Design and Synthesis of 2-Phenylindolizine Acetamides: Molecular Docking, in Vitro Antimicrobial and Anticancer Activity Evaluation

In the present work, we synthesized a small library of 2-phenylindolizine acetamide derivatives 7a-i and studied their biological activity. The synthesis was accomplished starting with easily available starting material phenacyl bromide 1 proceeding through the key intermediate 6-methyl-7-nitro-2-phenylindolizine 4. All the compounds 7a-i were characterized using spectroscopy viz., 1H-NMR, 13C NMR, FTIR, and mass spectrometry. Interestingly, 2-phenylindolizine scaffolds 7c, 7f and 7g revealed a remarkable antibacterial activity against relevant organisms S. aureus, E. coli, S. pneumoniae, P. aeruginosa. The target compounds 7e and 7h showed excellent anticancer activity against Colo-205 and MDA-MB-231 cell lines with IC50 values of 68.62, 62.91, 54.23 and 46.34 μM respectively. Additionally, all the 2-phenylindolizine acetamide derivatives 7a-i were subjected to molecular docking prediction by Autodock 4.2. Compounds 7a, 7f and 7c exhibited very good hydrogen bonding amino acid interactions Asp83 (2.23 Å), Asp83 (2.08 Å), His74 (2.05 Å), His76 (1.71 Å), Ser80 (1.05 Å) with active site of Topoisomerase-IV from S. pneumoniae (4KPE). Further, the compounds 7a-i have revealed acceptable ranges for drug-likeliness properties upon evaluation using SwissADME for ADMET and physiochemical properties.

An interdisciplinary course on computer-aided drug discovery to broaden student participation in original scientific research

We present a new highly interdisciplinary project-based course in computer aided drug discovery (CADD). This course was developed in response to a call for alternative pedagogical approaches during the COVID-19 pandemic, which caused the cancellation of a face-to-face summer research program sponsored by the Louisiana Biomedical Research Network (LBRN). The course integrates guided research and educational experiences for chemistry, biology, and computer science students. We implement research-based methods with publicly available tools in bioinformatics and molecular modeling to identify and prioritize promising antiviral drug candidates for COVID-19. The purpose of this course is three-fold: I. Implement an active learning and inclusive pedagogy that fosters student engagement and research mindset; II. Develop student interdisciplinary research skills that are highly beneficial in a broader scientific context; III. Demonstrate that pedagogical shifts (initially incurred during the COVID-19 pandemic) can furnish longer-term instructional benefits. The course, which has now been successfully taught a total of five times, incorporates four modules, including lectures/discussions, live demos, inquiry-based assignments, and science communication.

A multi-modal approach to investigate Desmodium gangeticum's influence on stress-induced male infertility: In vivo, in vitro, and in silico assessments

Physical and psychological stress has an inverse relation with male libido and sperm quality. The present study investigates the potential fertility-enhancing properties of Desmodium gangeticum (DG) root extracts in male Wister rats subjected to immobilization-induced stress (SIMB). DG roots were extracted using n-hexane (HEDG), chloroform (CEDG), and water (AEDG). In the pilot study, aphrodisiac protentional was investigated at two doses (125 and 250 mg kg-1) of each extract. In the main study, the HEDG and AEDG at 125 and 250 mg kg-1 were challenged for the stress by immobilization (SIMB), for 6 h daily over 28 days. Parameters assessed included aphrodisiac effects, gonadosomatic index (GSI), semen quality, sperm quantity, fructose content, serum hormonal levels, testicular oxidative stress, and testicular histopathology. Additional in silico studies, including the lipid solubility index, molecular docking, molecular dynamics, and SymMap studies were conducted for validation. HEDG demonstrated significant aphrodisiac activity, improved - GSI, sperm quality and quantity, and fructose content, serum testosterone levels, histological changes induced by SIMB in the testes. Swiss ADME studies indicated Gangetin (a pterocarpan) had a high brain permeation index (4.81), a superior docking score (-8.22), and higher glide energy (-42.60), compared with tadalafil (-7.17). The 'Lig fit Prot' plot in molecular dynamics simulations revealed a strong alignment between Gangetin and phosphodiesterase type 5 (PDE5). HEDG exerts aphrodisiac effects by increasing blood testosterone levels and affecting PDE5 activity. The protective effects on spermatozoa-related parameters and testicular histological changes are attributed to the antioxidant and anti-inflammatory properties, of pterocarpan (gangetin).

Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach

CONTEXT

The COVID-19 (coronavirus disease 19) pandemic brought on by the SARS-CoV-2 outbreak (severe acute respiratory syndrome coronavirus 2) has stimulated the exploration of various available chemical compounds that could be used to treat the infection. This has driven numerous researchers to investigate the antiviral potential of several bioactive compounds from medicinal plants due to their reduced adverse effects compared to chemicals. Some of the bioactive compounds used in folklore treatment strategies are reported as effective inhibitors against the proliferative and infective cycles of SARS-CoV-2. The secondary metabolites from plants are generally used to treat various diseases due to their intact medicinal properties. The present study analyzes the inhibitory potential of phytochemicals from medicinal plants like Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera against SARS-CoV-2 by molecular docking.

