Novel machine learning approach toward classification model of HIV-1 integrase inhibitors.

HIV-1 (human immunodeficiency virus-1) has been causing severe pandemics by attacking the immune system of its host. Left untreated, it can lead to AIDS (acquired immunodeficiency syndrome), where death is inevitable due to opportunistic diseases. Therefore, discovering new antiviral drugs against HIV-1 is crucial. This study aimed to explore a novel machine learning approach to classify compounds that inhibit HIV-1 integrase and screen the dataset of repurposing compounds. The present study had two main stages: selecting the best type of fingerprint or molecular descriptor using the Wilcoxon signed-rank test and building a computational model based on machine learning. In the first stage, we calculated 16 different types of fingerprint or molecular descriptors from the dataset and used each of them as input features for 10 machine-learning models, which were evaluated through cross-validation. Then, a meta-analysis was performed with the Wilcoxon signed-rank test to select the optimal fingerprint or molecular descriptor types. In the second stage, we constructed a model based on the optimal fingerprint or molecular descriptor type. This data followed the machine learning procedure, including data preprocessing, outlier handling, normalization, feature selection, model selection, external validation, and model optimization. In the end, an XGBoost model and RDK7 fingerprint were identified as the most suitable. The model achieved promising results, with an average precision of 0.928 ± 0.027 and an F1-score of 0.848 ± 0.041 in cross-validation. The model achieved an average precision of 0.921 and an F1-score of 0.889 in external validation. Molecular docking was performed and validated by redocking for docking power and retrospective control for screening power, with the AUC metrics being 0.876 and the threshold being identified at -9.71 kcal mol-1. Finally, 44 compounds from DrugBank repurposing data were selected from the QSAR model, then three candidates were identified as potential compounds from molecular docking, and PSI-697 was detected as the most promising molecule, with in vitro experiment being not performed (docking score: -17.14 kcal mol-1, HIV integrase inhibitory probability: 69.81%).

Integration of the Butina algorithm and ensemble learning strategies for the advancement of a pharmacophore ligand-based model: an in silico investigation of apelin agonists.

Introduction: 3D pharmacophore models describe the ligand's chemical interactions in their bioactive conformation. They offer a simple but sophisticated approach to decipher the chemically encoded ligand information, making them a valuable tool in drug design. Methods: Our research summarized the key studies for applying 3D pharmacophore models in virtual screening for 6,944 compounds of APJ receptor agonists. Recent advances in clustering algorithms and ensemble methods have enabled classical pharmacophore modeling to evolve into more flexible and knowledge-driven techniques. Butina clustering categorizes molecules based on their structural similarity (indicated by the Tanimoto coefficient) to create a structurally diverse training dataset. The learning method combines various individual pharmacophore models into a set of pharmacophore models for pharmacophore space optimization in virtual screening. Results: This approach was evaluated on Apelin datasets and afforded good screening performance, as proven by Receiver Operating Characteristic (AUC score of 0.994 ± 0.007), enrichment factor of (EF1% of 50.07 ± 0.211), Güner-Henry score of 0.956 ± 0.015, and F-measure of 0.911 ± 0.031. Discussion: Although one of the high-scoring models achieved statistically superior results in each dataset (AUC of 0.82; an EF1% of 19.466; GH of 0.131 and F1-score of 0.071), the ensemble learning method including voting and stacking method balanced the shortcomings of each model and passed with close performance measures.

Acute and sub-acute toxicity evaluation of Merremia tridentata (L.) stem extract on mice.

The acute and sub-acute toxicity studies were performed in male and female Swiss albino mice as per the guidelines mentioned in OECD. The oral administration of M. tridentata stem extract (MSE) showed no treatment-related mortality and body weight change in mice up to the single dose of 30,000 mg/kg body weight in the acute toxicity study and up to a dose of 30,000 mg/kg/day body weight in the sub-acute toxicity study. Moreover, the clinical signs, body weight, gross pathology, organ weight, hematology (except for platelet count), biochemical analysis, and histopathology did not show significant variation at a medium dose of 15,000 mg/kg/day body weight compared to the control group. However, toxicological signs in behavior, very mild interstitial nephritis, as well as significant variation in platelet count and total protein parameters were observed at a dose of 30,000 mg/kg/day in the 28-day oral toxicity study. Thus, the no-observed-adverse-effect level was determined at a dose of 15,000 mg/kg/day body weight. Based on study results, it is concluded that MSE showed LD50 of greater than 5000 mg/kg/day body weight. Hence, this could be a potential candidature as a future safe pharmaceutical product.

