Conceptual DFT study of the local chemical reactivity of the dilysyldipyrrolones A and B intermediate melanoidins

Talarolide A and Talaropeptides A-D: Potential Marine-Derived Therapeutic Peptides with Interesting Chemistry and Biological Activity Studied through Density Functional Theory (DFT) and Conceptual DFT

Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The molecular geometry optimizations and frequency calculations were conducted using the Density Functional Tight Binding (DFTBA) method. This was followed by a subsequent round of geometry optimization, frequency analysis, and computation of electronic properties and chemical reactivity descriptors. We employed the MN12SX/Def2TZVP/H2O model chemistry, utilizing the Gaussian 16 program and the SMD solvation model. The analysis of the global reactivity descriptors arising from CDFT was achieved as well as the graphical comparison of the dual descriptor DD revealing the areas of the molecules with more propensity to suffer a nucleophilic or electrophilic attack. Additionally, Molinspiration and SwissTargetPrediction were considered for the calculation of molecular characteristics and predicted biological targets. These include enzymes, nuclear receptors, kinase inhibitors, GPCR ligands, and ion channel modulators. The graphical results show that Talarolide A and the Talaropeptides A-D are likely to behave as protease inhibitors.

1,3 Dipolar Cycloaddition of Münchnones: Factors behind the Regioselectivity

The 1,3 dipolar cycloaddition reactions of münchnones and alkenes provide an expedite synthetic way to substituted pyrroles, an exceedingly important structural motif in the pharmaceutical and material science fields of research. The factors governing their regioselectivity rationalization are not well understood. Using several approaches, we investigate a set of 14 reactions (featuring two münchnones, 12 different alkenes, and two alkynes). The Natural Bond Theory and the Non-Covalent Interaction Index analyses of the noncovalent interaction energies fail to predict the experimental major regioisomer. Employing global cDFT descriptors or local ones such as the Fukui function and dual descriptor yields similarly inaccurate predictions. Only the local softness pairing, within Pearson's Hard and Soft Acids and Bases principle, constitutes a reliable predictor for the major reaction product. By taking into account an estimator for the steric effects, the correct regioisomer is predicted. Steric effects play a major role in driving the regioselectivity, as was corroborated by energy decomposition analysis of the transition states.

Application of the oxycodone templated molecular imprinted polymer in adsorption of the drug from human blood plasma as the real biological environment; a joint experimental and density functional theory study

In this project, we have synthesized and used a molecular imprinted polymer (MIP) for adsorption of oxycodone residue from the biological samples. Indeed, this study aims to develop a suitable method for determination of oxycodone drug residue in the human plasma using the common analysis methods. Therefore, the MIP was used for the solid phase extraction (MIP-SPE) approach in order to collect the oxycodone opioid and to concentrate it in the blood plasma samples. The extraction parameters such as adsorption time, pH, and the amount of sorbent in blood plasma were optimized and the capacity of loading amount (LA) for adsorbing it was determined. Moreover, a high performance liquid chromatography (HPLC)-UV detector method was validated and used for analyzing of the mentioned opioid extracted from plasma. The results showed that the limit of detection (LOD), and the limit of quantization (LOQ) for the developed MIP-SPE method were 1.24 ppb, and 3.76 ppb, respectively. Moreover, both of the MIP-, and non-imprinted polymers (NIP)-drug complexes were designed and were then optimized by the density functional theory (DFT) method. The results showed that the theoretical calculations supported the experimental data, confirming the favorability of adsorption of the drug by MIP compared to NIP.