METHODS

Ten druggable protein targets from SARS-CoV-2 are docked against the phytochemicals from the selected medicinal plants. The phytocompounds astragalin, isoquercetin, and 5-hydroxy-7-methoxy-6-c-glycosy flavone were found to have lower binding energy depicting their inhibitive potential compared with the reported inhibitors that are used in the treatment of SARS-CoV-2 infection. The phytocompounds found to have the least binding energy were selected for further analyses. To assess the compounds' potential as drugs, their ADMET characteristics were also examined. Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera six possible compounds were separately screened for ADME and toxicity characteristics; then, the results were analyzed. To assess the impact of the phytocompound binding on the dynamics of SARS-CoV-2 ribonuclease protein NSP15, microsecond-level all atomistic molecular dynamics simulations were performed, and their dynamics were analyzed. Microsecond-level molecular dynamics simulations of both the ligands complexed with NSP15 revealed that the ligand induces allosteric effects on NSP15, which could lead to destabilization of NSP15 hexameric interface and loss of RNA binding. The low binding energy exhibited by the phytochemicals from Lantana camera, Sphaeranthus indicus, and Nelumbo nucifera against the protein targets of SARS-CoV-2 showed inhibitory potential by the selected molecules. Their predicted interference of the enzymes involved in the molecular mechanisms aiding the proliferation of SARS-CoV-2 indicated the inhibitive ability of the phytochemicals.

Tacrolimus and Azole Derivatives of Agricultural and Human Health Importance: Prediction of ADME Properties

INTRODUCTION

Agricultural chemicals are impacting health nowadays. Recently, promising synergistic antifungal interaction between tacrolimus and some azole compounds was studied.

OBJECTIVE

To determine ADME parameters, potential side effects of test substances to reduce time and resources in the future.

METHODS

All descriptors and molecular parameters were obtained by the protocols of SwissADME and ProTox II.

RESULTS

In the result, the following physicochemical and drug-likeness parameters were calculated.

CONCLUSION

Studied triazoles 1 and 2 showed good ADME characteristics and promising toxicity levels suitable to be checked for in vitro toxicology in case of future advanced results in the agricultural field.

Molecular dynamics simulation and pharmacokinetics studies of ombuin and quercetin against human pancreatic α-amylase

Diabetes mellitus (DM) is a group of metabolic disorders characterised by chronic hyperglycaemia. DM is currently one of the top ten causes of death in humans. Chronic hyperglycaemia in DM leads to long-term damage and failure of different organs in the body. Type 2 DM (T2D) is the most common DM form, characterised by peripheral insulin resistance, relative insulin deficiency, impaired hepatic glucose production regulation and pancreatic β cell dysfunction. The human pancreatic α-amylase (HPA) inhibitor is currently one of the most effective methods developed to inhibit hyperglycaemia in T2D patients. However, the current standard drug available, acarbose, has been associated with severe side effects following prolonged use in patients. Therefore, an alternative drug capable of effectively inhibiting HPA with minimal side effects is required. Based on our previous study, we further explored the therapeutic potential of quercetin and ombuin via molecular dynamics (MD) simulation. The Desmond Simulation Package was used to run 100-ns MD simulations to examine the steady nature and conformational stability of the ligand-HPA complexes. Post-simulation molecular mechanics-generalised born surface area (MM-GBSA) analysis of HPA's binding free energy with quercetin and ombuin was explored. The lead compounds' drug-likeness, absorption, distribution, metabolism and elimination properties were also studied using the SwissADME tool. These results indicate that quercetin and ombuin have great potential as anti-DM drugs with more favourable properties than acarbose.Communicated by Ramaswamy H. Sarma.

New tetrazolopyrrolidine-1,2,3-triazole analogues as potent anticancer agents: design, synthesis and molecular docking studies

1,2,3-Triazole and tetrazole derivatives bearing pyrrolidines are found to exhibit notable biological activity and have become useful scaffolds in medicinal chemistry for application in lead discovery and optimization. We report design, synthesis and molecular docking studies of tetrazolyl-1,2,3-triazole derivatives (7a-i) bearing pyrrolidine moiety and evaluating their anticancer activity against four cancer cell lines viz. Hela, MCF-7, HCT-116 and HepG2. The structures of the new compounds were ascertained by spectral means IR, NMR: 1H &13C and Mass spectrum. From the studies compounds7a and 7i exhibited significant anticancer activity against the Hela cell line with IC50 = 0.32 ± 1.00, 1.80 ± 0.22 μM when compared to reference drug Doxorubicin (IC50 = 2.34 ± 0.11 μM), whereas 7h, 7i, and 7b were found to be active against MCF-7, HCT-116 and HepG2 cell lines with IC50 = 3.20 ± 1.40, 1.38 ± 0.06 and 0.97 ± 0.12 μM respectively. Notably 7a exhibited highest conventional hydrogen bondings TyrA:40, SerA:17, LysA:117, AlaA:146, Tyr218 with 3HB4and SerA:17, LysA:117, AlaA:146, TyrA:40 with 6IBZ and docking energy - 10.85, - 8.21 kcal/mol respectively. These compounds were further evaluated for their ADMET and physicochemical properties by using SwissADME. The results of the in vitro and in silico studies suggest that the tetrazole incorporated pyrrolidine-triazoles may possess the ideal structural requirements for further developing new anticancer agents.

