Computational investigation of pyrrolidin derivatives as novel GPX4/MDM2–p53 inhibitors using 2D/3D-QSAR, ADME/toxicity, molecular docking, molecular dynamics simulations, and MM-GBSA free energy

Copper(II)-photocatalyzed Hydrocarboxylation of Schiff bases with CO2: antimicrobial evaluation and in silico studies of Schiff bases and unnatural α-amino acids

We synthesized and characterized two copper(II) complexes: [CuL2Cl]Cl and [CuL'2Cl]Cl, where L = 2,2'-bipyridine and L' = 4,4'-dimethyl-2,2'-bipyridine. We evaluated their photocatalytic hydrocarboxylation properties on a series of synthesized Schiff bases (SBs): (E)-1-(4-((5-bromo-2-hydroxybenzylidene)amino)phenyl)ethanone (SB1), (E)-N-(4-(dimethylamino)benzylidene)benzo[d]thiazol-2-amine (SB2), (E)-4-Bromo-2-((thiazol-2-ylimino)methyl)phenol (SB3), and (E)-4-((5-bromo-2-hydroxybenzylidene)amino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (SB4). Under mild photocatalytic reaction conditions (room temperature, 1 atm CO2, 30-watt Blue LED light), the derivatives of α-amino acids UAA1-4 were obtained with yields ranging from 5% to 44%. Experimental results demonstrated that [CuL2Cl]Cl exhibited superior photocatalytic efficiency compared to [CuL'2Cl]Cl, attributed to favourable electronic properties. In silico studies revealed strong binding strengths with E. faecalis DHFR (4M7U) for docked Schiff bases (SB) and unnatural α-amino acids (UAAs). In vitro studies further demonstrated significant antimicrobial and antifungal activity for SB2, SB3, and SB4, while none of the synthesized UAAs exhibited such properties, primarily due to the electronic and binding properties of these molecules.

Benzothiazole derivatives as p53-MDM2 inhibitors: in-silico design, ADMET predictions, molecular docking, MM-GBSA Assay, MD simulations studies

Breast cancer stands as the most prevalent malignancy among the female populace. One of the pivotal domains in the therapeutic landscape of breast cancer revolves around the precise targeting of the p53-MDM2 inhibitory pathway. The advent of p53-MDM2 inhibition in the context of developing treatments for breast cancer marks a significant stride. In the quest for enhancing the efficacy of p53-MDM2 inhibition against breast cancer, a new series of benzothiazole compounds (B1-B30) was designed through in-silico methodologies in the present work. Using Schrodinger Maestro, the compounds underwent molecular docking assessments against the p53-MDM2 target (PDB: 4OGT). Compared to reference compounds, B25 and B12 exhibited notably elevated glide scores. Extensive in-silico studies, including ADMET and toxicity evaluations, were performed to predict pharmacokinetics, drug likeness, and toxicity. All compounds adhered to Lipinski criteria, signifying favorable oral drug properties. The MM-GBSA analysis indicated consistent binding free energies. Molecular dynamics simulations for B25 over 200 ns assessed complex stability and interactions. In summary, these compounds exhibit potential for future cancer therapy medication development.

Computational evaluation of 1,2,3-triazole-based VEGFR-2 inhibitors: anti-angiogenesis potential and pharmacokinetic assessment

The vascular endothelial growth factor (VEGF) and its cell surface receptor, as well as the human VEGFR-2 domain kinase, are some of the signaling pathways that have received the most attention in this field. This study aimed to identify novel molecules as VEGFR-2 inhibitors using 3D-QSAR modeling based on 1,2,3-triazole. Docking studies and dynamic simulations were performed to analyze novel interactions with the inhibitors and validate the molecular docking, dynamic simulations, and ADMET analyses. The optimized CoMSIA/SEH model showed good statistical results, and molecular docking and molecular dynamics simulations demonstrated stability of M3 ligand with the receptor and provided insight into ligand-receptor interactions. The newly developed compounds performed well in ADMET evaluations and showed promising results using Lipinski's rule of five, suggesting that the molecule M3 could be a useful anti-angiogenesis agent. In conclusion, this study provides insights into the structure-activity relationship of VEGFR-2 inhibitors and identifies M3 as a potential new anti-angiogenesis drug. The methodology used in this study can be applied to other similar drug targets to discover new and potent inhibitors.

