Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

Rojas‐Valencia, Natalia; Gómez, Sara; Núñez‐Zarur, Francisco; Cappelli, Chiara; Hadad, C. Z.; Restrepo, Albeiro

doi:10.1021/acs.jpcb.1c06766

Cited by 13 publications

(21 citation statements)

References 64 publications

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“…(2) d→a energy values, calculated for the interactions in that snapshot, are in the same ranges as those found in a-Ibu/water clusters coming from exhaustive explorations of the PESs, reinforcing the fact that randomly choosing configurations from classical mechanics simulations are reliable sources to gain deep insight about inter-fragment bonding, a strategy that has been recently used in several works [10,[77][78][79][80].…”

Section: Hydration Patternssupporting

confidence: 56%

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

et al. 2022

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We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C–C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.

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Section: Hydration Patternssupporting

confidence: 56%

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

et al. 2022

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“…Following the procedures introduced in a previous study of virus•••cell intermolecular interactions for the wild-type SARS-COV-2, [15] the strength of bonding interactions is described and quantified in terms of a set of QTAIM (first three items below) and NBO indexes rooted in quantum chemistry and firmly linked to the physicochemical nature of the interaction. In particular, [19][20][21][22][23][24][25][26] (i) Accumulation of electron densities at the bond critical points for intermolecular contacts. Larger densities indicate stronger interactions.…”

Section: Introductionmentioning

confidence: 99%

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

et al. 2021

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Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS‐COV‐2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (α or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (β or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (γ or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (ζ, or P.2 or 20B/S484K, also first reported in Brazil). From the analysis of a set of bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO‐CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells. This results in significantly improved initial virus⋅⋅⋅cell molecular recognition and attachment at the microscopic level, which trigger the infectious cycle.

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“…Gratifyingly, this procedure seems to remove all structural bias and ambiguity because all quantum descriptors calculated a posteriori indicate that the intermolecular contacts indeed exist. We proceeded to dissect virus⋯cell bonding interactions following these steps: [18,19,[50][51][52] 1. A 3.5 Å separation between residues in the E-protein and the GAG was used to establish a persistent (> 10% occupancy) intermolecular contact.…”

Section: Methodsmentioning

confidence: 99%

Initial Recognition and Attachment of the Zika Virus to Host Cells: A Molecular Dynamics and Quantum Interaction Approach

et al. 2022

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The zika virus (ZIKV), transmitted to humans from the bites of Aedes Aegypti and Aedes Albopictus mosquitoes produces Zika fever and neurodegenerative disorders that despite affecting millions of people, most recently in Africa and the Americas, has been declared a neglected tropical disease by the World Health Organization. In this work, atomistic molecular dynamics simulations followed by rigorous analysis of the intermolecular interactions reveal crucial aspects of the initial virus⋯cell molecular recognition and attachment, events that trigger the infectious cycle. Previous experimental studies have shown that Dermatan Sulfate (DS) and Chondroitin Sulfate A (CSA), two glycosaminoglycans which are actually epimers to each other and that are structural constituents of receptors expressed in cell membranes, are the preferred anchorage sites, with a marked preference for DS. Our calculations rationalize this preference from a molecular perspective as follows: when free of the virus, DS has one sulfate group that does not participate in intramolecular strong hydrogen bonds, thus, it is readily available to interact with the envelope protein of the virus (Zika−E), then, after formation of the complexes, Zika−E⋯DS exhibits ten strong salt brides connecting the two fragments against only six salt bridges and two hydrogen bonds in Zika−E⋯CSA. Our results complement the current view of the interaction between the virus and the receptor glycosoaminoglycans revealing that the negatively charged carboxylate groups in CSA and DS are just as important as the sulfates because of the formation of equally strong salt bridges with the positively charged Arginine and Lysine aminoacids in the envelope protein of the virus.

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Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

Cited by 13 publications

References 64 publications

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

Initial Recognition and Attachment of the Zika Virus to Host Cells: A Molecular Dynamics and Quantum Interaction Approach

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