Elbehairi S, Achar RR, Silina E, Stupin V, Manturova N, Glossman-Mitnik D, Shivamallu C, Kollur SP. Anticholinesterase activity of Areca Catechu: In Vitro and in silico green synthesis approach in search for therapeutic agents against Alzheimer's disease

For many years, the primary focus has been on finding effective treatments for Alzheimer's disease (AD), which has led to the identification of promising therapeutic targets. The necessity for AD stage-dependent optimal settings necessitated a herbal therapy strategy. The plant species Areca Catechu L. (AC) was selected based on the traditional uses against CNS-related diseases. AC leaf extract were prepared using a Soxhlet extraction method and hydroxyapatite nanoparticles (HAp-NPs) were synthesized from the same (AC-HAp-NPs). Powder X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED) and fourier transform infrared spectroscopy (FTIR) were used to confirm the structure and morphology of the as-prepared AC-HAp-NPs. The crystalline character of the AC-HAp-NPs was visible in the XRD pattern. The synthesized material was found to be nanoflake, with an average diameter of 15-20 nm, according to SEM analysis. The TEM and SAED pictures also revealed the form and size of AC-HAp-NPs. In vitro anti-acetylcholinesterase and butyrylcholinesterase (AChE and BChE) activities of hydroxyapatite nanoparticles produced from an AC leaf extract was tested in this study. When compared to control, AC-HAp-NPs had higher anti-AChE and BChE activity. The anti-acetylcholinesterase action of phytoconstituents generated from AC leaf extract was mediated by 4AQD and 4EY7, according to a mechanistic study conducted utilizing in silico research. The global and local descriptors, which are the underpinnings of Conceptual Density Functional Theory (CDFT), have been predicted through the MN12SX/Def2TZVP/H2O model chemistry to help in the comprehension of the chemical reactivity properties of the five ligands considered in this study. The CDFT experiments are supplemented by the calculation of several useful calculated pharmacokinetics indices, their expected biological targets connected to the bioavailability of the five ligands in order to further the goal of studying their bioactivity.

Virtual Screening for Potential Phytobioactives as Therapeutic Leads to Inhibit NQO1 for Selective Anticancer Therapy

NAD(P)H:quinone acceptor oxidoreductase-1 (NQO1) is a ubiquitous flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory two-electron reductions of quinones, quinonimines, nitroaromatics, and azo dyes. NQO1 is a multifunctional antioxidant enzyme whose expression and deletion are linked to reduced and increased oxidative stress susceptibilities. NQO1 acts as both a tumor suppressor and tumor promoter; thus, the inhibition of NQO1 results in less tumor burden. In addition, the high expression of NQO1 is associated with a shorter survival time of cancer patients. Inhibiting NQO1 also enables certain anticancer agents to evade the detoxification process. In this study, a series of phytobioactives were screened based on their chemical classes such as coumarins, flavonoids, and triterpenoids for their action on NQO1. The in silico evaluations were conducted using PyRx virtual screening tools, where the flavone compound, Orientin showed a better binding affinity score of -8.18 when compared with standard inhibitor Dicumarol with favorable ADME properties. An MD simulation study found that the Orientin binding to NQO1 away from the substrate-binding site induces a potential conformational change in the substrate-binding site, thereby inhibiting substrate accessibility towards the FAD-binding domain. Furthermore, with this computational approach we are offering a scope for validation of the new therapeutic components for their in vitro and in vivo efficacy against NQO1.

Computational Pharmacokinetics Report, ADMET Study and Conceptual DFT-Based Estimation of the Chemical Reactivity Properties of Marine Cyclopeptides

Homophymines A-E and A1-E1 are bioactive natural cyclodepsipeptides with a complex molecular architecture. These molecules could have a potential use as antimicrobial, antiviral, and anticancer substances. We have carried out a computational study of the properties of this family of marine peptides using 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 cheminformatics tools. The latter can be used to estimate the associated physicochemical parameters and to improve the process of virtual screening through a similarity search. Using this approach, the ability of the peptides to behave as a potentially useful drugs can be investigated. An analysis of their bioactivity and pharmacokinetics indices related to the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) features has also been carried out.

