scholarly journals Conceptual DFT-Based Computational Peptidology of Marine Natural Compounds: Discodermins A–H

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4158
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Homology Model ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Qsar Studies ◽  
Biological Targets

A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A–H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kinds of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity, some parameters of usefulness for future QSAR studies, their predicted biological targets, and the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A–H pharmacokinetics are also reported.

scholarly journals Conceptual DFT-based Computational Peptidology of Marine Natural Compounds: Discodermins A–H

2020 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Homology Model ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Qsar Studies ◽  
Biological Targets

A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A-H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kind of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A-H pharmacokinetics are also reported.

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.

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.

Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors

2015 ◽  
pp. 123-179 ◽  
Author(s):  
Sudip Pan ◽  
Ashutosh Gupta ◽  
Venkatesan Subramanian ◽  
Pratim K. Chattaraj
Keyword(s):  
Density Functional Theory ◽  
Biological Activity ◽  
Density Functional ◽  
Successful Implementation ◽  
Quantitative Structure ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Structure Activity ◽  
Regular Change

Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.

scholarly journals Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors

2017 ◽  
pp. 1517-1572 ◽  
Author(s):  
Sudip Pan ◽  
Ashutosh Kumar Gupta ◽  
Venkatesan Subramanian ◽  
Pratim K. Chattaraj
Keyword(s):  
Density Functional Theory ◽  
Biological Activity ◽  
Density Functional ◽  
Successful Implementation ◽  
Quantitative Structure ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Structure Activity ◽  
Regular Change

Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.

scholarly journals In Silico Pharmacokinetics, ADMET Study and Conceptual DFT Analysis of Two Plant Cyclopeptides Isolated From Rosaceae as a Computational Peptidology Approach

2021 ◽  
Vol 9 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Local Descriptors ◽  
Molecular Systems ◽  
Biological Targets ◽  
Global And Local

This research presents the outcomes of a computational determination of the chemical reactivity and bioactivity properties of two plant cyclopeptides isolated from Rosaceae through the consideration of Computational Peptidology (CP), a protocol employed previously in the research of similar molecular systems. CP allows the prediction of the global and local descriptors that are the integral foundations of Conceptual Density Functional Theory (CDFT) and which could help in getting in the understanding of the chemical reactivity properties of the two plant cyclopeptides under study, hoping that they could be related to their bioactivity. The methodology based on the Koopmans in DFT (KID) approach and the MN12SX/Def2TZVP/H2O model chemistry has been successfully validated. Various Chemoinformatics tools have been used to improve the process of virtual screening, thus identifying some additional properties of these two plant cyclopeptides connected to their ability to behave as potentially useful drugs. With the further objective of analyzing their bioactivity, the CP protocol is complemented with the estimation of some useful parameters related to pharmacokinetics, their predicted biological targets, and the Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) parameters related to the bioavailability of the two plant cyclopeptides under study are also reported.

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 Conceptual density functional theory based electronic structure principles

2021 ◽  
Author(s):  
Debdutta Chakraborty ◽  
Pratim Kumar Chattaraj
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Review Article ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Reactivity Descriptors

In this review article, we intend to highlight the basic electronic structure principles and various reactivity descriptors as defined within the premise of conceptual density functional theory (CDFT).

Solvent effect on the Molecular structure and Global, Local and Dual Descriptors: A Density Functional Theory Study

2021 ◽  
pp. 305-315
Author(s):  
Faiza Lehraki ◽  
Nadjib Melkemi
Keyword(s):  
Density Functional Theory ◽  
Dipole Moment ◽  
Density Functional ◽  
Basis Set ◽  
Frontier Molecular Orbital ◽  
Nucleophilic Attack ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Polarized Continuum Model

This study aims to explore the effects of solvent polarity on the geometry, energy of solvation, dipole moment, polarizability, charge distribution, frontier molecular orbital analysis, and global, local, and dual descriptors for β Carboline. The effects of eight solvents were treated using a conductor-like polarized continuum model. Density Functional Theory calculations were performed at B3LYP level at 6-311++g (d,p) basis set. The computed results showed that the dipole moment, polarizability, the solvation free energy, and atomic charge of β Carboline increased with the increasing polarity of the solvent. Also, the solvation modified the values of the reactivity descriptors as a result of the interaction between the solvent and β Carboline. The dual descriptor provided a clearer difference between electrophilic and nucleophilic attack at specific atomic site than presented by Fukui functions of β Carboline.

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