NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study.

Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe3O4_A and Fe3O4_B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe3O4_A and Fe3O4_B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

Review of the Phytochemistry and Biological Activity of Cissus incisa Leaves.

BACKGROUND: Cissus incisa is a Vitaceae with a pantropical distribution. In northern Mexico, its leaves have traditionally been used to treat skin infections, abscesses and tumors. Despite its medicinal uses, few studies have been reported. OBJECTIVE: The objective of this study is to summarize the phytochemical and biological studies carried out so far on the leaves of C. incisa, since this part of the plant is the one frequently used, and awaken scientific interest towards the plant. METHODS: Since C. incisa was an undocumented species, most of the information comes from reports of our research group. Databases, books, and websites were also consulted. The information collected was organized and presented in a synthesized way. Plant name was checked with the database "The Plant List". RESULTS: 171, 260, and 114 metabolites were identified by UHPLC-QFTOF-MS in the hexane, chloroform/ methanol, and aqueous extracts, respectively. Fatty acyls, sphingolipids, sterols, glycerolipids, prenol lipids, and terpenes are common metabolites found in these extracts. 2-(2´-hydroxydecanoyl amino)-1,3,4-hexadecanotriol-8-ene, 2,3-dihydroxypropyl tetracosanoate, ß-sitosterol, ß-sitosterol-D-glucopyranoside, α-amyrin-3-O-ß-D-glucopyranoside were also isolated and characterized. Extracts, phytocompounds and semi-synthetic derivatives showed antimicrobial activity against multi-drug resistant bacteria and various cancer cell lines. Results from Perturbation- Theory-Machine Learning-Information-Fusion model (PTMLIF), molecular docking, and vesicular contents assay identified potential targets on the cell membrane, suggesting an antibacterial mechanism of action for ceramides from C. incisa leaves. CONCLUSION: This review reports the efforts of the scientific community in authenticating species used in traditional medicine. Moreover, it gives a compendium of phytochemistry and the biological activities of the components from C. incisa leaves.

Metabolomic Profile and Cytotoxic Activity of Cissus incisa Leaves Extracts.

Cissus incisa leaves have been traditionally used in Mexican traditional medicine to treat certain cancerous illness. This study explored the metabolomic profile of this species using untargeted technique. Likewise, it determined the cytotoxic activity and interpreted all data by computational tools. The metabolomic profile was developed through UHPLC-QTOF-MS/MS for dereplication purposes. MetaboAnalyst database was used in metabolic pathway analysis and the network topological analysis. Hexane, chloroform/methanol, and aqueous extracts were evaluated on HepG2, Hep3B, HeLa, PC3, A549, and MCF7 cancer cell lines and IHH immortalized hepatic cells, using Cell Titer proliferation assay kit. Hexane extract was the most active against Hep3B (IC50 = 27 ± 3 µg/mL), while CHCl3/MeOH extract was the most selective (SI = 2.77) on the same cell line. A Principal Component Analysis (PCA) showed similar profiles between the extracts, while a Venn diagram revealed 80 coincident metabolites between the bioactive extracts. The sesquiterpenoid and triterpenoid biosynthesis pathway was the most significant identified. The Network Pharmacology (NP) approach revealed several targets for presqualene diphosphate, phytol, stearic acid, δ-tocopherol, ursolic acid and γ-linolenic acid, involved in cellular processes such as apoptosis. This work highlights the integration of untargeted metabolomic profile and cytotoxic activity to explore plant extracts, and the NP approach to interpreting the experimental results.

Palladium-mediated synthesis and biological evaluation of C-10b substituted Dihydropyrrolo[1,2-b]isoquinolines as antileishmanial agents.