Bioactive compounds from four Indian medicinal plants have different potency to induce sex reversal in Nile tilapia: A chromatographic, molecular docking and in silico analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Herbal plants such as Basella alba (Family: Basellaceae), Tribulus terrestris (Family: Zygophyllaceae), Asparagus racemosus (Family: Asparagaceae) and Mucuna pruriens (Family: Fabaceae) are mentioned in Indian traditional system of medicine Ayurveda to possess androgenic activity and increase male virility. The plants have been reported to improve testosterone level and sperm production in experimental male rodents as well.

AIM OF THE STUDY

Male Nile tilapias grow more quickly than females and hence are preferred for monosex Nile tilapia culture. Ethanol extracts of B. alba leaves (EB) and T. terrestris seeds (ET), and methanol extract of A. racemosus roots (MA) and M. pruriens seeds (MM) were found effective to induce masculinization in Nile tilapia. The present study intends to evaluate the anti-aromatase activity of EB, ET, MA and MM, to identify the androgenic bioactive compounds in the extracts, and to determine their pharmacokinetics. The study may validate the use of those plant extracts and their major bioactive phytoconstituents in the field of aquaculture and pharmaceuticals.

MATERIALS AND METHODS

The four crude plant extracts were first fractioned through column and thin layer chromatography (TLC). Three days old Nile tilapia juveniles (mean weight 0.025 ± 0.009g; mean length 12.50 ± 0.12 mm; n = 50 fish/replicate, 3 replicates/treatment) were then fed diets fortified with the obtained fractions for 30 days. After 30 days, fish were sacrificed and gonad aromatase mRNA expression, and 11-ketotestosterone (11-KT) and estradiol (E₂) levels were measured. Fractions yielding the highest male percentage for each plant were subject to gas chromatography-mass spectrometry (GC-MS) analysis. The in silico docking and SwissADME study were conducted with the components showing higher peak percentage in chromatogram.

RESULTS

After column chromatography and TLC analysis, EB, ET, MM and MA yielded 6 (EB1 - EB6), 8 (ET1- ET8), 14 (MM1-MM14) and 5 (MA1- MA5) fractions, respectively. Fish fed EB2, ET2, MA2 and MM13 fraction fortified diets showed significantly (p < 0.05) higher male percentage (92.32%-98.39%) compared to other treatment groups. EB2, ET2, MA2 and MM13 fed fish showed significantly (p < 0.05) higher 11-KT level compared to control male (+247.52 - +397.76%) and lower E₂ level compared to control female (-95.92% to -90.65%). Aromatase mRNA expression was significantly (p < 0.05) down-regulated by all these four fractions (-1.32 to -5.65 fold) with respect to control female. GC-MS analysis revealed the presence of 1-Octadecene (OD) in EB2, Phenol, 2,4-bis(1,1-dimethylethyl) (PD) in ET2 and MA2, 9,12-Octadecadienoic acid (Z,Z)- (ODDA) in MM13. In silico molecular docking indicated that PD is more effective than ODDA and OD to inhibit aromatase. In addition, PD showed better pharmacokinetics and more drug-likeness compared to OD and ODDA in SwissADME analysis.

CONCLUSION

The present results indicate that ET and MA are more potent to produce all-male tilapia by means of aromatase inhibition. PD can be an ideal compound to achieve masculinization in Nile tilapia through dietary administration, but further investigation is required.

Quantitative structure activity relationship studies of androgen receptor binding affinity of endocrine disruptor chemicals with index of ideality of correlation, their molecular docking, molecular dynamics and ADME studies

Endocrine disrupter chemicals (EDCs) are both natural and man-made chemicals that mimic, block or interfere with human hormonal system. In the present manuscript, QSAR modeling was performed for the androgen disruptors that interfere with biosynthesis, metabolism or action of androgens that causes adverse effects on male reproductive system. A set of 96 EDCs that exhibited affinity towards androgen receptors (Log RBA) in rats were employed for carrying out QSAR studies using Hybrid descriptors (combination of HFG and SMILES) through Monte Carlo Optimization. Using index of ideality of correlation (TF2), five splits were formed and predictability of five models resulting from these splits was assessed by various validation parameters. Models resulted from first split was the top most one with R2validation = 0.7878. Structural attributes responsible for change in endpoint were studied by employing correlation weights of structural attributes. In order to further validate the model, new EDCs were designed using these attributes. In silico molecular modelling studies were performed to assess the detailed interactions with the receptor. The binding energies of all the designed compounds were observed to be better than lead and are in the range of -10.46 to -14.80. Molecular dynamics simulation of 100 ns was performed for ED01 and NED05. The results revealed that the protein-ligand complex bearing NED05 was more stable than lead ED01 exhibiting better interactions with the receptor. Further, in an attempt to assess their metabolism, ADME studies were evaluated using SwissADME. The developed model enables to predict the characteristics of designed compounds in an authentic way.Communicated by Ramaswamy H. Sarma.

