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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.

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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.

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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.

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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.

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Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules.Communicated by Ramaswamy H. Sarma.

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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.

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As a continuation of our research on the chemical reactivity, pharmacokinetics and ADMET properties of cyclopeptides of marine origin with potential therapeutic abilities, in this work our already presented integrated molecular modeling protocol has been used for the study of the chemical reactivity and bioactivity properties of the Veraguamides A-G family of marine natural drugs. This protocol results from the estimation of the conceptual density functional theory (CDFT) chemical reactivity descriptors together with several chemoinformatics tools commonly considered within the process of development of new therapeutic drugs. CP-CDFT is a branch of computational chemistry and molecular modeling dedicated to the study of peptides, and it is a protocol that allows the estimation with great accuracy of the CDFT-based reactivity descriptors and the associated physical and chemical properties, which can aid in determining the ability of the studied peptides to behave as potential useful drugs. Moreover, the superiority of the MN12SX density functional over other long-range corrected density functionals for the prediction of chemical and physical properties in the presence of water as the solvent is clearly demonstrated. The research was supplemented with an investigation of the bioactivity of the molecular systems and their ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as is customary in medicinal chemistry. Some instances of the CDFT-based chemical reactivity descriptors' capacity to predict the pKas of peptides as well as their potential as AGE inhibitors are also shown.

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Aspergillipeptide 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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Oxidative stress plays an essential role in the regulation of vital processes in living organisms. Reactive oxygen species can react chemically with the constituents of the cells leading to irreversible damage. The first structure of the cell in contact with the environment that surrounds it is the membrane, which protects it and allows the exchange of substances. Some signals manifest when the components of a bilayer are undergoing oxidation, like an increase in the lipid area, decrease in the thickness of the bilayer, and exchange of the oxidized groups toward the bilayer surface. In this investigation, a molecular dynamics simulation was done on a set of Dioleoylphosphatidylcholine membranes with different percentage of oxidized lipids, in order to observe the effect of the oxidation degree on the membrane structure. It was found that, as higher the concentration of oxidized lipids is, the larger the damage of the membrane. This is reflected in the increase in the lipid area and the decrease in the thickness and membrane packing. Also, it was observed that hydrophobicity inside the membrane decreases as the oxidation percentage increases.Communicated by Ramaswamy H. Sarma.

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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.

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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.

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The KID (Koopmans in DFT) protocol usually applies in organic molecules of the closed-shell type. We used the KID procedure on an open-shell Mo-based system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors obtained from the conceptual density-functional theory (DFT). From a set of 18 density functionals, spread from the second until the fourth rung of Jacob's ladder: BLYP, BP86, B97-D, MN12-L, MN15-L, M06-L, M11-L, CAM-B3LYP, PBE0, B3LYP, N12-SX, M06-2X, MN15, MN12-SX, ωB97X-D, M11, LC-ωHPBE, and APFD, we concluded that CAM-B3LYP provides the best outcome, and in the second place, M06-2X. Because the vertical first ionization potential and vertical first electron affinity in the ground state (gs) are defined as follows I = E gs(N - 1) - E gs(N) and A = E gs(N) - E gs(N + 1), where E gs(N - 1), E gs(N), and E gs(N + 1) correspond to energies of the system bearing N, N + 1, and N - 1 electrons, along with Koopmans' theorem (KT) given by I ≈ -εHOMO (εHOMO, highest occupied molecular orbital energy) and A ≈ -εLUMO (εLUMO, lowest unoccupied molecular orbital energy), the deviation from the KT was performed by the use of the index, such that J I = |E gs(N - 1) - E gs(N) + εHOMO| and J A = |E gs(N) - E gs(N + 1) + εLUMO|, which are absolute deviations from the perspective of I and A, respectively. Furthermore, the εSOMO (SOMO: singly-occupied molecular orbital energy) leads us to another index given by |ΔSL| = |εSOMO - εLUMO|. Therefore, J HL and |ΔSL| are indexes defined to evaluate the quality of the KT when employed within the context of quantum chemical calculations based on DFT and not the Hartree-Fock theory. We propose the index that could be more suitable to choose the most proper density functional because the J HL and |ΔSL| are independent indexes.

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This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the theopapuamides A-D family of marine peptides by making use of our proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular system. CP allows for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea about the chemical reactivity properties of the marine natural products under study, which are expected to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans In DFT) technique, as well as the MN12SX/Def2TZVP/H2O model chemistry is successfully verified. Together with several chemoinformatic tools that can be used to improve the process of virtual screening, some additional properties of these marine peptides are identified related to their ability to behave as useful drugs. With the further objective of analyzing their bioactivity, some useful parameters for future QSAR studies, their predicted biological targets, and the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the theopapuamides A-D pharmacokinetics are also reported.

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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.

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Eight novel metal-free organic sensitizers were proposed for dye-sensitized solar cells (DSSCs), theoretically calculated and studied via density functional theory with D-π-A structure. These proposals were formed to study the effect of novel π-bridges, using carbazole as the donor group and cyanoacrylic acid as the anchorage group. Through the M06/6-31G(d) level of theory, ground state geometry optimization, vibrational frequencies, the highest occupied molecular orbital, the lowest unoccupied molecular orbital, and their energy levels were calculated. Further, chemical reactivity parameters were obtained and analyzed, such as chemical hardness (η), electrophilicity index (ω), electroaccepting power (ω+) and electrodonating power (ω-). Free energy of electron injection (ΔGinj) and light-harvesting efficiency (LHE) also were calculated and discussed. On the other hand, absorption wavelengths, oscillator strengths, and electron transitions were calculated through time-dependent density functional theory with the M06-2X/6-31G(d) level of theory. In conclusion, the inclusion of thiophene groups and the Si heteroatom in the π-bridge improved charge transfer, chemical stability, and other optoelectronic properties of carbazole-based dyes.

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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.

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Ten molecules were theoretically calculated and studied through density functional theory with the M06 density functional and the 6-31G(d) basis set. The molecular systems have potential applications as sensitizers for dye-sensitized solar cells. Three molecules were taken from the literature, and seven are proposals inspired in the above, including the azomethine group in the π-bridge expecting a better charge transfer. These molecular structures are composed of triphenylamine (donor part); different combinations of azomethine, thiophene, and benzene derivatives (π-bridge); and cyanoacrylic acid (acceptor part). This study focused on the effect that the azomethine group caused on the π-bridge. Ground-state geometry optimization, the highest occupied molecular orbital, the lowest unoccupied molecular orbital, and their energy levels were obtained and analyzed. Absorption wavelengths, oscillator strengths, and electron transitions were obtained via time-dependent density functional theory using the M06-2X density functional and the 6-31G(d) basis set. The free energy of electron injection (ΔGinj) was calculated and analyzed. As an important part of this study, chemical reactivity parameters are discussed, such as chemical hardness, electrodonating power, electroaccepting power, and electrophilicity index. In conclusion, the inclusion of azomethine in the π-bridge improved the charge transfer and the electronic properties of triphenylamine-based dyes.

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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.

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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.