Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations.

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Chemical reactivity of graphene doped with 3d transition metals: nothing compares to a single vacancy.

CONTEXT: Finding catalysts that do not rely on the use of expensive metals is one of the requirements to achieve sustainable production. The reactivity of graphene doped with 3d transition metals was studied. All dopants enhanced the reactivity of graphene and performed better than Stone-Wales defects and divacancies, but were inferior to monovacancies. For hydrogenation of doped-monovacancies, Sc, Ti, Cr, Co, and Ni induced more prominent reactivity on the carbon atoms. However, the metals were the most reactive center for V, Mn, and Fe-doped graphene. Cu and Zn turned the four neighboring carbon atoms into the preferred sites for hydrogenation. The addition of oxygen to doped graphene with Ti, V, Cr, Mn, Fe, Co, and Ni on a monovacancy revealed a more uniform pattern since the metal, preferred to react with oxygen. However, Sc induced a larger reactivity on the carbon atoms. The affinity of the 3d metal-doped graphene systems towards oxygen was inferior to that observed for single-vacancies. Therefore, vacancy engineering is the most favorable and least expensive method to enhance the reactivity of graphene. METHODS: We applied Truhlar's M06-L method accompanied by the 6-31G* basis sets to perform periodic boundary conditions calculations as implemented in Gaussian 09. The ultrafine grid was employed and the unit cells were sampled employing 100 k-points. Results were visualized employing Gaussview 5.0.1.

Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator.

The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general-purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz-Singh-Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions.

Marine Toxins as Pharmaceutical Treasure Troves: A Focus on Saxitoxin Derivatives from a Computational Point of View.

This work highlights the significant potential of marine toxins, particularly saxitoxin (STX) and its derivatives, in the exploration of novel pharmaceuticals. These toxins, produced by aquatic microorganisms and collected by bivalve mollusks and other filter-feeding organisms, offer a vast reservoir of chemical and biological diversity. They interact with sodium channels in physiological processes, affecting various functions in organisms. Exposure to these toxins can lead to symptoms ranging from tingling sensations to respiratory failure and cardiovascular shock, with STX being one of the most potent. The structural diversity of STX derivatives, categorized into carbamate, N-sulfocarbamoyl, decarbamoyl, and deoxydecarbamoyl toxins, offers potential for drug development. The research described in this work aimed to computationally characterize 18 STX derivatives, exploring their reactivity properties within marine sponges using conceptual density functional theory (CDFT) techniques. Additionally, their pharmacokinetic properties, bioavailability, and drug-likeness scores were assessed. The outcomes of this research were the chemical reactivity parameters calculated via CDFT as well as the estimated pharmacokinetic and ADME properties derived using computational tools. While they may not align directly, the integration of these distinct datasets enriches our comprehensive understanding of the compound's properties and potential applications. Thus, this study holds promise for uncovering new pharmaceutical candidates from the considered marine toxins.

Exploring marine toxins: comparative analysis of chemical reactivity properties and potential for drug discovery.

Marine toxins, produced by various marine microorganisms, pose significant risks to both marine ecosystems and human health. Understanding their diverse structures and properties is crucial for effective mitigation and exploration of their potential as therapeutic agents. This study presents a comparative analysis of two hydrophilic and two lipophilic marine toxins, examining their reactivity properties and bioavailability scores. By investigating similarities among these structurally diverse toxins, valuable insights into their potential as precursors for novel drug development can be gained. The exploration of lipophilic and hydrophilic properties in drug design is essential due to their distinct implications on drug distribution, elimination, and target interaction. By elucidating shared molecular properties among toxins, this research aims to identify patterns and trends that may guide future drug discovery efforts and contribute to the field of molecular toxinology. The findings from this study have the potential to expand knowledge on toxins, facilitate a deeper understanding of their bioactivities, and unlock new therapeutic possibilities to address unmet biomedical needs. The results showcased similarities among the studied systems, while also highlighting the exceptional attributes of Domoic Acid (DA) in terms of its interaction capabilities and stability.

Computational Discovery of Marine Molecules of the Cyclopeptide Family with Therapeutic Potential.

