Virtual Prospection of Marine Cyclopeptides as Therapeutics by Means of Conceptual DFT and Computational ADMET.

Bioactive peptides are chemical compounds created through the covalent bonding of amino acids, known as amide or peptide bonds. Due to their unusual chemistry and various biological effects, marine bioactive peptides have garnered considerable research. The effectiveness of a bioactive marine peptide is attributed to its structural features, such as amino acid content and sequence, which vary depending on the degree of action. Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that render them an attractive modality for the development of therapeutics. The apratoxins are a class of molecules formed by a series of cyclic depsipeptides with potent cytotoxic activities. The objective of this research is to pursue a computational prospection of the molecular structures and properties of several cylopeptides of marine origin with potential therapeutic applications. The methodology will be based on the determination of the chemical reactivity descriptors of the studied molecules through the consideration of the Conceptual DFT model and validation of a particular model chemistry, MN12SX/Def2TZVP/H2O. These studies will be complemented by a determination of the pharmacokinetics and ADMET parameters by resorting to certain cheminformatics tools.

Conceptual DFT-Based Computational Peptidology of Marine Natural Compounds: Discodermins A-H.

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.

Calculation of the Global and Local Conceptual DFT Indices for the Prediction of the Chemical Reactivity Properties of Papuamides A-F Marine Drugs.

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.

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

Global and local charge transfer in electron donor-acceptor complexes.

The formation of electron donor-acceptor complexes is studied with global and local charge transfer partitionings. The 1-parabola model is applied to the bromination reaction of alkenes and the correlations found between the global and local charge transferred with the transition energy of the charge transfer bands and the kinetic rate constants indicate that the nucleophilic attack of alkenes to bromine is the electronic process controlling the reactivity in the formation of the electron donor-acceptor complexes in this reaction. The 2-parabolas model is used in studying the nitrosation of aromatic compounds where colorful electron donor-acceptor complexes are formed. In this case, and like previous applications of the 2-parabolas model, the consistent usage of the model mandates the explicit consideration of reaction conditions in preparing the reactants to have a direction of electron transfer that is consistent with the chemical potential differences. For the nitrosation reaction this implies considering the nitrosonium cation as the charge acceptor. Both applications support that the charge transferred predicted from chemical reactivity models can be used as a scale to measure the nucleophilicity in reactivity trends. Graphical Abstract ᅟ.