scholarly journals Chemical Reactivity Properties, Solubilities, and Bioactivity Scores of Some Pigments Derived from Carotenoids of Marine Origin through Conceptual DFT Descriptors

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Carotenoid Pigments ◽  
Density Functionals ◽  
Solvation Model ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors

Five density functionals, CAM-B3LYP, LC-ωHPBE, MN12SX, N12SX, and ωB97XD, in connection with the Def2TZVP basis set were assessed together with the SMD solvation model for the calculation of the molecular properties, chemical reactivities, and solubilities of some pigments derived from astaxanthin, β-cryptoxanthin, fucoxanthin, myxol, siphonaxanthin, siphonein, and zeaxanthin marine carotenoids in the presence of different solvents (hexane, methanol, ethanol, and water). All the chemical reactivity descriptors for the systems were calculated via conceptual density functional theory (CDFT). Finally, the potential bioavailability and druggability as well as the bioactivity scores for the marine carotenoid pigments were predicted through different methodologies already reported in the literature, which have been previously validated during the study of other natural products obtained from marine sources.

scholarly journals Local Molecular Reactivity of the Colored Dansylglycine in Water and Dioxane Studied through Conceptual DFT

2018 ◽  
Vol 2018 ◽  
pp. 1-7
Author(s):  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Solvation Model ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Molecular Reactivity ◽  
Chemical Reactivity Descriptors

This study evaluated a fixed long-range corrected range-separated hybrid (RSH) density functional associated with the Def2TZVP basis set alongside the SMD solvation model for the computation of the structure, molecular properties, and chemical reactivity of the M8 intermediate melanoidin pigment in the presence of water and dioxane. The preference of the active sites pertinent to radical, nucleophilic, and electrophilic attacks is made through linking them with the electrophilic and nucleophilic Parr functions, Fukui function indices, and condensed dual descriptor which are chemical reactivity descriptors that arise from conceptual density functional theory. The study confirmed the results from previous works showing that the MN12SX density functional is the most appropriate in predicting the chemical reactivity of this molecule in both solvents.

scholarly journals A CDFT-Based Computational Peptidology (CDFT-CP) Study of the Chemical Reactivity and Bioactivity of the Marine-Derived Alternaramide Cyclopentadepsipeptide

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Chemical Reactivity ◽  
Therapeutic Drug ◽  
Inhibitory Effects ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors ◽  
And Staphylococcus Aureus

Alternaramide is a cyclic pentadepsipeptide isolated from marine sources that has been shown to present weak antibiotic activity against Bacillus subtilis and Staphylococcus aureus as well as inhibitory effects on inflammatory mediator expressions. Thus, this work reports the results of a computational study of the chemical reactivity and bioactivity properties of this cyclopentadepsipeptide considering a CDFT-based computational peptidology (CDFT-CP) methodology that results from the combination of the chemical reactivity descriptors that arise from conceptual density functional theory (CDFT) together with some cheminformatics tools that can be used to estimate the associated physicochemical parameters, to improve the process of virtual screening through a similarity search, and to identify the ability of the peptide to behave as a potential useful drug, complemented with an analysis of its bioactivity and pharmacokinetics indices related to the ADMET (absorption, distribution, metabolism, excretion, and toxicity) features. The results represent a new confirmation of the superiority of the MN12SX density functional in the fulfilment of the Janak and ionization energy theorems through the proposed KID procedure. This has been useful for the accurate prediction of the CDFT reactivity descriptors that help in understanding the chemical reactivity. The computational pharmacokinetics study revealed the potential ability of alternaramide as a therapeutic drug by interacting with GPCR ligands and protease inhibitors. The ADMET indices confirm this assertion through the absence of toxicity and good absorption and distribution properties.

scholarly journals Chemical Reactivity Properties, pKa Values, AGEs Inhibitor Abilities and Bioactivity Scores of the Mirabamides A–H Peptides of Marine Origin Studied by Means of Conceptual DFT

Marine Drugs ◽  
2018 ◽  
Vol 16 (9) ◽  
pp. 302 ◽  
Author(s):  
Juan Frau ◽  
Norma Flores-Holguín ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Advanced Glycation Endproducts ◽  
Great Accuracy ◽  
Basis Set ◽  
Solvation Model ◽  
Conceptual Density Functional Theory ◽  
Marine Origin ◽  
Reactivity Descriptors

The MN12SX density functional, in connection with the Def2TZVP basis set, was assessed, together with the SMD solvation model (Solvation Model based on the Density), for calculation of the molecular properties and structure of a group of peptides of marine origin named Mirabamides A–H. All the chemical reactivity descriptors for the systems were calculated via Conceptual Density Functional Theory (CDFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks were chosen by linking them with the Fukui function indices, nucleophilic and electrophilic Parr functions, and condensed Dual Descriptor Δ f ( r ) , respectively. Additionally, the p K a values for the different peptides are predicted with great accuracy as well as the ability of the studied molecule in acting as an efficient inhibitor of the formation of Advanced Glycation Endproducts (AGEs), which constitutes a useful knowledge for the development of drugs for fighting Diabetes, Alzheimer and Parkinson diseases. Finally, the bioactivity scores for the Mirabamides A–H are predicted through different methodologies.

scholarly journals Calculation of the Global and Local Conceptual DFT Indices for the Prediction of the Chemical Reactivity Properties of Papuamides A–F Marine Drugs

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3312 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Active Regions ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Global And Local

A well-behaved model chemistry previously validated for the study of the chemical reactivity of peptides was considered for the calculation of the molecular properties and structures of the Papuamide family of marine peptides. A methodology based on Conceptual Density Functional Theory (CDFT) was chosen for the determination of the reactivity descriptors. The molecular active sites were associated with the active regions of the molecules related to the nucleophilic and electrophilic Parr functions. Finally, the drug-likenesses and the bioactivity scores for the Papuamide peptides were predicted through a homology methodology relating them with the calculated reactivity descriptors, while other properties such as the pKas were determined following a methodology developed by our group.

