Probing the dynamical interaction of the <i>para</i>-sulfonato-calix[4]arene with an antifungal protein

Bartocci, Alessio; Dumont, Élise

doi:10.1039/d3cp01202f

Cited by 3 publications

(4 citation statements)

References 47 publications

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“…Indeed, these positively charged residues have already been reported as bridge residues between binding sites, due to their ability to coordinate ligands at the protein surface. 42–44 We surmise that the use of a non-polarizable force field may also lead to overshooting the formation of salt-bridges with respect to other non-covalent interactions. Our MD simulations in the μs-time range are not prone to capture all microsecond-to-millisecond motions.…”

Section: Discussionmentioning

confidence: 99%

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One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

Dos Santos,

Bartocci,

Gillet

et al. 2024

Phys. Chem. Chem. Phys.

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Section: Discussionmentioning

confidence: 99%

“…Binding site search onto the protein surfaces follows a computational protocol recently exploited. [42][43][44]50 Ubiquitin monomer structure with 76 residues was taken from an unpublished, high-resolution PDB provided by Dr E. Girard IBS, Grenoble. Protonation states of ubiquitin residues were assigned using the H++ server 48 at pH 6.5.…”

Section: Methodsmentioning

confidence: 99%

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

Dos Santos,

Bartocci,

Gillet

et al. 2024

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The optimized structures were used as input for MM‐GBSA calculations, [133] to obtain the binding affinity of the different protein‐calix[4]arene systems [132] . This procedure was recently validated to calculate the binding energy of calixarene derivatives to proteins [134–136] . Electrostatic and van der Waals (vdW) interactions were calculated considering an infinite cut‐off.…”

Section: Methodsmentioning

confidence: 99%

“…[132] This procedure was recently validated to calculate the binding energy of calixarene derivatives to proteins. [134][135][136] Electrostatic and van der Waals (vdW) interactions were calculated considering an infinite cut-off. The polar solvation term was calculated using the GB model, whereas the non-polar solvation term was determined using solvent-accessible, surfacearea-dependent terms.…”

Section: Virtual Screeningmentioning

confidence: 99%

Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking

Giugliano,

Gajo,

Marforio

et al. 2024

Chemistry A European J

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Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5%), isoleucine (11.3%), phenylalanines (11.3%) and valine (9.5%) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator‐activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer‐related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well‐defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.

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Situating the phosphonated calixarene–cytochrome C association by molecular dynamics simulations

Bartocci,

Dumont

2024

The Journal of Chemical Physics

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Protein–calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as “molecular glue.” Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

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Probing the dynamical interaction of the para-sulfonato-calix[4]arene with an antifungal protein

Abstract: Calixarenes are hallmark molecules in supramolecular chemistry as guest cages for small ligands. They have also conversely proved their interest as auxiliary ligands toward assisted co-crystallization of proteins. These functionalized...

Cited by 3 publications

References 47 publications

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics

Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking

Situating the phosphonated calixarene–cytochrome C association by molecular dynamics simulations

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