Design, Microwave-Assisted Synthesis, Antimicrobial and Anticancer Evaluation, and In Silico Studies of Some 2-Naphthamide Derivatives as DHFR and VEGFR-2 Inhibitors.

Naphthamide is a common structural framework with diverse pharmacological activities. Ten novel 2-naphthamide derivatives have been designed, synthesized, and evaluated for their in vitro antibacterial, antifungal, and anticancer activities. The title compounds were synthesized from dimethoxybenzaldehyde derivatives through a four-step microwave-assisted synthesis process. The structures were confirmed by 1H NMR, 13C NMR, and MS spectra. Compound 8b showed good antibacterial activity against Escherichia coli, Streptococcus faecalis, Salmonella enterica, MSSA, and MRSA with MIC values of 16, 16, 16, 8, and 16 µg/mL, respectively, compared to ciprofloxacin (MIC = 8-16 µg/mL). Compounds 5b (IC50 = 3.59-8.38 µM) and 8b (IC50 = 2.97-7.12 µM) exhibited good cytotoxic activity against C26, HepG2, and MCF7 cancer cell lines as compared to paclitaxel (IC50 = 2.85-5.75 µM). Moreover, compounds 5b and 8b exhibited better anticancer activity than PTX against the C26 cell line. In particular, compound 8b showed potent in vitro VEGFR-2 inhibitory activity with the IC50 value of 0.384 µM compared with sorafenib (IC50 = 0.069 µM). Therefore, compound 8b is the most potent compound for anticancer activity as indicated by in vitro cell line inhibition, in silico ADMET, molecular docking, and in vitro VEGFR-2 inhibition studies.

Design, synthesis, bio-evaluation, and in silico studies of some N-substituted 6-(chloro/nitro)-1H-benzimidazole derivatives as antimicrobial and anticancer agents.

A new series of 6-substituted 1H-benzimidazole derivatives were synthesized by reacting various substituted aromatic aldehydes with 4-nitro-o-phenylenediamine and 4-chloro-o-phenylenediamine through condensation using sodium metabisulfite as the oxidative reagent. The N-substituted 6-(chloro/nitro)-1H-benzimidazole derivatives were prepared from the 6-substituted 1H-benzimidazole derivatives and substituted halides using potassium carbonate by conventional methods as well as by exposure to microwave irradiation. Seventy-six 1H-benzimidazole derivatives have been synthesized in moderate to excellent yields with the microwave-assisted method (40 to 99%). Compounds 1d, 2d, 3s, 4b, and 4k showed potent antibacterial activity against Escherichia coli, Streptococcus faecalis, MSSA (methicillin-susceptible strains of Staphylococcus aureus), and MRSA (methicillin-resistant strains of Staphylococcus aureus) with MIC (the minimum inhibitory concentration) ranging between 2 and 16 µg mL-1 as compared to ciprofloxacin (MIC = 8-16 µg mL-1), in particular compound 4k exhibits potent fungal activity against Candida albicans and Aspergillus niger with MIC ranging between 8 and 16 µg mL-1 compared with the standard drug fluconazole (MIC = 4-128 µg mL-1). In addition, compounds 1d, 2d, 3s, 4b, and 4k also showed the strongest anticancer activity among the synthesized compounds against five tested cell lines with IC50 (half-maximal inhibitory concentration) ranging between 1.84 and 10.28 µg mL-1, comparable to paclitaxel (IC50 = 1.38-6.13 µM). Furthermore, the five most active compounds showed a good ADMET (absorption, distribution, metabolism, excretion, and toxicity) profile in comparison to ciprofloxacin, fluconazole, and paclitaxel as reference drugs. Molecular docking predicted that dihydrofolate reductase protein from Staphylococcus aureus is the most suitable target for both antimicrobial and anticancer activities, and vascular endothelial growth factor receptor 2 and histone deacetylase 6 are the most suitable targets for anticancer activity of these potent compounds.

In vitro and in vivo antidiabetic activity, isolation of flavonoids, and in silico molecular docking of stem extract of Merremia tridentata (L.).

