Development of artificial neural network models to predict the PAMPA effective permeability of new, orally administered drugs active against the coronavirus SARS-CoV-2.

Responding to the pandemic caused by SARS-CoV-2, the scientific community intensified efforts to provide drugs effective against the virus. To strengthen these efforts, the "COVID Moonshot" project has been accepting public suggestions for computationally triaged, synthesized, and tested molecules. The project aimed to identify molecules of low molecular weight with activity against the virus, for oral treatment. The ability of a drug to cross the intestinal cell membranes and enter circulation decisively influences its bioavailability, and hence the need to optimize permeability in the early stages of drug discovery. In our present work, as a contribution to the ongoing scientific efforts, we employed artificial neural network algorithms to develop QSAR tools for modelling the PAMPA effective permeability (passive diffusion) of orally administered drugs. We identified a set of 61 features most relevant in explaining drug cell permeability and used them to develop a stacked regression ensemble model, subsequently used to predict the permeability of molecules included in datasets made available through the COVID Moonshot project. Our model was shown to be robust and may provide a promising framework for predicting the potential permeability of molecules not yet synthesized, thus guiding the process of drug design. Supplementary Information: The online version contains supplementary material available at 10.1007/s13721-023-00410-9.

Computational Analysis of LOX1 Inhibition Identifies Descriptors Responsible for Binding Selectivity.

Lipoxygenases are a family of cytosolic, peripheral membrane enzymes, which catalyze the hydroperoxidation of polyunsaturated fatty acids and are implicated in the pathogenesis of major human diseases. Over the years, a substantial number of scientific reports have introduced inhibitors active against one or another subtype of the enzyme, but the selectivity issue has proved to be a major challenge for drug design. In the present work, we assembled a dataset of 317 structurally diverse molecules hitherto reported as active against 15S-LOX1, 12S-LOX1, and 15S-LOX2 and identified, using supervised machine learning, a set of structural descriptors responsible for the binding selectivity toward the enzyme 15S-LOX1. We subsequently incorporated these descriptors in the training of QSAR models for LOX1 activity and selectivity. The best performing classifiers are two stacked models that include an ensemble of support vector machine, random forest, and k-nearest neighbor algorithms. These models not only can predict LOX1 activity/inactivity but also can discriminate with high accuracy between molecules that exhibit selective activity toward either one of the isozymes 15S-LOX1 and 12S-LOX1.

Iridoid glucosides in the genus Veronica (Plantaginaceae) from New Zealand.

Four simple iridoid glucosides, three known esters of catalpol, seven esters of aucubin, and two phenylethanoids were isolated from Veronica hookeri (syn. Hebe ciliolata; Plantaginaceae). Of these, none of four aromatic (p-methoxybenzoyl, isovanilloyl, veratroyl, caffeoyl) 6-O-esters of aucubin and 6″-O-benzoyl mussaenosidic acid, had been reported from nature before. Similarly, three simple iridoid glucosides, two esters of 6-O-rhamnopyranosylcatapol, and two phenylethanoid glucosides, as well as 1-O-benzoyl-3-α-glucuronosylglycerol, and 1-O-ß-benzoyl rutinoside were isolated from Veronica pinguifolia (syn. Hebe pinguifolia). The compound 3″-O-benzoyl-2″-O-caffeoyl 6-O-rhamnopyranosylcatalpol had not been reported previously. The pattern of the structural features of the iridoid glucosides is overlaid onto the latest molecular phylogenetic framework of Veronica sects. Hebe and Labiatoides, and discussed in the context of evolutionary trends.

LOX1 inhibition with small molecules.

Lipoxygenases (LOXs) are nonheme, iron-containing dioxygenases that catalyze the dioxygenation of polyunsaturated fatty acids and are widely distributed among plant and animal species. Human LOXs, now identified as key enzymes in the pathogenesis of major disorders, have increasingly drawn the attention as targets and great effort has been made for the discovery and design of suitable inhibitors, to which end both pharmacological and computational methods have been employed. In the present work, using pharmacophore modeling and docking, we attempt to elucidate the inhibition of LOX1 with a new inhibitor, albidoside, an iridoid glucoside isolated from plants of the Scutellaria genus. Through a pharmacophore approach, complementarities between the ligand and the binding site are explored and a plausible mode of binding with the protein is suggested for albidoside.

Iridoid glucosides in the endemic Picconia azorica (Oleaceae).