Switching of newly synthesized linker-based derivatives of non-steroidal anti-inflammatory drugs toward anti-inflammatory and anticancer activity

A new series of linker-based derivatives of non-steroidal anti-inflammatory drugs were designed and synthesized. All the compounds were well characterized with the help of various spectroscopic techniques such as FT-IR, ¹H NMR, ¹³C NMR, and HRMS. The main emphasis of this paper is to understand the switching of the most promising compounds 8 and 10 towards anti-inflammatory and anticancer activity in terms of in-silico and in-vitro studies in detail. During the molecular docking study, compounds 8 and 10 demonstrated the importance of hetero atoms as well as the perfect alignment of a compound in the binding pocket of a target site, which may affect their bioactivity. Here, the presence of 1,3‑dicarbonyl interactions with ASN 351 in compound 8 (not found in compound 10) may be responsible for its better inhibitory activity against the COX-2 target site. On the other hand, a slight increase in the potency of compound 10 towards anticancer activity may be due to the instantaneous participation of the OH group and carbonyl group to give conventional hydrogen bonds towards THR 149 amino acid residue, which was missing in compound 8. Molecular dynamics simulation was also performed for compounds 10 and 8 toward COX-2 and HER-2 protein sites. Further, compounds 8 and 10 were subjected to in-vitro COX-2 inhibition and cytotoxicity assay and the results obtained were in accordance with the in-silico study. Thus, compound 8 become more potent towards COX-2 inhibition with IC₅₀ value of 48.51 µg/ml and compound 10 showed good bioactivity toward cytotoxic activity with IC₅₀ value of 93.03 µg/ml.

In Silico Molecular Docking Approach of Melanin Against Melanoma Causing MITF Proteins and Anticancer, Oxidation-Reduction, Photoprotection, and Drug-Binding Affinity Properties of Extracted Melanin from Streptomyces sp. strain MR28

Melanin is a biopolymer reported for diverse biological actions to secure organisms over adverse environmental factors. In the last decade, melanin attributed considerable attention for its use in bioelectronics, photoprotection, environmental bioremediation, and drug discovery. Molecular docking study is the emerging trend in drug discovery for drug designing by targeting proteins. Considering the therapeutic nature of the melanin, we extracted melanin from Streptomyces sp. strain MR28, and it was tested for various biological activities, viz., DPPH free radical scavenging potency, sun protection factor (SPF), drug likeness by SwissADME, molecular docking of melanin on melanocyte-inducing transcription factor (MITF) proteins, cytotoxic activity on A375 malignant melanoma with induction of apoptosis study by flow cytometry, and adsorption study of melanin on doxorubicin and camptothecin drug for drug uptake by melanin. The melanin showed good scavenging potency of DPPH free radicals in a concentration-dependent manner. SPF of 38.64 ± 0.63, 55.53 ± 0.53, and 67.07 ± 0.82 were recorded at 0.06, 0.08, and 0.1 µg/mL, concentrations, respectively. SwissADME screening confirms the drug likeness of melanin. Docking of melanin with MITF proteins exhibited a maximum of - 9.2 kcal/mol binding affinity for 4ATK protein. Cytotoxicity of the melanin drug exhibited good inhibition of melanoma cells in dose-dependent way with significant IC₅₀ of 65.61 µg/mL; apoptotic study reveals melanin showed 64.02% apoptosis for melanin and 33.8% apoptosis for standard drug (doxorubicin). The maximum adsorptions for selected drugs camptothecin and doxorubicin to melanin were recorded at 90 min. In conclusion, the extracted melanin showed significant results over many biological applications and it can be used in the pharmaceutical field to avoid chemical-based drugs.

ADME Prediction, Structure-activity Relationship of Boswellic Acid Scaffold for the Aspect of Anticancer & Anti-inflammatory Potency

Nature is the chief source of various remedies which are used to cure various diseases. Boswellic acid (BA) is a secondary metabolite from the pentacyclic terpenoid compound groups that are derived from the plant genus Boswellia. The oleo gum resins of these plants are primarily composed of polysaccharides, with the remaining amounts of resin (30-60%) and essential oils (5-10%) soluble in organic solvents. BA and its analogs are also reported to exhibit various in vivo and biological responses for example anti-inflammatory, anti-tumor, free radical scavenging activity, etc. Among all analogs, 11-keto-β-boswellic acid (KBA) and 3-O-acetyl-11-keto-β-boswellic acid (AKBA) has been demonstrated to be the most effective at reducing cytokine production and inhibiting the inflammatory responsecausing enzymes. In this review, we summarized the computational ADME prediction via the SwissADME computational tool and the structure-activity relationship of the Boswellic acid scaffold for the aspect of anticancer and antiinflammatory potency. In addition to these research findings which are associated with the therapy of acute inflammation and some cancers, the potential of boswellic acids against other disorders was also discussed.