Theoretical study ofFeB35+nN36-n(n = 0, 1) nanocages: Chemical reactivity descriptors

2015 ◽  
Vol 14 (04) ◽  
pp. 1550026 ◽  
Author(s):  
Davood Farmanzadeh ◽  
Hamid Rezainejad
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Chemical Species ◽  
Dft Method ◽  
High Reactivity ◽  
Binding Energies ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
The Density Functional Theory ◽  
Chemical Reactivity Descriptors

In this study, by the density functional theory (DFT) method-based reactivity descriptors, the electronic properties and chemical reactivity of Fe substituted nanocage, FeB35+nN36-n(n = 0, 1), were investigated in gaseous and aqueous phases. The calculated binding energies of Fe atoms revealed that the substituting Fe atom in some locations of nanocage make the system more stable. The calculated global descriptors showed that the substituted Fe remarkably increases the chemical reactivity of B36N36. Also, local descriptors showed that the high reactivity of substituted nanocages is mainly related to Fe atom and these chemical species are more talented for nucleophilic attacks. The results of this work may be useful to investigate the effects of substituted metals in chemical reactivity of BN nanostructures.

scholarly journals CDFT-Based Reactivity Descriptors as a Useful MEDT Chemoinformatics Tool for the Study of the Virotoxin Family of Fungal Peptides

Molecules ◽  
2019 ◽  
Vol 24 (15) ◽  
pp. 2707 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Medicinal Chemistry ◽  
Chemical Reactivity ◽  
Computational Studies ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Toxic Peptides

Virotoxins are monocyclic peptides formed by at least five different compounds: alaviroidin, viroisin, deoxoviroisin, viroidin and deoxovirodin. These are toxic peptides singularly found in Amanita virosa mushrooms. Here we perform computational studies on the structural and electronic conformations of these peptides using the MN12SX/Def2TZVP/H2O chemistry model to investigate their chemical reactivity. CDFT-based descriptors (for Conceptual Density Functional Theory) (e.g., Parr functions and Nucleophilicity) are also considered. At the same time, other properties (e.g., pKas) will be determined and used to study virotoxins solubility and to inform decisions about repurposing these agents in medicinal chemistry.

scholarly journals Chemical-Reactivity Properties, Drug Likeness, and Bioactivity Scores of Seragamides A–F Anticancer Marine Peptides: Conceptual Density Functional Theory Viewpoint

Computation ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 52 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Drug Repurposing ◽  
Chemical Hardness ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors

A methodology based on concepts that arose from Density Functional Theory (CDFT) was chosen for the calculation of global and local reactivity descriptors of the Seragamide family of marine anticancer peptides. Determination of active sites for the molecules was achieved by resorting to some descriptors within Molecular Electron Density Theory (MEDT) such as Fukui functions. The pKas of the six studied peptides were established using a proposed relationship between this property and calculated chemical hardness. The drug likenesses and bioactivity properties of the peptides considered in this study were obtained by resorting to a homology model by comparison with the bioactivity of related molecules in their interaction with different receptors. With the object of analyzing the concept of drug repurposing, a study of potential AGE-inhibition abilities of Seragamides peptides was pursued by comparison with well-known drugs that are already available as pharmaceuticals.

Computational peptidology approach to the study of the chemical reactivity and bioactivity properties of Aspergillipeptide D, a cyclopentapeptide of marine origin

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Chemical Reactivity ◽  
Therapeutic Drug ◽  
Moderate Activity ◽  
Conceptual Density Functional Theory ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors ◽  
Aspergillus Sp

AbstractAspergillipeptide D is a cyclic pentapeptide isolated from the marine gorgonian Melitodes squamata-derived fungus Aspergillus sp. SCSIO 41501 that it has been shown to present moderate activity against herpes virus simplex type 1 (HSV-1). Thus, this paper presents the results of a computational study of this cyclopentapeptide’s chemical reactivity and bioactivity properties using a CDFT-based computational peptidology (CDFT-CP) methodology, which is derived from combining chemical reactivity descriptors derived from Conceptual Density Functional Theory (CDFT) and some Cheminformatics tools which may be used. This results in an improvement of the virtual screening procedure by a similarity search allowing the identification and validation of the known ability of the peptide to act as a possible useful drug. This was followed by an examination of the drug’s bioactivity and pharmacokinetics indices in relation to the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics. The findings provide further evidence of the MN12SX density functional’s superiority in proving the Janak and Ionization Energy theorems using the proposed KID approach. This has proven to be beneficial in accurately predicting CDFT reactivity characteristics, which aid in the understanding of chemical reactivity. The Computational Pharmacokinetics study revealed the potential ability of Aspergillipeptide D as a therapeutic drug through the interaction with different target receptors. The ADMET indices confirm this assertion through the absence of toxicity and good absorption and distribution properties.

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