Stellatolides are natural compounds that have shown promising biological activities, including antitumor, antimicrobial, and anti-inflammatory properties, making them potential candidates for drug development. Chemical Reactivity Theory (CRT) is a branch of chemistry that explains and predicts the behavior of chemical reactions based on the electronic structure of molecules. Conceptual Density Functional Theory (CDFT) and Computational Peptidology (CP) are computational approaches used to study the behavior of atoms, molecules, and peptides. In this study, we present the results of our investigation of the chemical reactivity and ADMET properties of Stellatolides A-H using a novel computational approach called Conceptual DFT-based Computational Peptidology (CDFT-CP). Our study uses CDFT and CP to predict the reactivity and stability of molecules and to understand the behavior of peptides at the molecular level. We also predict the ADMET properties of the Stellatolides A-H to provide insight into their effectiveness, potential side effects, and optimal dosage and route of administration, as well as their biological targets. This study sheds light on the potential of Stellatolides A-H as promising candidates for drug development and highlights the potential of CDFT-CP for the study of other natural compounds and peptides.

Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors.

Background: A coronavirus identified in 2019, SARS- CoV- 2, has caused a pandemic of respiratory illness, called COVID- 19. Most people with COVID-19 experience mild to moderate symptoms and recover without the need for special treatments. The SARS­CoV­2 RNA­dependent RNA polymerase (RdRp) plays a crucial role in the viral life cycle. The active site of the RdRp is a very accessible region, so targeting this region to study the inhibition of viral replication may be an effective therapeutic approach. For this reason, this study has selected and analysed a series of ligands used as SARS-CoV-2 virus inhibitors, namely: the Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir and Zalcitabine. Methods: These ligands were analyzed using molecular docking, Receptor-Based Pharmacophore Modelling. On the other hand, these outcomes were supported with chemical reactivity indices defined within a conceptual density functional theory framework. Results: The results show the conformations with the highest root-mean-square deviation (RMSD), have π-π stacking interaction with residue LEU141, GLN189, GLU166 and GLY143, HIE41, among others. Also was development an electrostatic potential comparison using the global and local reactivity indices. Conclusions: These studies allow the identification of the main stabilizing interactions using the crystal structure of SARS­CoV­2 RNA­dependent RNA polymerase. In this order of ideas, this study provides new insights into these ligands that can be used in the design of new COVID-19 treatments. The studies allowed us to find an explanation supported in the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.

Conceptual DFT, QTAIM, and Molecular Docking Approaches to Characterize the T-Type Calcium Channel Blocker Anandamide.

The anandamide is a relevant ligand due to its capacity of interacting with several proteins, including the T-type calcium channels, which play an important role in neuropathic pain and depression disorders. Hence, a detailed characterization of the chemical properties and conformational stability of anandamide may provide valuable information to understand its behavior in a biological context. Herein, conceptual DFT and QTAIM analyses were performed to theoretically characterize the chemical reactivity properties and the structural stability of conformations of anandamide, using the BP86/cc-pVTZ level of theory. Global reactivity description, based on conceptual DFT, indicates that the hardness increases and the electrophilicity index decreases for both, the hairpin and U-shape conformers relative to the extended conformers. Also, an increase in the chemical potential value and a decrease in the electronegativity and the electrophilicity index is observed in the ethanolamide open ring conformers in comparison with the corresponding closed ring structures. In addition, regarding the characterization of local reactivity descriptors, the maximum values of the Fukui and Parr functions indicate that the most probable location for a nucleophilic attack is either the hydroxyl oxygen located in the ethanolamide closed ring conformers or the carbonyl oxygen present in the open ring conformers. The most probable location for an electrophilic attack is in the alkyl double bond region in all anandamide conformers. According to the QTAIM results, the intramolecular hydrogen bond formation stabilizing the structure of anandamide has interaction energy values for the closed ring conformations of 12.33-12.46 kcal mol-1, indicating a strong interaction. Lastly, molecular docking calculations determined that a region in the pore, denominate as pore-blocking, is a probable site for the interaction of anandamide with the human Cav3.2 isoform of the T-type calcium channel family. The pore-blocking site contains hydrophobic residues where the non-polar part in the final alkyl region of anandamide established mainly alkyl-alkyl interactions, while the polar part (the ethanolamide group) interacts with the polar residue S900. The information based on conceptual DFT presented may aid in the design of drugs with similar chemical characteristics as those identified in anandamide so as to bind anandamide-interacting proteins, including the T-type calcium channels.