Synthesis and biological evaluation of thiosemicarbazone derivatives

In this study, firstly, 22 thiosemicarbazone derivatives (3a-y) were synthesized. Then, ADME parameters, pharmacokinetic properties, drug-like structures, and suitability for medicinal chemistry of these molecules were studied theoretically by using SwissADME and admetSAR programs. According to the results of these theoretical studies, it can be said that the bioavailability and bioactivity of these compounds may be high. In silico molecular docking between ligands (thiosemicarbazone derivatives) and targeted proteins (protein-78 (GRP78) for C6 and quinone reductase-2 (4ZVM for MCF 7) was analyzed using Hex 8.0.0 docking software. According to the docking data, almost all molecules had higher negative E values than Imatinib (already used as a drug). For this, in vitro anticancer studies of these molecules were done. The cytotoxic activities of thiosemicarbazone derivatives (3a-y) were evaluated on C6 glioma and MCF7 breast cancer cell lines at 24 h, and Imatinib was used as the positive control. According to the results of the cytotoxicity assay, it can be said that the five compounds (3b, c, f, g, and m with IC₅₀ = 10.59-9.08 μg/mL; Imatinib IC₅₀ = 11.68 μg/mL) showed more potent cytotoxic activity than Imatinib on C6 cell line. Together with to these results ten compounds (3b, d, f, g, I, k, l, m, n, and r with IC₅₀ = 7.02-9.08 μg/mL; Imatinib IC₅₀ = 9.24 μg/mL) had a more effective cytotoxic activity against MCF7 cell line than Imatinib. Compound 3 m showed the highest antiproliferative effect against C6 and MCF7 cell lines.

Molecular Descriptors as a Facile Tool toward Designing Surface-Functionalized Nanoparticles for Drug Delivery

Modulating the surface chemistry of nanoparticles, often by grafting hydrophilic polymer brushes (e.g., polyethylene glycol) to prepare nanoformulations that can resist opsonization in a hematic environment and negotiate with the mucus barrier, is a popular strategy toward developing biocompatible and effective nano-drug delivery systems. However, there is a need for tools that can screen multiple surface ligands and cluster them based on both structural similarity and physicochemical attributes. Molecular descriptors offer numerical readouts based on molecular properties and provide a fertile ground for developing quick screening platforms. Thus, a study was conducted with 14 monomers/repeating blocks of polymeric chains, namely, oxazoline, acrylamide, vinylpyrrolidone, glycerol, acryloyl morpholine, dimethyl acrylamide, hydroxypropyl methacrylamide, hydroxyethyl methacrylamide, sialic acid, carboxybetaine acrylamide, carboxybetaine methacrylate, sulfobetaine methacrylate, methacryloyloxyethyl phosphorylcholine, and vinyl-pyridinio propanesulfonate, capable of imparting hydrophilicity to a surface when assembled as polymeric brushes. Employing free, Web-based, and user-friendly platforms, such as SwissADME and ChemMine tools, a series of molecular descriptors and Tanimoto coefficient of molecular pairs were determined, followed by hierarchical clustering analyses. Molecular pairs of oxazoline/dimethyl acrylamide, hydroxypropyl methacrylamide/hydroxyethyl methacrylamide, acrylamide/glycerol, carboxybetaine acrylamide/vinyl-pyridinio propanesulfonate, and sulfobetaine methacrylate/methacryloyloxyethyl phosphorylcholine were clustered together. Similarly, the molecular pair of hydroxypropyl methacrylamide/hydroxyethyl methacrylamide demonstrated a high Tanimoto coefficient of >0.9, whereas the pairs oxazoline/vinylpyrrolidone, acrylamide/dimethyl acrylamide, acryloyl morpholine/dimethyl acrylamide, acryloyl morpholine/hydroxypropyl methacrylamide, acryloyl morpholine/hydroxyethyl methacrylamide, carboxybetaine methacrylate/sulfobetaine methacrylate, and glycerol/hydroxypropyl methacrylamide had a Tanimoto coefficient of >0.8. The analyzed data not only demonstrated the ability of such in silico tools as a facile technique in clustering molecules of interest based on their structure and physicochemical characteristics but also provided vital information on their behavior within biological systems, including the ability to engage an array of possible molecular targets when the monomers are self-assembled on nanoparticulate surfaces.

In search of HIV entry inhibitors using molecular docking, ADME and toxicity studies of some Thiazolidinone-Pyrazine derivatives against CXCR4 co-receptor

BACKGROUND

Entry inhibitors prevent binding of human immunodeficiency virus protein to the chemokine receptor CXCR4 and are used along with conventional anti-HIV therapy. They aid in restoring immunity and can prevent the development of HIV-TB co-infection.

AIM

In the present study various thiazolidinone-pyrazine derivatives earlier studied for NNRT inhibition activity were gauged for their entry inhibitor potential.

OBJECTIVE

Objective of the study is to perform molecular docking, ADME, toxicity studies of some Thiazolidinone-Pyrazine Derivatives as entry inhibitors targeting CXCR4 co-receptors.

METHODS

In-silico docking studies were performed using AutoDock Vina software and compounds were further studied for ADME and toxicity using SwissADME and pkCSM software respectively.