Chemical reactivity and binding interactions in ribonucleic acid-peptide complexes

The covalent and noncovalent backbone binding interactions in RNA-peptide complexes were studied by DFT methods. Four RNA structures R1(GGCUAGCC), R2(AAUCGAUU), R3(GGGAUCCC), and R4(AAAGCUUU) has been selected for eight protonated peptides (DR, ER, GR, KR, NGR, RR, tmeGnd (tme), and VR) interactions based on an experimental study (Anal Chem. 2019; 91:1659-1664). Chemical reactivity theory is used to study the reactivity of eight peptides with global descriptors. Lower hardness values reflected low stability and high reactivity for the protonated peptides. DR, ER, GR, KR, NGR, RR, and VR show lower value of ω, μ while tme has high value of ω, μ. Larger highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap for ER, GR, and KR showed greater structural stability for peptides. AutoDock and PatchDock results indicated that R1, R2, and R4 retain hairpin structures while interacting with peptide complexes. The calculated binding energies of (R1-R4)-peptide complexes from AutoDock tools are (1.49-11.12) kcal/mol. Results showed that the noncovalent interactions are stronger than the covalent interactions for R1-peptide complexes. The reason might be the transfer of proton from protonated ligand to deprotonated RNA, which has initiated the loss of the ligand. Also it has been observed that proton transfer has become energetically unfavorable in presence of additional hydrogen bonds which is predicted in the experimental results.

Synthesis, Computational Pharmacokinetics Report, Conceptual DFT-Based Calculations and Anti-Acetylcholinesterase Activity of Hydroxyapatite Nanoparticles Derived From Acorus Calamus Plant Extract

Over the years, Alzheimer's disease (AD) treatments have been a major focus, culminating in the identification of promising therapeutic targets. A herbal therapy approach has been required by the demand of AD stage-dependent optimal settings. Present study describes the evaluation of anti-acetylcholinesterase (AChE) activity of hydroxyapatite nanoparticles derived from an Acorus calamus rhizome extract (AC-HAp NPs). The structure and morphology of as-prepared (AC-HAp NPs) was confirmed using powder X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HR-TEM). The crystalline nature of as-prepared AC-HAp NPs was evident from XRD pattern. The SEM analysis suggested the spherical nature of the synthesized material with an average diameter between 30 and 50 nm. Further, the TEM and HR-TEM images revealed the shape and size of as-prepared (AC-HAp NPs). The interplanar distance between two lattice fringes was found to be 0.342 nm, which further supported the crystalline nature of the material synthesized. The anti-acetylcholinesterase activity of AC-HAp NPs was greater as compared to that of pure HAp NPs. The mechanistic evaluation of such an activity carried out using in silico studies suggested that the anti-acetylcholinesterase activity of phytoconstituents derived from Acorus calamus rhizome extract was mediated by BNDF, APOE4, PKC-γ, BACE1 and γ-secretase proteins. The global and local descriptors, which are the underpinnings of Conceptual Density Functional Theory (CDFT), have been predicted through the MN12SX/Def2TZVP/H2O model chemistry to help in the comprehension of the chemical reactivity properties of the five ligands considered in this study. With the further objective of analyzing their bioactivity, the CDFT studies are complemented with the estimation of some useful computed pharmacokinetics indices, their predicted biological targets, and the ADMET parameters related to the bioavailability of the five ligands are also reported.

Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments

The physicochemical and antioxidant properties of seven carotenoids: antheraxanthin, β-carotene, neoxanthin, peridinin, violaxanthin, xanthrophyll and zeaxanthin were studied by theoretical means. Then the Optoelectronic properties and interaction of chlorophyll-carotenoid complexes are analysed by TDDFT and IGMPLOT. Global reactivity descriptors for carotenoids and chlorophyll (Chla, Chlb) are calculated via conceptual density functional theory (CDFT). The higher HOMO-LUMO (HL) gap indicated structural stability of carotenoid, chlorophyll and chlorophyll-carotenoid complexes. The chemical hardness for carotenoids and Chlorophyll is found to be lower in the solvent medium than in the gas phase. Results showed that carotenoids can be used as good reactive nucleophile due to lower µ and ω. As proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs), it is anticipated that direct antioxidant activity in these carotenoids is mainly due to the sequential proton loss electron transfer (SPLET) mechanism with dominant solvent effects. Also lower PAs of carotenoid suggest that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivities to transfer protons. Reaction rate constant with Transition-State Theory (TST) were estimated for carotenoid-Chlorophyll complexes in gas phase. Time dependent Density Functional Theory (TDDFT) showed that all the chlorophyll (Chla, Chlb)-carotenoid complexes show absorption wavelength in the visible region. The lower S1-T1 adiabatic energy gap indicated ISC transition from S1 to T1 state.

