Synthesis, PASS predication, in vitro antimicrobial evaluation and pharmacokinetic study of novel n-octyl glucopyranoside esters

Synthesis and PASS-assisted evaluation of new heterocyclic compounds containing hydroquinoline scaffolds

Currently, there is a growing interest in the synthesis of heterocyclic compounds containing hydroquinoline fragments. This surge can be attributed to the broad range of pharmaceutical and industrial applications that these compounds possess. In this study, the synthesis of both linear and fused heterocyclic systems that incorporate hydroquinoline fragments was described. Furthermore, the pharmacological activity spectra of the synthesized compounds were predicted using the in silico method, employing the Prediction of Activity Spectra of Substances (PASS) program. Hydroquinolines containing the nitrile functionality 7 and 8 were synthesized through the reaction of the corresponding hydroquinolinecarbaldehyde 5a, 6b with hydroxylamine hydrochloride and iodine in aqueous ammonia under ambient conditions, respectively. 2-Phenyl-1,3-oxazol-5(4 H)-ones 9a, b and 10a, b were synthesized via the condensation of compounds 5a, b and 6a, b with hippuric acid in acetic acid in 30-60% yield. When the methyl activated 7-methylazolopyrimidines 11a, b were reacted with N-alkyl-2,2,4-trimethyl-1,2,3,4-tetrahydroquinoline-6-carbaldehydes 6a, b, 60-70% yield of triazolo/pyrazolo[1,5-a]pyrimidin-6-yl carboxylic acids 12a, b were obtained. The condensation of 7-hydroxy-1,2,3,4-tetramethyl-1,2-dihydroquinoline 3 h with dimethylacetylenedicarboxylate (DMAD) and ethyl acetoacetate afforded cyclic products 16 and 17, respectively. The condensation reaction of 6-formyl-7-hydroxy-1,2,2,4-tetramethyl-1,2-dihydroquinoline 5e with methylene-active compounds such as ethyl cyanoacetate/dimethyl-3-oxopentanedioate/ethyl acetoacetate/diethylmalonate/Meldrum's acid afforded 3-substituted coumarins 19 and 21 containing dihydroquinoline moiety. The pentacyclic coumarin 22 was obtained via the tandom condensation reaction of malononitrile with 5e in the presence of a catalytic amount of piperidine in ethanol. The biological activities of the synthesized compounds were predicted using the PASS program. Based on the prognosis, compounds 13a, b, and 14 exhibited a high likelihood of being active as inhibitors of gluconate 2-dehydrogenase, as well as possessing antiallergic, antiasthmatic, and antiarthritic properties, with a probability value (Pa) ranging from 0.849 to 0.870. Furthermore, it was discovered that compounds 7 and 8 tended to act as effective progesterone antagonists and displayed antiallergic, antiasthmatic, and antiarthritic effects (Pa = 0.276-0.827). Among the hydroquinolines containing coumarin moieties, compounds 17, 19a, and 19c were predicted to be potent progesterone antagonists, with Pa values of 0.710, 0.630, and 0.615, respectively.

Computer-Aided Strategy on 5-(Substituted benzylidene) Thiazolidine-2,4-Diones to Develop New and Potent PTP1B Inhibitors: QSAR Modeling, Molecular Docking, Molecular Dynamics, PASS Predictions, and DFT Investigations

A set of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives was explored to study the main structural requirement for the design of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Utilizing multiple linear regression (MLR) analysis, we constructed a robust quantitative structure-activity relationship (QSAR) model to predict inhibitory activity, resulting in a noteworthy correlation coefficient (R2) of 0.942. Rigorous cross-validation using the leave-one-out (LOO) technique and statistical parameter calculations affirmed the model's reliability, with the QSAR analysis revealing 10 distinct structural patterns influencing PTP1B inhibitory activity. Compound 7e(ref) emerged as the optimal scaffold for drug design. Seven new PTP1B inhibitors were designed based on the QSAR model, followed by molecular docking studies to predict interactions and identify structural features. Pharmacokinetics properties were assessed through drug-likeness and ADMET studies. After that density functional theory (DFT) was conducted to assess the stability and reactivity of potential diabetes mellitus drug candidates. The subsequent dynamic simulation phase provided additional insights into stability and interactions dynamics of the top-ranked compound 11c. This comprehensive approach enhances our understanding of potential drug candidates for treating diabetes mellitus.