The development of new molecules for the treatment of leishmaniasis is, a neglected parasitic disease, is urgent as current anti-leishmanial therapeutics are hampered by drug toxicity and resistance. The pyrrolo[1,2-b]isoquinoline core was selected as starting point, and palladium-catalyzed Heck-initiated cascade reactions were developed for the synthesis of a series of C-10 substituted derivatives. Their in vitro leishmanicidal activity against visceral (L. donovani) and cutaneous (L. amazonensis) leishmaniasis was evaluated. The best activity was found, in general, for the 10-arylmethyl substituted pyrroloisoquinolines. In particular, 2ad (IC50 = 3.30 µM, SI > 77.01) and 2bb (IC50 = 3.93 µM, SI > 58.77) were approximately 10-fold more potent and selective than the drug of reference (miltefosine), against L. amazonensis on in vitro promastigote assays, while 2ae was the more active compound in the in vitro amastigote assays (IC50 = 33.59 µM, SI > 8.93). Notably, almost all compounds showed low cytotoxicity, CC50 > 100 µg/mL in J774 cells, highest tested dose. In addition, we have developed the first Perturbation Theory Machine Learning (PTML) algorithm able to predict simultaneously multiple biological activity parameters (IC50, Ki, etc.) vs. any Leishmania species and target protein, with high values of specificity (>98%) and sensitivity (>90%) in both training and validation series. Therefore, this model may be useful to reduce time and assay costs (material and human resources) in the drug discovery process.

Molecular docking, SAR analysis and biophysical approaches in the study of the antibacterial activity of ceramides isolated from Cissus incisa.

The developing of antibacterial resistance is becoming in crisis. In this sense, natural products play a fundamental role in the discovery of antibacterial agents with diverse mechanisms of action. Phytochemical investigation of Cissus incisa leaves led to isolation and characterization of the ceramides mixture (1): (8E)-2-(tritriacont-9-enoyl amino)-1,3,4-octadecanetriol-8-ene (1-I); (8E)-2-(2',3'-dihydroxyoctacosanoyl amino)-1,3,4-octadecanetriol-8-ene (1-II); (8E)-2-(2'-hydroxyheptacosanoyl amino)-1,3,4-octadecanetriol-8-ene (1-III); and (8E)-2-(-2'-hydroxynonacosanoyl amino)-1,3,4-octadecanetriol-8-ene (1-IV). Until now, this is the first report of the ceramides (1-I), (1-II), and (1-IV). The structures were elucidated using NMR and mass spectrometry analyses. Antibacterial activity of ceramides (1) and acetylated derivates (2) was evaluated against nine multidrug-resistant bacteria by Microdilution method. (1) showed the best results against Gram-negatives, mainly against carbapenems-resistant Acinetobacter baumannii with MIC = 50 µg/mL. Structure-activity analysis and molecular docking revealed interactions between plant ceramides with membrane proteins, and enzymes associated with biological membranes of Gram-negative bacteria, through hydrogen bonding of functional groups. Vesicular contents release assay showed the capacity of (1) to disturb membrane permeability detected by an increase of fluorescence probe over time. The membrane disruption is not caused for ceramides lytic action on cell membranes, according in vitro hemolyticactivity results. Combining SAR analysis, bioinformatics and biophysical techniques, and also experimental tests, it was possible to explain the antibacterial action of these natural ceramides.

Antibacterial and cytotoxic activities of new sphingolipids and other constituents isolated from Cissus incisa leaves.