RESULTS

Taking into consideration the docking results, pharmacokinetic behaviour and toxicity profile four molecules (compound 1, 9, 11 and 16) have shown potential as entry inhibitors.

CONCLUSION

These compounds have shown potential as both NNRTI and entry inhibitors and hence can be used in management of immune compromised diseases like TB-HIV coinfection.

In silico ADME/Pharmacokinetic and Target Prediction Studies of Ethambutol as Drug Molecule

BACKGROUND

The conventional approach for the development of any pharmaceutically active molecule is a time-consuming and costly process because the synthesis is followed by laboratory tests which are then followed by long clinical trials. Hence a faster approach is desired. This article discusses Ethambutol, a frontline anti-tubercular drug that has its properties predicted by the SwissADME tool and the results would be compared with the findings published in the literature.

OBJECTIVE

The main objective is to study the predicted and experimental ADME properties, compare them. As well as study the predicted targets and understand the use of SwissADME for designing other drug molecules.

METHOD

SwissADME, an online tool for ADME prediction was used along with Swiss Target Prediction to understand the targets of the drug. Further, experimental data was obtained from the available scientific literature.

RESULTS

We found certain similarities between the predicted and experimental data. However, there were some variations, depending on the testing conditions. The results are interpreted ahead in the article.

CONCLUSION

Ethambutol's predicted ADME properties are discussed and as per findings from results, it can be concluded that other drug molecules can be similarly predicted using these tools. Also, based on predicted data we can reformulate and prepare some different preparations of the drug.

GC-MS Analysis, Molecular Docking and Pharmacokinetic Properties of Phytocompounds from Solanum torvum Unripe Fruits and Its Effect on Breast Cancer Target Protein

This study was designed to identify phytocompounds from the aqueous extract of Solanum torvum unripe fruits using GC–MS analysis against breast cancer. For this, the identified phytocompounds were subjected to perform molecular docking studies to find the effects on breast cancer target protein. Pharmacokinetic properties were also tested for the identified phytocompounds to evaluate the ADMET properties. Molecular docking studies were done using docking software PyRx, and pharmacokinetic properties of phytocompounds were evaluated using SwissADME. From the results, ten best compounds were identified from GC–MS analysis against breast cancer target protein. Of which, three compounds showed very good binding affinity with breast cancer target protein. They are ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) (− 7.3 kcal/mol), aspidospermidin-17-ol,1-acetyl-16-methoxy (− 6.7 kcal/mol) and 2-(3,4-dichlorophenyl)-4-[[2-[1-methyl-2-pyrrolidinyl]ethyl amino]-6-[trichloromethyl]-s-triazine (− 6.7 kcal/mol). Further, docking study was performed for the synthetic drug doxorubicin to compare the efficiency of phytocompounds. The binding affinity of ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) is higher than the synthetic drug doxorubicin (− 7.2 kcal/mol), and the binding affinity of other compounds is also very near to the drug. Hence, the present study concludes that the phytocompounds from the aqueous extract of Solanum torvum unripe fruits have the potential ability to treat breast cancer.

Novel 6-hydroxyquinolinone derivatives: Design, synthesis, antimicrobial evaluation, in silico study and toxicity profiling

Infectious diseases of bacteria and fungi have become a major risk to public health because of antibiotic and antifungal resistance. However, the availability of effective antibacterial and antifungal agents is becoming increasingly limited with growing resistance to existing drugs. In response to that, novel agents are critically needed to overcome such resistance. A new series of 6-hydroxyquinolinone 3, 4, 5a, 5b, 6a and 6b bearing different side chains were synthesized and evaluated as antimicrobials against numbers of bacteria and fungi, using inhibition zone technique. As one of these derivatives, compound 3 was identified as a potent antibacterial and antifungal agent against all tested microorganisms with good minimum inhibitory concentration values comparable to reference drugs. Molecular docking studies were performed on antibacterial and antifungal targets; microbial DNA gyrase B of Staphylococcus aureus (PDB ID: 4URO); N-myristoyltransferase of Candida albicans (PDB ID: 1IYK), respectively, to predict the most probable type of interaction at the active site of the target protein in addition to binding affinities and orientations of docked ligands. Additionally, in silico prediction in terms of detailed physicochemical ADME and toxicity profile relating drug-likeness as well as medicinal chemistry friendliness was performed to all synthesized compounds. The results indicated that a novel 4,6-dihydroxyquinolin-2(1H)-one (3) is likely to be a newly synthesized drug candidate, indicating low toxicity in addition to good in silico absorption. In order to pave the way for more logical production of such compounds, structure-activity and toxicity relationships are also discussed.