Novel potent and selective dual acetylcholinesterase inhibitors: N-substituted theobromine and theophylline derivatives

Methylxanthines and their derivatives are of great interest due to their diverse biological activities. In this work, a new series of twenty-eight semisynthetic theobromine and theophylline derived compounds were designed and synthesized by applying a simple and efficient strategy. First, the corresponding methylxanthine was reacted with a dibromoalkane (n = 3, 5-8) and subsequently, the brominated intermediate was reacted with an amine, including pyrrolidine, piperidine, diethylamine, methylpiperazine, 1-(2-aminoethyl)pyrrolidine, 1-(2-aminoethyl)piperidine, 2-(1-methylpyrrolidin-2-yl)ethanamine, 1-benzylpiperidin-4-amine, 1-benzylpiperidin-4-yl-methanamine, and 2-(1-benzylpiperidin-4-yl)ethan-1-amine. The two synthetic steps were carried out in very short times using a microwave reactor. The biological activity of the new compounds was evaluated on acetylcholinesterase (AChE), butyrylcholinesterase (BChE), monoamine oxidases (MAO-A, MAO-B) and beta-secretase (BACE-1). The majority of the new derivatives showed potent and selective in vitro AChE inhibition. Compounds 21, 28 and 30 exhibited the strongest effect on both electric eel and human AChE enzyme, with IC50 values on the low nanomolar scale. The kinetic study of compound 28 in hAChE displayed a mixed inhibition mechanism, suggesting a simultaneous interaction with both the CAS and PAS of the enzyme. This experimental binding mode is consistent with the results of docking and molecular dynamics modelling studies, where it was observed that the piperidinium fragment of 16, 21, 28 and 32 was located at the CAS, whereas the xanthine fragment of each inhibitor interacted with Trp286 in the PAS. These results indicate that these novel xanthine analogues act as selective and potent AChE inhibitors that could also prevent the precipitation of the aberrant Aβ peptide. These properties, in conjunction with their in silico good pharmacokinetic profiles, make these molecules promising lead compounds for the development of new effective drugs against several forms of dementia.

Alsfouk B, Eddamsyry B, Khamar H, Zair T, Alaoui El Belghiti M. Chemical composition, antimicrobial, and antioxidant properties of essential oils from Artemisia herba-alba asso. and Artemisia huguetii caball. from Morocco: in vitro and in silico evaluation

Introduction

Morocco is home to a remarkable diversity of flora, including several species from the Artemisia genus. This study aims to thoroughly examine the chemical composition of essential oils derived from Artemisia species and assess their antibacterial and antioxidant properties through in vitro experiments and in silico simulations.

Methods

Samples of Artemisia herba-alba Asso. were collected from Boulemane and Ifrane in Morocco, while Artemisia huguetii Caball. was sampled from Tata, representing regions of the Central Middle Atlas and Western Anti-Atlas. Essential oils were extracted using hydrodistillation, and their chemical composition was analyzed by gas chromatography-mass spectrometry (GC-MS). Antibacterial and antifungal activities were evaluated, and antioxidant properties were assessed using the DPPH assay. In silico predictions of antibacterial and antioxidant activities were performed using computational models.

Results

The extraction yields varied depending on the geographical origin, ranging from 1.54% to 2.78%. GC-MS analysis revealed significant differences in the chemical composition of the oils from different Artemisia species and regions, with a notable prevalence of oxygenated monoterpenes. Specifically, the oil from Boulemane was rich in thujone, the oil from Ifrane was predominantly composed of camphor, and the oil from Tata contained both camphor and thujone. The oils exhibited stronger antifungal than antibacterial properties, with Enterobacter cloacae strains showing high sensitivity, with minimum inhibitory concentrations (MIC) of approximately 12.5 mg/mL. The Boulemane oil of A. herba-alba displayed the highest antioxidant activity, effectively inhibiting DPPH at a concentration of 13.501 μg/mL.

Discussion

The in silico simulations predicted that the primary compounds in these essential oils, such as davanone, eucalyptol, camphor, and thujone, would exhibit potent antibacterial and antioxidant properties. These compounds were found to have favorable ADMET characteristics, including good blood-brain barrier permeability, gastrointestinal absorption, and skin penetration. Molecular docking studies revealed strong interactions between these compounds and key target proteins, such as NADPH-dependent catalase and dihydrofolate reductase. The stability of the protein-ligand complexes was confirmed by molecular dynamics, with davanone showing a significant impact. Overall, this study provides a comprehensive understanding of the biological potential of Artemisia essential oils, highlighting davanone as a promising molecule for medicinal or pharmaceutical applications.

