Computational peptidology approach to the study of the chemical reactivity and bioactivity properties of Aspergillipeptide D, a cyclopentapeptide of marine origin

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.

Revisiting The Trapping of Noble Gases (He – Kr) By The Triatomic H3+ and Li3+ Species: A Density Functional Reactivity Theory Study

Small atomic clusters with exotic stability, bonding, aromaticity and reactivity properties can be made use of for various purposes. In this work, we revisit the trapping of noble gas atoms (He – Kr) by the triatomic H3+ and Li3+ species by using some analytical tools from density functional theory, conceptual density functional theory, and the information-theoretic approach. Our results showcase that though similar in geometry, H3+ and Li3+ exhibit markedly different behaviour in bonding, aromaticity, and reactivity properties after the addition of noble gas atoms. Moreover, the exchange-correlation interaction and steric effect are key energy components in stablizing the clusters. This study also finds that the origin of the molecular stability of these species is due to the spatial delocalization of the electron density distribution. Our work provides an additional arsenal towards better understanding of small atomic clusters capturing noble gases.

Aromatic Clusters as Potential Hydrogen Storage Materials

The scientific community is engrossed in the thought of a probable solution to the future energy crisis keeping in mind a better environment-friendly alternative. Although there are many such alternatives, the green hydrogen energy has occupied most of the brilliant minds due to its abundance and numerous production resources. For the advancement of hydrogen economy, Government agencies are funding pertinent research projects. There is an avalanche of molecular systems which are studied by several chemists for storing atomic and molecular hydrogens. The present review on molecular hydrogen storage focuses on all-metal and nonmetal aromatic clusters. In addition to the effect of aromaticity on hydrogen trapping potential of different molecular moieties, the importance of using the conceptual density functional theory based reactivity descriptors is also highlighted. Investigations from our group have been revealing the fact that several aromatic metal clusters, metal doped nonmetal clusters as well as pure nonmetal clusters can serve as potential molecular hydrogen trapping agents. Reported systems include N4Li2, N6Ca2 clusters, Mgn, and Can (n = 8–10) cage-like moieties, B12N12 clathrate, transition metal doped ethylene complexes, M3+ (M = Li, Na) ions, E3-M2 (E = Be, Mg, Al; M = Li, Na, K) clusters, Li3Al4− ions, Li decorated star-like molecules, BxLiy (x = 3–6; y = 1, 2), Li-doped annular forms, Li-doped borazine derivatives, C12N12 clusters (N4C3H)6Li6 and associated 3-D functional material, cucurbiturils, lithium–phosphorus double-helices. Ni bound C12N12 moieties are also reported recently.

Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain

Coronavirus disease-2019 (COVID-19) has caused a severe impact on almost all aspects of human life and economic development. Numerous studies are being conducted to find novel therapeutic strategies to overcome COVID-19 pandemic in a much effective way. Ulva intestinalis L. (Ui), a marine microalga, known for its antiviral property, was considered for this study to determine the antiviral efficacy against severe acute respiratory syndrome-associated Coronavirus-2 (SARS-CoV-2). The algal sample was dried and subjected to ethanolic extraction, followed by purification and analysis using gas chromatography-coupled mass spectrometry (GC-MS). Forty-three known compounds were identified and docked against the S1 receptor binding domain (RBD) of the spike (S) glycoprotein. The compounds that exhibited high binding affinity to the RBD of S1 protein were further analyzed for their chemical behaviour using conceptual density-functional theory (C-DFT). Finally, pharmacokinetic properties and drug-likeliness studies were carried out to test if the compounds qualified as potential leads. The results indicated that mainly phenols, polyenes, phytosteroids, and aliphatic compounds from the extract, such as 2,4-di-tert-butylphenol (2,4-DtBP), doconexent, 4,8,13-duvatriene-1,3-diol (DTD), retinoyl-β-glucuronide 6′,3′-lactone (RBGUL), and retinal, showed better binding affinity to the target. Pharmacokinetic validation narrowed the list to 2,4-DtBP, retinal and RBGUL as the possible antiviral candidates that could inhibit the viral spike protein effectively.

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.

Unveiling the Different Reactivity of Bent and Linear Three-Atom-Components Participating in [3 + 2] Cycloaddition Reactions

The reactivity of a series of pairs of bent and linear three-atom-component (B-TACs and L-TACs) participating in [3 + 2] cycloaddition (32CA) reactions towards ethylene and electrophilic dicyanoethylene (DCE) have been studied within the Molecular Electron Density Theory. While the pseudodiradical structure of B-TACs changes to that of pseudoradical or carbenoid L-TACs upon dehydrogenation, zwitterionic B-TACs remain unchanged. Conceptual Density Functional Theory (CDFT) indices characterize five of the nine TACs as strong nucleophiles participating in polar reactions towards electrophilic ethylenes. The activation energies of the 32CA reactions with electrophilic DCE range from 0.5 to 22.0 kcal·mol−1, being between 4.3 and 9.1 kcal·mol−1 lower than those with ethylene. In general, B-TACs are more reactive than their L-TAC counterparts. A change in the regioselectivity is found in these polar 32CA reactions; in general, while B-TACs are meta regioselective, L-TACs are ortho regioselective. The geometrical parameters of the transition state structures suggest that the formation of the single bond involving the most electrophilic carbon of DCE is more advanced. A change in the asynchronicity in the reactions involving B-TACs and L-TACs is also found.