Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters

Tiwari, Vikas; Garg, Sonali; Karmakar, Tarak

doi:10.1021/acsabm.2c00997

Cited by 7 publications

(8 citation statements)

References 30 publications

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“…Therefore, the same fluorophore gives different responses with different DNA structures and their sequence variants. Several laboratories, including us, have used this differential fluorescence response of a fluorophore to tentatively rank the preferred nucleic acid structures of the same [59–62] …”

Section: Resultsmentioning

confidence: 99%

Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G‐Quadruplex

Metangle,

Ranjan

2023

ChemBioChem

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The therapeutic potential of G‐quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine‐based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G‐quadruplex. The binding of compound 1 to Pu22 G‐quadruplex, initially identified through a fluorescence‐based screening, was further confirmed by UV‐vis, fluorescence spectroscopy, and circular dichroism‐based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G‐quadruplex revealed a concentration‐dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence‐based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka) of 5.67×106 M−1. CD experiments displayed that the parallel conformation of the G‐quadruplex was retained on compound 1’s binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close‐distance interactions involving the quinolinium nitrogen atom.

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Section: Resultsmentioning

confidence: 99%

Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G‐Quadruplex

Metangle,

Ranjan

2023

ChemBioChem

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“…During the production run, the coordinates were saved every 10 ps. As the TIP3P water model is more compatible with the AMBER force field, 36,39,40 some systems were simulated for 500 ns again in such water. In contrast to SPC, the TIP3P water model possesses a larger dipole moment and has a bond angle and dielectric constant closer to the experimental values.…”

Section: Methodsmentioning

confidence: 99%

Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings

Panda,

Karmakar,

Sen Gupta

et al. 2024

Phys. Chem. Chem. Phys.

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“…27 Some recent reports have shown biological applications of water-dispersible MPCs including anticancer activity, 30 anti-Alzheimer's drug, 31 and as a delivery vehicle for an anticancer drug. 32,33 Recently some insights into the aggregation of MPCs and their interaction with the biological environment have been provided using experimental as well as computational methods at atomistic and coarse-grained levels. [34][35][36][37][38][39][40][41][42] Vanzan et al, studied the dimerization of three different Au 25 -based nanoclusters functionalized with hydrophobic ligands in dichloromethane solvent using metadynamics (MetaD)simulations.…”

Section: Introductionmentioning

confidence: 99%

Understanding Molecular Aggregation of Ligand-protected Atomically-Precise Metal Nanoclusters

Tiwari

Karmakar

2023

Preprint

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Atomically precise ligand-protected nanoclusters (MPC) have emerged as an important class of molecules due to their unique structural features and diverse potential applications, including nano-electronics, bio-imaging, as sensors and drug carriers. Understanding the atomistic details of their intermolecular interaction is of paramount interest for designing, synthesizing, and system-specific applications. Crystal structures of various MPCs provide details related to molecular packing and intermolecular interactions. While these experiments reveal macroscopic, mostly static properties, they are often limited by the spatial and temporal resolutions in delineating the microscopic dynamical details. Here we apply molecular dynamics and enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in the solution phase. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and periodic crystals. The free energy profiles obtained from enhanced sampling simulations of dimerization reveal a pivotal role of the protonated states of the ligands as well as the solvation shell in mediating the molecular aggregation process in solution. In the solid phase, the MPCs’ ligands have suppressed conformational flexibility owing to many facile intermolecular hydrogen bonds and π- stacks. Our work provides unprecedented molecular-level details of the aggregation process and conformational dynamics of MPCs ligands in the solution and crystalline phases, which will help rational design of new MPCs with specific properties.

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Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters

Cited by 7 publications

References 30 publications

Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G‐Quadruplex

Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G‐Quadruplex

Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings

Understanding Molecular Aggregation of Ligand-protected Atomically-Precise Metal Nanoclusters

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