Harnessing a Biocatalyst to Bioremediate the Purification of Alkylglycosides

As the world moves towards net-zero carbon emissions, the development of sustainable chemical manufacturing processes is essential. Within manufacturing, purification by distillation is often used, however this process is energy intensive and methods that could obviate or reduce its use are desirable. Developed herein is an alternative, oxidative biocatalytic approach that enables purification of alkyl monoglucosides (essential bio-based surfactant components). Implementing an immobilised engineered alcohol oxidase, a long-chain alcohol by-product derived from alkyl monoglucoside synthesis (normally removed by distillation) is selectively oxidised to an aldehyde, conjugated to an amine resin and then removed by simple filtration. This affords recovery of the purified alkyl monoglucoside. The approach lays a blueprint for further development of sustainable alkylglycoside purification using biocatalysis and, importantly, for refining other important chemical feedstocks that currently rely on distillation.

Enzymatic and selective production of alkyl α-d-glucopyranosides by the α-glucosyl transfer enzyme derived from Xanthomonas campestris WU-9701

Several alkyl glucosides exhibit various bioactivities. 1-Octyl β-d-glucopyranoside produced by organic synthesis is used as a nonionic surfactant. However, no convenient method has been developed for the selective production of alkyl α-glucosides (α-AGs), such as 1-octyl α-d-glucopyranoside (α-OG). Therefore, we developed a simple method for selective production of α-AGs using the glucosyl transfer enzyme XgtA, (E.C. 3.2.1.20), derived from Xanthomonas campestris WU-9701. When 0.80 M alkyl alcohol and 2.5 units XgtA were incubated in 2.0 mL of 30 mM HEPES-NaOH buffer (pH 8.0) containing 1.2 M maltose at 45 °C, a specific α-AG corresponding to each alkyl alcohol (C2-C10) was detected. Under the standard conditions, we examined the selective production of α-OG from 1-octanol and maltose using XgtA. The reaction product was isolated and identified as α-OG via 1H nuclear magnetic resonance and nuclear overhauser effect spectroscopy analyses. No other glucosylated products, such as maltotriose, were detected in the reaction mixture. Under the standard conditions at 45 °C for 96 h, 243 mM α-OG (71 g/L) was produced in one batch production. Moreover, the addition of glucose isomerase to the reaction mixture decreased the concentration of glucose released via the reaction and increased the amount of α-OG produced; 359 mM α-OG (105 g/L) was maximally produced at 96 h. In conclusion, this study demonstrates the selective production of α-AGs using a simple enzymatic reaction, and XgtA has the potential to selectively produce various α-AGs.

Computer-aided anti-cancer drug discovery of EGFR protein based on virtual screening of drug bank, ADMET, docking, DFT and molecular dynamic simulation studies

Numerous malignancies, including breast cancer, non-small cell lung cancer, and chronic myeloid leukemia, are brought on by aberrant tyrosine kinase signaling. Since the current chemotherapeutic medicines are toxic, there is a great need and demand from cancer patients to find novel chemicals that are toxic-free or have low toxicity and that can kill tumor cells and stop their growth. This work describes the in-silico examination of substances from the drug bank as EGFR inhibitors. Firstly, drug-bank was screened using the pharmacophore technique to select the ligands and Erlotinib (DB00530) was used as matrix compound. The selected ligands were screened using ADMET and the hit compounds were subjected to docking. The lead compound from the docking was subjected to DFT and MD simulation study. Using the pharmacophore technique, 23 compounds were found through virtual drug bank screening. One hit molecule from the ADMET prediction was the subject of docking study. According to the findings, DB03365 molecule fits to the EGFR active site by several hydrogen bonding interactions with amino acids. Furthermore, DFT analysis revealed high reactivity for DB03365 compound in the binding pocket of the target protein, based on ELUMO, EHOMO and band energy gap. Furthermore, MD simulations for 100 ns revealed that the ligand interactions with the residues of EGFR protein were part of the essential residues for structural stability and functionality. However, DB03365 was a promising lead molecule that outperformed the reference compound in terms of performance and in-vitro and in-vivo experiments needs to validate the study.Communicated by Ramaswamy H. Sarma.