Thiazole-Chalcone Hybrids as Prospective Antitubercular and Antiproliferative Agents: Design, Synthesis, Biological, Molecular Docking Studies and In Silico ADME Evaluation

Compounds bearing thiazole and chalcone pharmacophores have been reported to possess excellent antitubercular and anticancer activities. In view of this, we designed, synthesized and characterized a novel series of thiazole-chalcone hybrids (1-20) and further evaluated them for antitubercular and antiproliferative activities by employing standard protocols. Among the twenty compounds, chalcones 12 and 7, containing 2,4-difluorophenyl and 2,4-dichlorophenyl groups, showed potential antitubercular activity higher than the standard pyrazinamide (MIC = 25.34 µM) with MICs of 2.43 and 4.41 µM, respectively. Chalcone 20 containing heteroaryl 2-thiazolyl moiety exhibited promising antiproliferative activity against the prostate cancer cell line (DU-145), higher than the standard methotrexate (IC50 = 11 ± 1 µM) with an IC50 value of 6.86 ± 1 µM. Furthermore, cytotoxicity studies of these compounds against normal human liver cell lines (L02) revealed that the target molecules were comparatively less selective against L02. Additional computational studies using AutoDock predicted the key binding interactions responsible for the activity and the SwissADME tool computed the in silico drug likeliness properties. The lead compounds generated through this study, create a way for the optimization and development of novel drugs against tuberculosis infections and prostate cancer.

Synthesis and anticancer potential of novel 5,6-oxygenated and/or halogenated steroidal d-homo lactones

A series of 5,6-modified steroidal d-homo lactones, comprising of halogenated and/or oxygenated derivatives, was synthesized and evaluated for potential anticancer properties. Preparation of many of these compounds involved investigating alternative synthetic pathways. In silico ADME testing was performed for both novel and some previously synthesized compounds. Calculated physicochemical properties were in accordance with the Lipinski, Veber, Egan, Ghose and Muegge criteria, suggesting the potential of these molecules as orally active agents. Cytotoxicity of the synthesized steroid derivatives was tested on six tumor and one normal human cell line. None of the investigated derivatives was toxic to non-cancerous MRC-5 control cells. Most of the compounds showed significant cytotoxicity against the treated cancer cell lines. Most notably, the 3β,5α,6β-trihydroxy derivative exhibited strong cytotoxicity against multiple cell lines (MCF-7, MDA-MB-231 and HT-29), with the highest effect observed for lung adenocarcinoma (A549) cells, for which this steroid was more cytotoxic than all of the three commercial chemotherapeutic agents used as reference compounds. Molecular docking suggests the 3β,5α,6β-trihydroxy derivative could bind the EGFR tyrosine kinase domain with high affinity, providing a potential mechanism for its cytotoxicity via inhibition of EGFR signaling. The most active compounds were further studied for their potential to induce apoptosis by the double-staining fluorescence method; where the 5α,6β-dibromide, 5α,6β-dichloride and 3β,5α,6β-triol induced apoptotic changes in all three treated cell lines: MDA-MB-231, HT-29 and A549. To predict interactions with nuclear steroidal receptors, affinity for the ligand binding domains of ERα, ERβ and AR was measured using a yeast-based fluorescence assay. The 5β,6β-epoxide, dibromide and 5α-hydroxy-3,6-dioxo derivatives showed affinity for ERα, while the 5α-fluoro-6β-hydroxy and 3β-acetoxy-5α,6β-dihydroxy derivatives were identified as ERβ ligands. None of the tested compounds showed affinity for AR. Structure-activity relationships of selected compounds were also examined.

Application of QSAR Method in the Design of Enhanced Antimalarial Derivatives of Azetidine-2-carbonitriles, their Molecular Docking, Drug-likeness, and SwissADME Properties

The resistance of the P. falciparum strain to some of the antimalarial drugs has been a dominant dilemma facing the treatment of this fetid disease. This necessitates the detection and development of new antimalarial agents targeting the P. falciparum. Azetidine-2-carbonitriles reported for its antimalarial activities, could provide an alternative to the customized antimalarial drugs. Leading to the use of quantitative structure-activity relationship (QSAR) studies, which relates the structures of Azetidine-2-carbonitriles with their activities to generate predictive models. The structures were optimized using density functional theory (DFT) DFT/B3LYP/6-31G* basis set to generate their molecular descriptors, where five predictive models were constructed using the generated descriptors. The models were constructed using the genetic function algorithm component of a material studio, where the model with good statistical parameters, high coefficient of determination (R2) = 0.9465, cross-validated R2 (Q2cv) = 0.8981, Q2 (L4O)cv = 0.9272, and highest external validated R2 (R2 pred) = 0.6915 was selected as the best model. These statistical results show the robustness, excellent power of prediction, and validity of the selected model. The descriptor, SpMax2_Bhp (the maximum absolute eigenvalue of Barysz matrix for n = 2 was weighted by polarizability), was revealed to be the most influential in the model due to its highest mean effect. The descriptor played a role in the design of sixteen (16) theoretical derivatives of Azetidine-2-carbonitriles using compound 25 as the design template by increasing polarizability of the compounds through substitution of the various group with electron deactivating groups (F, I, Cl, SO3H, CN, NO2, etc.) at different position of the template. The designed compounds were docked with Plasmodium falciparum dihydroorotate dehydrogenase (Pf-DHODH), giving compound D9 the highest binding energy. The designed compounds were further screened for their drug-likeness, where they all pass Lipinski's RO5. All the compounds show good skin permeability coefficient and have low Gastrointestinal absorption while few compounds D1, D2, D3, D14, and D15 inhibiting the CYP1A2.