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

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.

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

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.

Investigation of Antifungal Properties of Synthetic Dimethyl-4-Bromo-1-(Substituted Benzoyl) Pyrrolo[1,2-a] Quinoline-2,3-Dicarboxylates Analogues: Molecular Docking Studies and Conceptual DFT-Based Chemical Reactivity Descriptors and Pharmacokinetics Evaluation

Candida albicans, an opportunistic fungal pathogen, frequently colonizes immune-compromised patients and causes mild to severe systemic reactions. Only few antifungal drugs are currently in use for therapeutic treatment. However, evolution of a drug-resistant C. albicans fungal pathogen is of major concern in the treatment of patients, hence the clinical need for novel drug design and development. In this study, in vitro screening of novel putative pyrrolo[1,2-a]quinoline derivatives as the lead drug targets and in silico prediction of the binding potential of these lead molecules against C. albicans pathogenic proteins, such as secreted aspartic protease 3 (SAP3; 2H6T), surface protein β-glucanase (3N9K) and sterol 14-alpha demethylase (5TZ1), were carried out by molecular docking analyses. Further, biological activity-based QSAR and theoretical pharmacokinetic analysis were analyzed. Here, in vitro screening of novel analogue derivatives as drug targets against C. albicans showed inhibitory potential in the concentration of 0.4 µg for BQ-06, 07 and 08, 0.8 µg for BQ-01, 03, and 05, 1.6 µg for BQ-04 and 12.5 µg for BQ-02 in comparison to the standard antifungal drug fluconazole in the concentration of 30 µg. Further, in silico analysis of BQ-01, 03, 05 and 07 analogues docked on chimeric 2H6T, 3N9K and 5TZ1 revealed that these analogues show potential binding affinity, which is different from the therapeutic antifungal drug fluconazole. In addition, these molecules possess good drug-like properties based on the determination of conceptual Density Functional Theory (DFT)-based descriptors, QSAR and pharmacokinetics. Thus, the study offers significant insight into employing pyrrolo[1,2-a]quinoline analogues as novel antifungal agents against C. albicans that warrants further investigation.

Tuning the transition barrier of H2 dissociation in the hydrogenation of CO2 to formic acid on Ti-doped Sn2O4 clusters

Schematic representation of Ti-doping on a pure Sn₂O₄ cluster for the hydrogenation of CO₂ to HCOOH via a hydride pathway.

Preparation, Spectroscopic Characterization, Theoretical Investigations, and In Vitro Anticancer Activity of Cd(II), Ni(II), Zn(II), and Cu(II) Complexes of 4(3H)-Quinazolinone-Derived Schiff Base

Herein, we report the synthesis and characterization of a new Schiff base ligand 3-[[(E)-(3-hydroxyphenyl)-methylidene]amino]-2-methyl-quinazolin-4(3H)-one (HAMQ) and its Cd(II), Ni(II), Zn(II), and Cu(II) complexes (C₁–C₄). The ligand HAMQ was synthesized by reacting 3-hydroxybenzaldehyde and 3-amino-2-methyl-4(3H)-quinazolinone in a 1:1 molar ratio. The structure of the ligand and its complexes (C₁–C₄) were evaluated using ultraviolet (UV)–visible (Vis) light spectroscopy, ¹H-NMR, Fourier-transform infrared (FT-IR) spectroscopy, MS, elemental analysis, conductance data, and thermogravimetric analysis (TGA). The characterization results suggested that the bidentate ligand, HAMQ, coordinated to the metal center through the lactum oxygen and the azomethine nitrogen. Moreover, all the metal complexes were analyzed using powder X-ray diffraction studies, which revealed that all of them belong to a triclinic crystal system. The research was supplemented by density functional theory (DFT) studies on the IR and UV–Vis spectra, as well as the chemical reactivity of the HAMQ and its four metallic derivatives making use of conceptual density functional theory (CDFT) by means of KID (Koopmans in DFT) methodology. The synthesized complexes displayed significant in vitro anticancer activity against human cancer cell lines (HeLa and HCT-115).