In our continued investigation of plants from the family Oleaceae we have now investigated Picconia azorica endemic to the Azores. Like most species within the family it contains the oleoside-based secoiridoid glucosides ligstroside and oleuropein as the main compounds and in addition verbascoside and echinacoside. As with the previously investigated Picconia excelsa, it also contained the carbocyclic iridoid glucosides involved in the biosynthetic pathway to the oleoside derivatives. However, while P. excelsa contained loganin esterified with some monoterpenoid acids, P. azorica contains similar esters of 7-epi-loganic acid named Picconioside A and B. In addition were found the two 7-O-E/Z-cinnamoyl esters of 7-epi-loganic acid named Picconioside C and D.

Further iridoid glucosides in the genus Manulea (Scrophulariaceae).

From Manulea altissima (Scrophulariaceae) were isolated five known secoiridoid glucosides sweroside, eustomoside, eustoside, secoxyloganin and secologanoside as well as the 4″-O-rhamnopyranosyl-feruloyl ester of adoxosidic acid, named altissimoside. Also, the caffeoyl phenylethanoid glycoside verbascoside was isolated. In addition two previously unknown terpenoid esters of 6ß-hydroxy 8-epi-boschnaloside, named manucoside A and B were isolated from a formerly obtained fraction from the work-up of Manulea corymbosa. The distribution of iridoid glucosides in the Scrophulariaceae is discussed.

Unexpected secoiridoid glucosides from Manulea corymbosa.

From an extract of Manulea corymbosa were isolated four known secoiridoid glucosides (1-4), 10 new monoterpenoid esters of secologanol, namely, manuleosides A-I (5-11, 13, and 14) and dimethyl rhodanthoside A (12), and four new phenylpropanoid esters of carbocyclic iridoid glucosides, manucorymbosides I-IV (15-18). Also, the caffeoyl phenylethanoid glycoside verbascoside was isolated. The presence of secoiridoids apparently derived from loganic acid in the family Scrophulariaceae is unprecedented and greatly unexpected.

Minor iridoids from Scutellaria albida ssp. albida. Inhibitory potencies on lipoxygenase, linoleic acid lipid peroxidation and antioxidant activity of iridoids from Scutellaria sp.

A new iridoid glycoside, 6'-O-E-caffeoyl-mussaenosidic acid , in addition to one known aglycon, four known triterpenes and one known flavonoid, were isolated from the aerial parts of Scutellaria albida subsp. albida. Furthermore, 12 iridoids with similar structures isolated from Scutellaria sp., were examined for their inhibitory potency on lipoxygenase and lipid peroxidation, as well as their antioxidant activity, in comparison to known antioxidants e.g. caffeic acid, nordihydroguaretic acid (NDGA) and trolox. AAPH, DPPH and soybean lipoxygenase (LOX) assays were used for the tests. This investigation led to interesting observations considering the Structure-Activity Relationship. According to our results, the presence of a p-coumaroyl group optimized and even dramatically changed the biological responses of the investigated iridoids.

Depsides and other polar constituents from Origanum dictamnus L. and their in vitro antimicrobial activity in clinical strains.

Phytochemical investigation of the polar extracts of the aerial parts of Origanum dictamnus afforded 15 secondary metabolites. One new depside was isolated, to which the trivial name salvianolic acid P (1) was given, in addition to the known depsides rosmarinic acid (2) and rosmarinic acid methyl ester (3), as well as two monoterpenes, thymoquinone (4) and thymoquinol 2-O-beta-glucopyranoside (5); two simple phenolic acids, oresbiusin A (6) and E-caffeic acid (7); six flavonoids, namely, apigenin (8), kaempferol (9), quercetin (10), eriodictyol (11), taxifolin (12), naringenin (13); and two alicyclic derivatives, that is, 12-hydroxyjasmonic acid (14) and its 12-O-beta-d-glucoside (15). The structures of all isolated compounds were established by spectroscopic methods, mainly 1D and 2D NMR, as well as HPLC-DAD-MS and HR-MS spectrometric analyses. The absolute configuration of compound 1 was determined by CD measurements as 7'R, 7''S, 8''S. Compound 1 is interesting as it contains a benzodioxane ring, which is unusual in natural products. Moreover, it has been proved to be active against the Gram-negative clinical strains Acinetobacter hemolyticus , Empedobacter brevis , Pseudomonas aeruginosa , and Klebsiella pneumoniae .

Iridoids from Scutellaria albida ssp. albida.

Three iridoid glycosides, 6'-O-E-p-coumaroylgardoside (1), 6'-O-p-E-coumaroyl-8-epi-loganic acid (2) and scutelloside (3) were isolated from the aerial parts of Scutellaria albida subsp. albida, in addition to an anomeric mixture in equilibrium of one iridoid aglycone (4, 4a), nine iridoid glycosides (5-13), four known phenylethanoid glycosides (14-17), and six known phenolic derivatives (18-23).