Novel Galactopyranoside Esters: Synthesis, Mechanism, In Vitro Antimicrobial Evaluation and Molecular Docking Studies

One-step direct unimolar valeroylation of methyl α-D-galactopyranoside (MDG) mainly furnished the corresponding 6-O-valeroate. However, DMAP catalyzed a similar reaction that produced 2,6-di-O-valeroate and 6-O-valeroate, with the reactivity sequence as 6-OH > 2-OH > 3-OH,4-OH. To obtain novel antimicrobial agents, 6-O- and 2,6-di-O-valeroate were converted into several 2,3,4-tri-O- and 3,4-di-O-acyl esters, respectively, with other acylating agents in good yields. The PASS activity spectra along with in vitro antimicrobial evaluation clearly indicated that these MDG esters had better antifungal activities than antibacterial agents. To rationalize higher antifungal potentiality, molecular docking was conducted with sterol 14α-demethylase (PDB ID: 4UYL, Aspergillus fumigatus), which clearly supported the in vitro antifungal results. In particular, MDG ester 7−12 showed higher binding energy than the antifungal drug, fluconazole. Additionally, these compounds were found to have more promising binding energy with the SARS-CoV-2 main protease (6LU7) than tetracycline, fluconazole, and native inhibitor N3. Detailed investigation of Ki values, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and the drug-likeness profile indicated that most of these compounds satisfy the drug-likeness evaluation, bioavailability, and safety tests, and hence, these synthetic novel MDG esters could be new antifungal and antiviral drugs.

In vitro antimicrobial, physicochemical, pharmacokinetics and molecular docking studies of benzoyl uridine esters against SARS-CoV-2 main protease

Different esters were found potential against microorganisms, and could be a better choice to solve the multidrug resistant (MDR) pathogenic global issue due to their improved biological and pharmacokinetic properties. In this view, several 4-t-butylbenzoyl uridine esters 4-15 with different aliphatic and aromatic groups were synthesized for antimicrobial, physicochemical and biological studies. In vitro antimicrobial tests against nine bacteria and three fungi along with prediction of activity spectra for substances (PASS) indicated promising antifungal functionality of these uridine esters compared to the antibacterial activities. In support of this observation their cytotoxicity and molecular docking studies have been performed against lanosterol 14α-demethylase (CYP51A1) and Aspergillus flavus (1R51). Significant binding affinities were observed against SARS-CoV-2 main protease (7BQY) considering hydroxychloroquine (HCQ) as standard. ADMET predictions were investigated to evaluate their absorption, metabolism and toxic properties. Most of the uridine esters showed better results than that of the HCQ. Overall, the present study might be useful for the development of uridine-based novel MDR antimicrobial and COVID-19 drugs.

DFT Based Comparative Studies of Some Glucofuranose and Glucopyranoside Esters and Ethers

Carbohydrate-based molecular scaffolding received significant interest due to its impact on the drug discovery and development in synthetic carbohydrate chemistry during the last couple of decades. In this respect, four glucose compounds in the furanose and pyranose forms with ester and ether functionality were selected for their structural, thermodynamic and chemical reactivity studies. PASS predication indicated that the glucose in the six-membered pyranose form was more prone to biological properties compared to their five-membered furanose form. Also, in the pyranose form acetate ester (3) had more potentiality than the ethyl ether (4). The HOMO-LUMO energy gaps were almost similar for both monosubstituted furanose and pyranose glucose indicating their almost similar reactivities. It was also inferred that these 6-O-substituted compounds followed Lipinski’s rule with the acceptable range of ADMET levels, and hence, safe from lethal proarrhythmic risks. Hopefully, these results can be used in the near future for their probable pharmaceutical use without any remarkable toxicity.

Chemical Reactivity Descriptors and Molecular Docking Studies of Octyl 6-O-hexanoyl-β-D-glucopyranosides

The present study describes different chemical reactivity predictions of 6-O-hexanoylation of octyl β-D-glucopyranosides prepared from octyl β-D-glucopyranoside (OBG). Also, molecular docking of the OBGs was conducted against SARS-CoV-2 main protease (6LU7), urate oxidase (Aspergillus flavus; 1R51) and glucoamylase (Aspergillus niger; 1KUL). DFT optimization indicated that glucoside 1 and its ester derivatives 2-7 exist in 4C1 conformation with C1 symmetry. Interestingly, the addition of ester group(s) decreased the HOMO-LUMO gap (Δԑ) of glucosides indicating their good chemical reactivities, whereas the other chemical reactivity descriptors indicated their moderate reactive nature. This fact of moderate reactivity was confirmed by their molecular docking with 6LU7, 1R51 and 1KUL. All the esters showed a moderate binding affinity with these three proteins. More importantly, incorporation of the ester group(s) increased binding affinity with 6LU7 and 1R51, whereas decreased with 1KUL as compared to non-ester OBG 1.