The antidiabetic activity of stem-ethanol extract (SE) and the flavonoid-rich fraction (FF) of Merremia tridentata (L.) were investigated on alloxan-induced diabetic mice. Apigenin, cosmosiin, and quercitrin are flavonoids isolated for the first time from stem extracts. In addition, cynaroside was found to be at the highest level in SE and FF with a percentage of 4.375% and 58.430%, respectively. The administration of SE (100 mg/kg) and FF (50, 75 mg/kg) daily for 20 days resulted in a better hypoglycemic effect than the reference drugs, glibenclamide (5 mg/kg), and metformin (10 mg/kg). Furthermore, SE and FF were shown to significantly improve the plasma lipid profiles at the end of the study. Docking's study suggests that cynaroside, cosmosiin, and quercitrin are the most desirable compounds for hypoglycemic effects in many antidiabetic targets. Especially, SE and FF showed strongly α-amylase and α-glucosidase inhibitory activities (IC50 = 1.61-1.72 mg/mL on α-amylase and IC50 = 0.24-0.44 mg/mL on α-glucosidase). Therefore, SE and FF of Merremia tridentata is a potential drug with antidiabetic and hypoglycemic action as indicated by in vivo, in silico, and in vitro studies.

N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies.

Compounds containing benzimidazole moiety occupy privileged chemical space for discovering new bioactive substances. In continuation of our recent work, 69 benzimidazole derivatives were designed and synthesized with good to excellent yields of 46-99% using efficient synthesis protocol i.e. sodium metabisulfite catalyzed condensation of aromatic aldehydes with o-phenylenediamines to form 2-arylbenzimidazole derivatives followed by N-alkylation by conventional heating or microwave irradiation for diversification. Potent antibacterial compounds against MSSA and MRSA were discovered such as benzimidazole compounds 3k (2-(4-nitrophenyl), N-benzyl), 3l (2-(4-chlorophenyl), N-(4-chlorobenzyl)), 4c (2-(4-chlorophenyl), 6-methyl, N-benzyl), 4g (2-(4-nitrophenyl), 6-methyl, N-benzyl), and 4j (2-(4-nitrophenyl), 6-methyl, N-(4-chlorobenzyl)) with MIC of 4-16 µg mL-1. In addition, compound 4c showed good antimicrobial activities (MIC = 16 µg mL-1) against the bacteria strains Escherichia coli and Streptococcus faecalis. Moreover, compounds 3k, 3l, 4c, 4g, and 4j have been found to kill HepG2, MDA-MB-231, MCF7, RMS, and C26 cancer cells with low µM IC50 (2.39-10.95). These compounds showed comparable drug-like properties as ciprofloxacin, fluconazole, and paclitaxel in computational ADMET profiling. Finally, docking studies were used to assess potential protein targets responsible for their biological activities. Especially, we found that DHFR is a promising target both in silico and in vitro with compound 4c having IC50 of 2.35 µM.

Synthesis of a Series of Novel 2-Amino-5-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole Derivatives as Potential Anticancer, Antifungal and Antibacterial Agents.

BACKGROUND: Many compounds containing a five-membered heterocyclic ring display exceptional chemical properties and versatile biological activities. OBJECTIVE: The objective of the present study was to prepare the 5-substituted 2-amino-1,3,4- oxadiazole and 2-amino-1,3,4-thiadiazole derivatives and evaluate their potential anticancer, antibacterial and antifungal activities. METHODS: Twenty-seven derivatives were synthesized by iodine-mediated cyclization of semicarbazones or thiosemicarbazones obtained from condensation of semicarbazide or thiosemicarbazide and aldehydes. The structures were confirmed by 1H-NMR, 13C-NMR and MS spectra. The antibacterial and antifungal activities were evaluated by diffusion method and the anticancer activities were evaluated by MTT assay. RESULTS: Twenty-seven derivatives have been synthesized in moderate to good yields. A number of derivatives exhibited potential antibacterial, antifungal and anticancer activities. CONCLUSION: Compounds (1b, 1e and 1g) showed antibacterial activity against Streptococcus faecalis, MSSA and MRSA with MIC value ranging between 4 to 64 µg/mL. Compound (2g) showed antifungal activity against Candida albicans (8 µg/mL) and Aspergillus niger (64 µg/mL). Compound (1o) exhibited high cytotoxic activity against HepG2 cell line (IC50 value 8.6 µM) which is comparable to the activity of paclitaxel, and is non-toxic on LLC-PK1 normal cell line. The structure activity relationship and molecular docking study of the synthesized compounds have also been reported.