A Network Pharmacology Identified Metastasis Target for Oral Squamous Cell Carcinoma Originating from Breast Cancer with a Potential Inhibitor from F. sargassaceae

This study aimed to identify specific therapeutic targets for oral squamous cell carcinoma (OSCC) that metastasize from breast cancer (BC) by using network pharmacology. The Gene Expression Omnibus for OSCC and BC served as the source of gene expression datasets and their analysis. Upregulated genes and the common intersecting genes of these cancers were determined along with that of the phytochemicals of F. sargassum to predict the pharmacological targets. Further, gene enrichment analysis revealed that their metastasis signature and metastasis targets were determined via a protein interaction network. Molecular docking and pharmacokinetic screening determined the potential therapeutic phytochemicals against the targets. The interaction network of 39 genes thus identified encoding proteins revealed HIF1A as a prominent metastasis target due to its high degree of connectivity and its involvement in cancer-related pathways. Molecular docking showed a strong binding affinity of isonahocol D2, a sargassum-derived compound with HIF1A, presenting a binding energy of -7.1 kcal/mol. Further, pharmacokinetic screening showed favorable ADME properties and molecular dynamics simulations showed stable interactions between isonahocol D2 and HIF1A, with significant stability over 100 ns. This study's results emphasized that isonahocol D2 is a promising therapeutic candidate against HIF1A in OSCC metastasized from breast cancer in translational medicine.

Unleashing Nature's potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

One of the characteristic features of cancer is angiogenesis, the process by which new, aberrant blood vessels are formed from pre-existing blood vessels. The process of angiogenesis begins when VEGF binds to its receptor, the VEGF receptor (VEGFR). The formation of new blood vessels provides nutrients that can promote the growth of cancer cells. When it comes to new blood vessel formation, VEGFR2 is a critical player. Therefore, inhibiting VEGFR2 is an effective way to target angiogenesis in cancer treatment. The aim of our research was to find new VEGFR-2 inhibitors by performing a virtual screening of 13313 from African natural compounds using different in silico techniques. Using molecular docking calculations and ADMET properties, we identified four compounds that exhibited a binding affinity ranging from -11.0 kcal/mol to -11.5 Kcal/mol when bound to VEGFR-2. These four compounds were further analyzed with 100 ns simulations to determine their stability and binding energy using the MM-PBSA method. After comparing the compounds with Regorafenib, a drug approved for anti-angiogenesis treatment, it was found that all the candidates (EANPDB 252, NANPDB 4577, and NANPDB 4580), with the exception of EANPDB 76, could target VEGFR-2 similarly effectively to Regorafenib. Therefore, we recommend three of these agents for anti-angiogenesis treatment because they are likely to deactivate VEGFR-2 and thus inhibit angiogenesis. However, it should be noted that the safety and suitability of these agents for clinical use needs further investigation, as the computer-assisted study did not include in vitro or in vivo experiments.

Analysis of the Chemical Composition and Evaluation of the Antioxidant, Antimicrobial, Anticoagulant, and Antidiabetic Properties of Pistacia lentiscus from Boulemane as a Natural Nutraceutical Preservative

Pistacia lentiscus L. has traditionally been employed as a diuretic and stimulant in the treatment of hypertension. Our interest centered on analyzing the chemical profile of the plant's leaves and its in vitro, in vivo, and in silico antioxidant, antimicrobial, anticoagulant, and antidiabetic effects in order to valorize this species and prepare new high-value products that can be used in the agro-food and pharmaceutical industries. When this species' essential oil was hydrodistilled and subjected to GC-MS analysis, the results showed that the principal components were germacrene D (17.54%), spathulenol (17.38%), bicyclogermacrene (12.52%), and terpinen-4-ol (9.95%). The extraction of phenolic compounds was carried out by decoction and Soxhlet. The determination of total polyphenols, flavonoids, and tannins of aqueous and organic extracts by spectrophotometric methods demonstrated the richness of this species in phenolic compounds. Chromatographic analysis by HPLC/UV-ESI-MS of the aqueous extract of P. lentiscus revealed the presence of 3,5-di-O-galloyl quinic acid, gallic acid, and 3,4,5-tri-O-galloyl quinic acid specific to this species. The study of antioxidant activity by three methods (DPPH, FRAP, and Total Antioxidant Capacity) revealed that P. lentiscus is a very promising source of natural antioxidants. The antimicrobial activity of the essential oil and aqueous extract (E0) was studied by microdilution on the microplate. The results revealed the effectiveness of the aqueous extract compared to the essential oil against Gram-negative bacteria (K. pneumoniae, A. baumannii, E. aerogenes, E. cloacae, P. fluorescence, Salmonella sp., Shigella sp., and Y. enterolitica) and candidoses (C. krusei and C. albicans). The measurements of prothrombin time (PT) and activated partial thromboplastin time (aPTT) of the aqueous extract (E0) can significantly prolong these tests from concentrations of 2.875 and 5.750 mg/mL, respectively. The antihyperglycemic effect of the aqueous extract (E0) showed a strong in vitro inhibitory activity of α-amylase and α-glucosidase compared to acarbose. Thus, it significantly inhibited postprandial hyperglycemia in Wistar albino rats. The in-silico study of the major compounds of the essential oil and extract (E0) carried out using PASS, SwissADME, pkCSM, and molecular docking tools confirmed our in vitro and in vivo results. The studied compounds showed a strong ability to be absorbed by the gastrointestinal tract and to passively diffuse through the blood-brain barrier, a similarity to drugs, and water solubility. Molecular docking experiments deduced the probable mode of action of the identified compounds on their respective target proteins, such as NADPH oxidase, thrombin, α-amylase, and α-glucosidase. Furthermore, given the demonstrated antioxidant, antimicrobial, anticoagulant, and antidiabetic effects, we can affirm the richness of P. lentiscus in bioactive molecules and its use in traditional medicine as a source of preservative agent.

Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques

A series of pyrrolidine derivatives have been used to study the main structural requirements for designing novel Mcl-1 inhibitors. For this purpose, three models CoMSIA, CoMFA and HQSAR were generated using QSAR molecular modeling techniques. The statistical results of the CoMFA (Q2 = 0.689; R = 0.999; R2pred = 0.986), CoMSIA (Q2 = 0.614; R2 = 0.923; R2pred = 0.815) and HQSAR (Q2= 0.603; R2 = 0.662; R2pred = 0.743) models showed good stability and predictability. The results of the models were presented as contours and colored fragments indicating the favorable and unfavorable contribution to the inhibitory activity of Mcl-1. Based on the obtained results, four new compounds were designed with more potent predicted pIC50 inhibitory activity. The ADME/Tox results and the pharmacokinetic properties revealed that these four compounds are orally bioavailable and show good permeability. In addition the four compounds showing non-inhibitors of CYP3A4 and CYP2D6 with the exception of Pred03. At the level of toxicity profile, the compounds Pred01, Pred02 and Pred03 showed interesting results and showed no AMES toxicity, no hERG inhibition and no skin sensitization. Molecular docking results were used to uncover the mode of interaction between the ligand and key residues of protein binding site. Molecular docking results were supported by molecular simulation and binding free energy estimation (MMPBSA). These results demonstrate the stability of the analyzed compounds in the target protein binding site during a 100 ns trajectory. Finally, all these results create a strong lead to develop promising new Pyrrolidine-based inhibitors against Mcl-1.Communicated by Ramaswamy H. Sarma.

In silico protein engineering shows that novel mutations affecting NAD+ binding sites may improve phosphite dehydrogenase stability and activity

Pseudomonas stutzeri phosphite dehydrogenase (PTDH) catalyzes the oxidation of phosphite to phosphate in the presence of NAD, resulting in the formation of NADH. The regeneration of NADH by PTDH is greater than any other enzyme due to the substantial change in the free energy of reaction (G°' = - 63.3 kJ/mol). Presently, improving the stability of PTDH is for a great importance to ensure an economically viable reaction process to produce phosphite as a byproduct for agronomic applications. The binding site of NAD⁺ with PTDH includes thirty-four residues; eight of which have been previously mutated and characterized for their roles in catalysis. In the present study, the unexplored twenty-six key residues involved in the binding of NAD⁺ were subjected to in silico mutagenesis based on the physicochemical properties of the amino acids. The effects of these mutations on the structure, stability, activity, and interaction of PTDH with NAD⁺ were investigated using molecular docking, molecular dynamics simulations, free energy calculations, and secondary structure analysis. We identified seven novel mutations, A155I, G157I, L217I, P235A, V262I, I293A, and I293L, that reduce the compactness of the protein while improving PTDH stability and binding to NAD⁺.

Synthesis of 4-(4-chlorophenyl)thiazole compounds: in silico and in vitro evaluations as leishmanicidal and trypanocidal agents

Neglected tropical diseases are a diverse group of communicable pathologies that mainly prevail in tropical and subtropical regions. Thus, the objective of this work was to evaluate the biological potential of eight 4-(4-chlorophenyl)thiazole compounds. Tests were carried out in silico to evaluate the pharmacokinetic properties, the antioxidant, cytotoxic activities in animal cells and antiparasitic activities were evaluated against the different forms of Leishmania amazonensis and Trypanosoma cruzi in vitro. The in silico study showed that the evaluated compounds showed good oral availability. In a preliminary in vitro study, the compounds showed moderate to low antioxidant activity. Cytotoxicity assays show that the compounds showed moderate to low toxicity. In relation to leishmanicidal activity, the compounds presented IC50 values that ranged from 19.86 to 200 µM for the promastigote form, while for the amastigote forms, IC50 ranged from 101 to more than 200 µM. The compounds showed better results against the forms of T. cruzi with IC50 ranging from 1.67 to 100 µM for the trypomastigote form and 1.96 to values greater than 200 µM for the amastigote form. This study showed that thiazole compounds can be used as future antiparasitic agents.