Antimicrobial Activity, in silico Molecular Docking, ADMET and DFT Analysis of Secondary Metabolites from Roots of Three Ethiopian Medicinal Plants

BACKGROUND

Uvaria scheffleri (Annonaceae), Clematis burgensis (Ranunculaceae), and Euphorbia schimperiana (Euphorbiaceae) are medicinal plants traditionally used to treat cough, tuberculosis, asthma, sore throat and skin infections.

METHODS

Silica gel column chromatographic separation was used to isolate compounds. Crude extract and isolated compounds were evaluated for antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Candida albicans via the broth dilution method. Docking studies were performed with E. coli DNA-Gyrase B and human DNA topoisomerase IIα by using AutoDock Vina. ADMET were predicted by SwissADME, PreADMET, and OSIRIS Property predictions. The optimized structures and molecular electrostatic potential surface of the isolated compounds were predicted by DFT analysis using B3LYP/6-31G basis levels.

RESULTS

Silica gel column chromatographic separation afforded five compounds 1-5 of which N-methyl-2,3-bis(2-hydroxybenzyl)-1Н-indol (1) is reported herein for the first time, along with known C-benzylated dihydrochalcone uvaretin (2), bis(2-ethylheptyl) phthalate (3), lupeol (4) and suberosin derivative (5). Dichloromethane roots extract of U. scheffleri showed potent antibacterial activity against S. aureus (MIC = 6.25 µg/mL) compared to gentamicin (MIC=5 µg/mL). In silico, molecular docking analysis of compounds (1and 3-5) showed strong interaction with E. coli DNA gyrase B with a binding energy value ranging from -6.9 to -6.0 kcal/mol compared to ciprofloxacin -7.2 kcal/mol, whereas analysis against human topoisomerase IIα showed binding energy value ranging from -5.9 to -5.3 kcal/mol compared to vosaroxin (-6.2 kcal/mol).

CONCLUSION

The results obtained suggest that N-methyl-2,3-bis(2-hydroxybenzyl)-1Н-indol (1) and coumarin (5) are potential topoisomerase II α inhibitors and might be used as anticancer agents. The ADMET studies showed the highest drug-likeness properties for studied compounds other than bis(2-ethylheptyl) phthalate (3). DFT calculations suggested that studied compounds showed the lowest gap energy and were chemically reactive, and isolated compounds may serve as potential drug candidates that corroborate with the traditional uses of studied plants.

Ziziphus oenoplia Mill.: A systematic review on ethnopharmacology, phytochemistry and pharmacology of an important traditional medicinal plant

BACKGROUND

Ziziphus oenoplia Mill. (Family- Rhamnaceae) an important shrub, often found throughout the hot regions of tropical Asia and northern Australia, is commonly well known as Jackal Jujube in English. It is a folk herbal medicine used as an abdominal pain killer and anti-diarrhoeal agent,.

OBJECTIVE

The review aims to provide up-to-date information on the vernacular information, botanical characterization, distribution, ethnopharmacological uses, pharmacological activities, and chemical constituents of Z. oenoplia for possible exploitation of treatment for various diseases and to suggest future investigations.

METHOD

This review was performed by studying online resources relating to Z. oenoplia and diverse resources, including scientific journals, books, and worldwide accepted databases from which information was assembled to accumulate significant information and relevant data at one place.

RESULTS

Investigations on Z. oenoplia have been focused on its pharmacological activities, including its antimicrobial, antidiabetic, antihepatotoxic, antiulcer, antiplasmodial, anticancer, wound healing, anthelmintic, antioxidant, analgesic and antinociceptive, hypolipidemic activity, anti-inflammatory, immunomodulatory and antidiarrheal activities. Phytochemical studies resulted in the isolation of fatty acids, flavonoids, phenols, pentacyclic triterpenes, hydroxy carboxylic acids, aliphatic hydroxy ether, and cyclopeptide alkaloids.

CONCLUSIONS

Most of the ethnopharmacological relevance of Z. oenoplia is justified but more need to be studied. Further investigations are necessary to fully understand the mode of action of the active constituents and to exploit its preventive and therapeutic potentials.