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.

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

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

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.

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.

Chemical reactivity and bioactivity properties of the Phallotoxin family of fungal peptides based on Conceptual Peptidology and DFT study

A methodology based on the concepts that arise from Density Functional Theory (CDFT) was chosen for the calculation of the global and local reactivity descriptors of the Phallotoxin family of fungal peptides. The determination of the active sites for the molecules has been achieved by resorting some descriptors within Molecular Electron Density Theory (MEDT) like the Dual Descriptor and the Parr functions. Phallosacin has been found as the most reactive of the peptides on the basis of the calculated Global Reactivity Descriptors. The pKas of the seven studied peptides were established using a proposed relationship between this property and the calculated Global Hardness. The 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.

Computational Peptidology Assisted by Conceptual Density Functional Theory for the Study of Five New Antifungal Tripeptides

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 a group of five new antifungal tripeptides, namely (2R)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]propanamido]-5-[(diaminomethylidene)amino]pentanoic acid, (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenyl propanamido]propanamido]-3-(4-hydroxyphenyl)propanoic acid, (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-methylbutanamido]-3-(4-hydroxyphenyl)propanoic acid, (2R)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-(1H-indol-3-yl)propanamido]-3-sulfanylpropanoic acid, and (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-(1H-indol-3-yl)propanamido]-3-(4-hydroxyphenyl)propanoic acid, according to their amino acid sequences. A methodology based on conceptual density functional theory was chosen for the determination of the reactivity descriptors. The molecular active sites were associated with the active regions of the molecules that were associated with the nucleophilic, electrophilic, and radical Fukui functions. Additionally, the pK a values for the different peptides are predicted with great accuracy, which constitutes a useful knowledge for the process of drug design. Finally, the bioactivity scores for the new antifungal peptides are predicted through a homology methodology relating them with the calculated reactivity descriptors.

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.

Conceptual DFT as a chemoinformatics tool for the study of the Taltobulin anticancer peptide

Objective

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 structure of the Taltobulin anticancer peptide. A methodology based on Conceptual Density Functional Theory (CDFT) was chosen for the determination of the reactivity descriptors.

Results

The molecular active sites were associated with the active regions of the molecule were associated with the nucleophilic and electrophilic Fukui functions. Finally, the bioactivity scores for the Taltobulin peptide are predicted through a homology methodology relating them with the calculated reactivity descriptors.

Chemical Reactivity Theory and Empirical Bioactivity Scores as Computational Peptidology Alternative Tools for the Study of Two Anticancer Peptides of Marine Origin

This work presents an account of the reactivity behavior of the anticancer marine drugs, Soblidotin and Tasidotin, based on the calculation of the global and local descriptors resulting from Chemical Reactivity Theory (CRT), also known as Conceptual DFT, for their consideration as a useful complement to approximations based on Molecular Docking. The information on the global and local reactivity descriptors of the Soblidotin and Tasidotin molecules, obtained through our proposed methodology, may be used for the design of new pharmaceutical analogs by relying on the chemical interactions between these peptides and their protein-type biological receptors. It can be concluded that the CRT approximation to the global and local chemical reactivity, based on the descriptors, can provide interesting information for the consideration of both molecules as potential therapeutic drugs. This is complemented by a study on Advanced Glycation Endproduct (AGE) inhibition, by comparison with the usual molecular systems considered for the task, as a re-purposing study. Finally, the bioactivity scores for Soblidotin and Tasidotin are predicted through an empirical procedure, based on comparison with molecular structures with well-known pharmacological properties.

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

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.

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

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.