Journal: Journal of Molecular Modeling

Abbreviation

J Mol Model

Publisher

Springer

Journal Volumes

ISSN

1610-2940
0948-5023

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Publications 1 - 5 of 5
  • Homology modeling and dynamics of the extracellular domain of rat and human neuronal nicotinic actylcholoine receptor suptypes α4β2 and α7
    Item type: Journal Article
    Bisson, William H.; Westera, Gerrit; Schubiger, Augustus P.; et al. (2008)
    Journal of Molecular Modeling
  • On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution
    Item type: Journal Article
    Leite, Elisa S.; Santana, Sidney R.; Hünenberger, Philippe H.; et al. (2007)
    Journal of Molecular Modeling
  • Structures and stabilities of naturally occurring cyclodextrins: a theoretical study of symmetrical conformers
    Item type: Journal Article
    Gamboa-Carballo, Juan J.; Rana, Vijay K.; Levalois-Grützmacher, Joëlle; et al. (2017)
    Journal of Molecular Modeling
  • Competitive formation of molecular inclusion complexes of chlordecone and beta-hexachlorocyclohexane with natural cyclodextrins: DFT and molecular dynamics study
    Item type: Journal Article
    Ferino-Pérez, Anthuan; Portorreal, Queiroz; Gamboa Carballo, Juan José; et al. (2023)
    Journal of Molecular Modeling
    Context: Chlordecone (CLD) and beta-hexachlorocyclohexane (beta-HCH) are chlorinated pesticides that coexist as persistent organic pollutants in the groundwater of several countries in the Caribbean, being an environmental issue. This work evaluates theoretically the competitive formation of host-guest complexes pesticides@cyclodextrines (CDs) as an alternative for water purification and selective separation of pesticides. Methods: Quantum mechanical calculations based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were used to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium, and in aqueous solutions. Results: DFT studies showed that interactions of both pesticides with CDs are mediated by steric factors and guided by maximization of the hydrophobic interactions either with the other pesticide or with the CD cavity's inner atoms. MD results corroborate the formation of stable complexes of both pesticides with the studied CDs. alpha-CD exhibited a preference for the smaller beta-HCH molecule over the CLD that could not perturb the formed complex. Conclusions: The simulation of competitive formation with gamma-CD illustrated that this molecule could accommodate both pesticides inside its cavity. These results suggest that CDs with smaller cavity sizes such as alpha-CD could be used for selective separation of beta-HCH from CLD in water bodies, while gamma-CD could be used for methods that aim to remove both pesticides at the same time.
  • De novo design of anticancer peptides by ensemble artificial neural networks
    Item type: Journal Article
    Grisoni, Francesca; Neuhaus, Claudia S.; Hishinuma, Miyabi; et al. (2019)
    Journal of Molecular Modeling
    Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present an ensemble machine learning model to design potent ACPs. Four counter-propagation artificial neural-networks were trained to identify peptides that kill breast and/or lung cancer cells. For prospective application of the ensemble model, we selected 14 peptides from a total of 1000 de novo designs, for synthesis and testing in vitro on breast cancer (MCF7) and lung cancer (A549) cell lines. Six de novo designs showed anticancer activity in vitro, five of which against both MCF7 and A549 cell lines. The novel active peptides populate uncharted regions of ACP sequence space.
Publications 1 - 5 of 5