DFT Based Pharmacokinetic, Molecular Docking, and ADMET Studies of Some Glucopyranoside Esters

Monosaccharide esters (MEs) are getting more attention from bioorganic chemists due to their biodegradable and drug-likeness properties. As a consequence, carbohydrate derivatives (sugar-based esters, SEs) are an essential part of medicinal chemistry. In this context, density functional theory (DFT) with B3LYP/ 3-21G has been employed to optimize the methyl 4,6-O-benzylidene-α-D-glucopyranoside (3) of methyl α-D-glucopyranoside (2) and its protected acyl esters 4-6. The prediction of activity spectra for substances (PASS) of these compounds showed better antifungal functionalities than the antibacterial potentiality. Thermodynamic properties and molecular electrostatic potential (MEP) of these MEs indicated their stability and both the electrophilic and nucleophilic attack sites. Due to their better antifungal potentiality, molecular docking was conducted against fungal protein lanosterol 14α-demethylase (3JUS), and SARS-CoV-2 main protease (6LU7) along with absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The study indicated a better binding affinity of some esters compared to the standard antifungal and COVID-19 related drug hydroxychloroquine (HCQ).

Efficient Synthetic Technique, PASS Predication, and ADMET Studies of Acylated n-Octyl Glucopyranosides

Direct dimolar pentanoylation of octyl β-D-glucopyranoside (OBG) in pyridine-chloroform solvent system furnished the corresponding 3,6-di-O-pentanoate in improved yield. The pentanoate was further converted into three 2,4-di-O-acyl esters to get novel octyl glucopyranosides. To explore medicinal probability of OBG-based esters all the synthesized compounds were subjected for in silico PASS (prediction of activity spectra for substances) predication and ADMET (absorption, distribution, metabolism, excretion, and toxicity) studies. Both the studies indicated that OBG derived carbohydrate fatty acid (CFA) esters are potential alternative for multidrug resistant (MDR) pathogens, especially for fungal infections.

Synthesis, PASS Predication, Antimicrobial, DFT, and ADMET Studies of Some Novel Mannopyranoside Esters

Due to the biodegradability and drug-likeness properties sugar esters (SEs) are getting especial attention to the synthetic and bioorganic chemists. In this context, we have synthesized several 6-O-pentanoyl mannopyranoside esters (5-9) with alkanoyl and sylfonyl chains reasonably in good yields. Both the prediction of activity spectra for substances (PASS) and in vitro tests indicated that these mannopyranoside esters possess better potentiality against fungal pathogens than the bacterial organisms. These SEs were also optimized with quantum chemical density functional theory (DFT), and various thermodynamic properties like frontier molecular orbital, and molecular electrostatic potential (MEP) were calculated and discussed. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) calculations indicated that these SEs can pass through blood brain barrier and less toxic. Drug-likeness results indicated good conditions for alkanoyl esters rather than sulfonyl esters despite their promising antifungal results. All the in vitro and in silico results indicated that the combination of pentanoyl (C5) and lauroyl (C12) chains in mannopyranoside framework, as in 9, might be a potential candidate for novel antifungal agent.

Novel mannopyranoside esters as sterol 14α-demethylase inhibitors: Synthesis, PASS predication, molecular docking, and pharmacokinetic studies

Direct unimolar one-step valeroylation of methyl α-d-mannopyranoside (MDM) furnished mainly 6-O-valeroate. However, similar reaction catalyzed by DMAP resulted 3,6-di-O-valeroate (21%) and 6-O-valeroate (47%) indicating reactivity sequence as 6-OH>3-OH>2-OH,4-OH. To get potential antimicrobial agents, 6-O-valeroate was converted into four 2,3,4-di-O-acyl esters, and 3,6-di-O-valeroate was converted into 2,4-di-O-acetate. Direct tetra-O-valeroylation of MDM gave a mixture of 2,3,4,6-tetra-O-valeroate and 2,3,6-tri-O-valeroate indicating that the C2-OH is more reactive than the equatorial C4-OH. The activity spectra analysis along with in vitro antimicrobial evaluation clearly indicated that these novel MDM esters had better antifungal activities over antibacterial agents. In this connection, molecular docking indicated that these MDM esters acted as competitive inhibitors of sterol 14α-demethylase (CYP51), an essential enzyme for clinical target to cure several infectious diseases. Furthermore, pharmacokinetic studies revealed that these MDM esters may be worth considering as potent candidates for oral and topical administration. Structure activity relationship (SAR) affirmed that saturated valeric chain (C5) in combination with caprylic (C8) chains was more promising CYP51 inhibitor over conventional antifungal antibiotics.