumawat et al 2021 ; Namsani et al 2021 ). Binding poses from ensemble docking were assessed by metadynamics to screen out false positives (Dandekar et al 2021 ). However, it is still difficult to apply the enhanced sampling to many systems because this method requires a long computation time.…”

Section: Enhanced Sampling Methods and Molecular Bindingmentioning

confidence: 99%

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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

2022

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Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.

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Section: Enhanced Sampling Methods and Molecular Bindingmentioning

confidence: 99%

“…, screen out false positives (Dandekar et al 2021). However, it is still difficult to apply the enhanced sampling to many systems because this method requires a long computation time.…”

Section: Enhanced Sampling Methods and Molecular Bindingmentioning

confidence: 99%

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

2022

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“…by using experimental techniques based on spectroscopy, calorimetry, polarimetry, and so on [4][5][6][7][8][9][10]. In recent times, a significant body of computational or theoretical research endeavors has also been dedicated toward a better understanding of the interaction phenomena [11][12][13][14][15][16][17]. The increasing growth of attention, within the scientific community, to this field of research is not surprising because the site-specific targeted delivery of drug molecules and their excretion from the human body via a benign mechanism pose very crucial research questions toward the successful implementation of the therapeutic actions of a drug.…”

Section: Introductionmentioning

confidence: 99%

Sequestration of Drugs from Biomolecular and Biomimicking Environments: Spectroscopic and Calorimetric Studies

Yadav

Paul²,

Mukherjee

2023

Colloids and Interfaces

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The binding of drugs to nucleic acids, proteins, lipids, amino acids, and other biological receptors is necessary for the transportation of drugs. However, various side effects may also originate if the bound drug molecules are not dissociated from the carrier, especially with the aid of non-toxic agents. The sequestration of small drug molecules bound to biomolecules is thus central to counter issues related to drug overdose and drug detoxification. In this article, we aim to present several methods used for the dissociation of small drug molecules bound to different biological and biomimicking assemblies under in vitro experimental conditions. To this effect, the application of various molecular assemblies, like micelles, mixed micelles, molecular containers, like β-cyclodextrin, cucurbit[7]uril hydrate, etc., has been discussed. Herein, we also try to shed light on the driving forces underlying such sequestration processes through spectroscopic and calorimetric techniques.

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Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods

Ormazábal,

Palma,

Pierdominici-Sottile

2024

Methods in Molecular Biology

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Role of molecular dynamics in optimising ligand discovery: Case study with novel inhibitor search for peptidyl t-RNA hydrolase

Cited by 3 publications

References 41 publications

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Sequestration of Drugs from Biomolecular and Biomimicking Environments: Spectroscopic and Calorimetric Studies

Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods

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