Cissus incisa is used in traditional Mexican medicine to treat certain ailments, infectious or cancerous diseases. Excepting for our previous research, this species had no scientific reports validating its traditional use. In this study, we evaluated the antibacterial and cytotoxic properties of the sphingolipids and others phytocompounds isolated from C. incisa leaves to increase the scientific knowledge of the Mexican flora. The antibacterial activity was evaluated against Gram-positive and Gram-negative bacteria by the Microdilution method. Meanwhile, the cytotoxic potential was determined on six human cancer cells: PC3, Hep3B, HepG2, MCF7, A549, and HeLa; using an aqueous solution cell proliferation assay kit. A cell line of immortalized human hepatocytes (IHH) was included as a control of non-cancerous cells. Selectivity index (SI) was determined only against the hepatocellular carcinoma cell lines. The phytochemical investigation of C. incisa leaves resulted in the isolation and characterization of five compounds: 2-(2'-hydroxydecanoyl amino)-1,3,4-hexadecanotriol-8-ene (1), 2,3-dihydroxypropyl tetracosanoate (2), ß-sitosterol-D-glucopyranoside (3), α-amyrin-3-O-ß-D-glucopyranoside (4), and a mixture of cerebrosides (5). Until now, this is the first report of the sphingolipids (1), (5-IV) and (5-V). Only the compound (4) and cerebrosides (5) exhibited antibacterial activity reaching a MIC value of 100 µg/mL against Pseudomonas aeruginosa resistant to carbapenems. While, the acetylated derivate of (3), compound (3Ac) showed the best cytotoxic result against PC3 (IC50 = 43 ± 4 µg/mL) and Hep3B (IC50 = 49.0 ± 4 µg/mL) cancer cell lines. Likewise, (3Ac) achieved better SI values on HepG2 and Hep3B cell lines. This research reveals the importance of study medicinal plants, to identify bioactive molecules as sources of potential drugs. The presence of these compounds allows us to justify the use of this plant in traditional Mexican medicine.

Antibacterial Activity of Cissus incisa Extracts against Multidrug- Resistant Bacteria.

AIMS: The need to find new antimicrobial agents to cope with this phenomenon increases. BACKGROUND: Infection diseases are illness caused by different microorganisms, such as bacteria, among those caused by resistant bacteria are associated with greater morbidity, mortality and cost of the treatment than those caused by sensitive bacteria of the same species. OBJECTIVE: Need to find new antimicrobial agents to cope with this phenomenon increases. METHODS: This work carried out the study of biological activities of Cissus incisa, taking account its traditional use. Three extracts were prepared from the leaves of this plant: hexane, chloroform methanol (1:1) and aqueous. Their antibacterial and antitubercular activities were evaluated using microdilution and alamar blue assays; respectively. RESULTS: The chloroform/methanol extract (1:1) was the most active of the three tested extracts for antimicrobial activity. In this way, the extract exhibits a broad spectrum of antimicrobial activity, against the Gram positive and Gram negative bacteria tested, with MIC values between 125 to 500 µg/mL. CONCLUSION: This research contributes both to the knowledge of the Mexican flora, as well as the discovery of potential antibacterial agents derivate from plants.

Modeling Antibacterial Activity with Machine Learning and Fusion of Chemical Structure Information with Microorganism Metabolic Networks.

Predicting the activity of new chemical compounds over pathogenic microorganisms with different metabolic reaction networks (MRN s) is an important goal due to the different susceptibility to antibiotics. The ChEMBL database contains >160 000 outcomes of preclinical assays of antimicrobial activity for 55 931 compounds with >365 parameters of activity (MIC, IC50, etc.) and >90 bacteria strains of >25 bacterial species. In addition, the Leong and Barabàsi data set includes >40 MRNs of microorganisms. However, there are no models able to predict antibacterial activity for multiple assays considering both drug and MRN structures at the same time. In this work, we combined perturbation theory, machine learning, and information fusion techniques to develop the first PTMLIF model. The best linear model found presented values of specificity = 90.31/90.40 and sensitivity = 88.14/88.07 in training/validation series. We carried out a comparison to nonlinear artificial neural network (ANN) techniques and previous models from the literature. Next, we illustrated the practical use of the model with an experimental case of study. We reported for the first time the isolation and characterization of terpenes from the plant Cissus incisa. The antibacterial activity of the terpenes was experimentally determined. The more active compounds were phytol and α-amyrin, with MIC = 100 µg/mL for Vancomycin-resistant Enterococcus faecium and Acinetobacter baumannii resistant to carbapenems. These compounds are already known from other sources. However, they have been isolated and evaluated for the first time here against several strains of multidrug-resistant bacteria including World Health Organization (WHO) priority pathogens. Last, we used the model to predict the activity of these compounds versus other microorganisms with different MRNs in order to find other potential targets.