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.

Revisiting the hydroxylation phenomenon of SiO2: a study through "hard-hard" and "soft-soft" interactions.

Surface hydroxylation has been extensively studied over the years for a variety of applications, and studies involving hydroxylation of different silica surfaces are still carried out due to the interesting properties obtained from those modified surfaces. Although a number of theoretical studies have been employed to evaluate details on the hydroxylation phenomenon on silica (SiO2) surfaces, most of these studies are based on computationally expensive models commonly based on extended systems. In order to circumvent such an aspect, here we present a low-cost theoretical study on the SiO2 hydroxylation process aiming to evaluate aspects associated with water-SiO2 interaction. Details about local reactivity, chemical softness, and electrostatic potential were evaluated for SiO2 model substrates in the framework of the density functional theory (DFT) using a molecular approach. The obtained results from this new and promising approach were validated and complemented by fully atomistic reactive molecular dynamics (FARMD) simulations. Furthermore, the implemented approach proves to be a powerful tool that is not restricted to the study of hydroxylation, opening a promising route for low computational cost to analyze passivation and anchoring processes on a variety of oxide surfaces.

Exploring the maximum Fukui function sites with the frontier-controlled soft-soft reactions using 1,3-dipolar cycloaddition reactions of nitrilium betaines.

According to P.K. Chattaraj. J Phys Chem A 2001, 105, 511-513 "the maximum Fukui function site is the best for the frontier-controlled soft-soft reactions whereas for the charge-controlled hard-hard interactions the preferred site is associated with the maximum net charge and not necessarily the minimum Fukui function". Taking into account these outcomes in this research is explored this reactivity scheme using in first case the reaction between fulminic acid with ethylene (reference reaction), after is varying the dipolarophile in the reaction between fulminic acid with acetylene, and finally is varying the dipole in the reaction between formonitrile imine with ethylene. These results allow study parameter such as charge transfer, polarizability, covalent character on bonding, among other; also shown the preference by the sf- / sf+ interactions in the transition state on the sf- / sf- interactions. On the other hand, these results also were justified using net electrophilicity which is defined as the electrophilic power of a system relative to its own nucleophilic power.

Theoretical Study of the Structural Stability, Chemical Reactivity, and Protein Interaction for NMP Compounds as Modulators of the Endocannabinoid System.

The cannabinoid receptors (CB1/CB2) and the T-type calcium channels are involved in disorders associated with both physiological pain and depressive behaviors. Valuable pharmacological species carbazole derivatives such as the NMP-4, NMP-7, and NMP-181 (Neuro Molecular Production) regulate both biological entities. In this work, DFT calculations were performed to characterize theoretically their structural and chemical reactivity properties using the BP86/cc-pVTZ level of theory. The molecular orbital contributions and the chemical reactivity analysis reveal that a major participation of the carbazole group is in the donor-acceptor interactions of the NMP compounds. The DFT analysis on the NMP compounds provides insights into the relevant functional groups involved during the ligand-receptor interactions. Molecular docking analysis is used to reveal possible sites of interaction of the NMP compounds with the Cav3.2 calcium channel. The interaction energy values and reported experimental evidence indicate that the site denominated as "Pore-blocking", which is formed mainly by hydrophobic residues and the T586 residue, is a probable binding site for the NMP compounds.

Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule.

This paper presents a brief summary of the difficulty that resides in the definition of the elusive concept of local chemical hardness. We argue that a definition of local hardness should be useful to a reactivity principle and not just as a mere definition. We then continue with a formal discussion about the benefits and difficulties of using the Fukui potential, which is interpreted as an alchemical derivative (alchemical hardness), as descriptor of local hardness of molecules. Computational evidence shows that the alchemical hardness is at least as good a descriptor as the combination of other two well-stabilized descriptors of local hardness, such as the Fukui function and grand canonical local hardness. Although our results are auspicious for the alchemical hardness as descriptor of local hardness, we finish by calling the attention of the community on the importance of discussing the raison d'être of a local hardness function and its main characteristics. We suggest that an axiomatic construction of local hardness could be they way of constructing a local hardness which is both useful and free of arbitrariness.

Reactivity of Aliphatic and Phenolic Hydroxyl Groups in Kraft Lignin towards 4,4' MDI.

Several efforts have been dedicated to the development of lignin-based polyurethanes (PU) in recent years. The low and heterogeneous reactivity of lignin hydroxyl groups towards diisocyanates, arising from their highly complex chemical structure, limits the application of this biopolymer in PU synthesis. Besides the well-known differences in the reactivity of aliphatic and aromatic hydroxyl groups, experimental work in which the reactivity of both types of hydroxyl, especially the aromatic ones present in syringyl (S-unit), guaiacyl (G-unit), and p-hydroxyphenyl (H-unit) building units are considered and compared, is still lacking in the literature. In this work, the hydroxyl reactivity of two kraft lignin grades towards 4,4'-diphenylmethane diisocyanate (MDI) was investigated. 31P NMR allowed the monitoring of the reactivity of each hydroxyl group in the lignin structure. FTIR spectra revealed the evolution of peaks related to hydroxyl consumption and urethane formation. These results might support new PU developments, including the use of unmodified lignin and the synthesis of MDI-functionalized biopolymers or prepolymers.

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.

Influence on the reactivity properties of the substitution by different halogens on the conjugated backbone of the 1,3,5-triaryl-2-pyrazoline skeleton in relation to the increasing alkyloxy chain length: a conceptual density functional theory study.

A series of non-substituted 1,3,5-triaryl-2-pyrazolines and pyrazolines substituted with Fluoro (-F), Chloro (-Cl) and Bromo (-Br) groups at the 3-aryl position were studied. All calculations were done using the conceptual framework of density functional theory. The geometries and reactivity properties were analyzed according to an increase from one to twelve alkyl units in the 5-aryl of 2-pyrazoline ring. In order to be able to apply the particular methodology named KID procedure (for Koopmans in DFT), the KID descriptors were calculated and the results showed that the use of this approximation (Koopmans' theorem in DFT studies) is feasible. The results for the geometries determined that the increase of the chain with alkyl units does not affect the geometry of the systems. However, the solvation energy also calculated is affected by this increase in the allyl chain length. Due to this, as the chains increases, the solubility of the molecular systems diminishes. The chemical reactivity properties were determined by calculating the descriptors that arise from conceptual DFT and it could be demonstrated that they are not affected by the chain growth. Slight differences were found due to the different halogen substitutions. Finally, it could be observed that all the pyrazolines present an important electrophilic behavior. Graphical Abstract Properties changes in relation to the increasing alkyloxy chain length and halogens presence.

Adenosine Derivates as Antioxidant Agents: Synthesis, Characterization, in Vitro Activity, and Theoretical Insights.

In this work, we present results about the synthesis and the antioxidant properties of seven adenosine derivatives. Four of these compounds were synthesized by substituting the N6-position of adenosine with aliphatic amines, and three were obtained by modification of the ribose ring. All compounds were obtained in pure form using column chromatography, and their structures were elucidated by infrared spectroscopy (IR) and Nuclear Magnetic Resonance (NMR). All adenosine derivatives were further evaluated in vitro as free radical scavengers. Our results show that compounds 1c, 3, and 5 display a potent antioxidant effect compared with the reference compound ascorbic acid. In addition, the absorption, distribution, metabolism and excretion (ADME) calculations show favorable pharmacokinetic parameters for the set of compounds analyzed, which guarantees their suitability as potential antioxidant drugs. Furthermore, theoretical analyses using Molecular Quantum Similarity and reactivity indices were performed in order to discriminate the different reactive sites involved in oxidative processes.

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.