The drug likeness analysis of anti-inflammatory clerodane diterpenoids

Inflammation is an active defense response of the body against external stimuli. Long term low-grade inflammation has been considered as a deteriorated factor for aging, cancer, neurodegeneration and metabolic disorders. The clinically used glucocorticoids and non-steroidal anti-inflammatory drugs are not suitable for chronic inflammation. Therefore, it's urgent to discover and develop new effective and safe drugs to attenuate inflammation. Clerodane diterpenoids, a class of bicyclic diterpenoids, are widely distributed in plants of the Labiatae, Euphorbiaceae and Verbenaceae families, as well as fungi, bacteria, and marine sponges. Dozens of anti-inflammatory clerodane diterpenoids have been identified on different assays, both in vitro and in vivo. In the current review, the up-to-date research progresses of anti-inflammatory clerodane diterpenoids were summarized, and their druglikeness was analyzed, which provided the possibility for further development of anti-inflammatory drugs.

In silico methods for metabolomic and toxicity prediction of zearalenone, α-zearalenone and β-zearalenone

Zearalenone (ZEA), α-zearalenol (α-ZEL) and β-zearalenol (β-ZEL) (ZEA's metabolites) are co/present in cereals, fruits or their products. All three with other compounds, constitute a cocktail-mixture that consumers (and also animals) are exposed and never entirely evaluated, nor in vitro nor in vivo. Effect of ZEA has been correlated to endocrine disruptor alterations as well as its metabolites (α-ZEL and β-ZEL); however, toxic effects associated to metabolites generated once ingested are unknown and difficult to study. The present study defines the metabolomics profile of all three mycotoxins (ZEA, α-ZEL and β-ZEL) and explores the prediction of their toxic effects proposing an in silico workflow by using three programs of predictions: MetaTox, SwissADME and PASS online. Metabolomic profile was also defined and toxic effect evaluated for all metabolite products from Phase I and II reaction (a total of 15 compounds). Results revealed that products describing metabolomics profile were: from O-glucuronidation (1z and 2z for ZEA and 1 ab, 2 ab and 3 ab for ZEA's metabolites), S-sulfation (3z and 4z for ZEA and 4 ab, 5 ab and 6 ab for ZEA's metabolites) and hydrolysis (5z and 7 ab for ZEA's metabolites, respectively). Lipinsky's rule-of-five was followed by all compounds except those coming from O-glucuronidation (HBA>10). Metabolite products had better properties to reach blood brain barrier than initial mycotoxins. According to Pa values (probability of activation) order of toxic effects studied was carcinogenicity > nephrotoxic > hepatotoxic > endocrine disruptor > mutagenic (AMES TEST) > genotoxic. Prediction of inhibition, induction and substrate function on different isoforms of Cytochrome P450 (CYP1A1, CYP1A2, CYP2C9 and CYP3A4) varied for each compounds analyzed; similarly, for activation of caspases 3 and 8. Relying to our findings, the metabolomics profile of ZEA, α-ZEL and β-ZEL analyzed by in silico programs predicts alteration of systems/pathways/mechanisms that ends up causing several toxic effects, giving an excellent sight and direct studies before starting in vitro or in vivo assays contributing to 3Rs principle; however, confirmation can be only demonstrated by performing those assays.

A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.

Xanthones, A Promising Anti-Inflammatory Scaffold: Structure, Activity, and Drug Likeness Analysis

Inflammation is the body's self-protective response to multiple stimulus, from external harmful substances to internal danger signals released after trauma or cell dysfunction. Many diseases are considered to be related to inflammation, such as cancer, metabolic disorders, aging, and neurodegenerative diseases. Current therapeutic approaches include mainly non-steroidal anti-inflammatory drugs and glucocorticoids, which are generally of limited effectiveness and severe side-effects. Thus, it is urgent to develop novel effective anti-inflammatory therapeutic agents. Xanthones, a unique scaffold with a 9H-Xanthen-9-one core structure, widely exist in natural sources. Till now, over 250 xanthones were isolated and identified in plants from the families Gentianaceae and Hypericaceae. Many xanthones have been disclosed with anti-inflammatory properties on different models, either in vitro or in vivo. Herein, we provide a comprehensive and up-to-date review of xanthones with anti-inflammatory properties, and analyzed their drug likeness, which might be potential therapeutic agents to fight against inflammation-related diseases.

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

Octyl β-d-glucopyranoside (OBG), prepared from d-glucose and octan-1-ol employing MW method, was subjected to direct dimolar valeroylation in pyridine at room temperature (25 °C) with valeroyl chloride. This mainly furnished the corresponding 3,6-di-O-valeroate in 57% yield indicating the regioselectivity at C-6 and C-3 positions. For structural elucidation and to get newer glucopyranosides of potential antimicrobial 3,6-di-O-valeroate was further converted into four novel 2,4-di-O-acyl esters reasonably in good yields. Per-O-acetate and per-O-benzoate of OBG were also prepared for SAR study. PASS predication and in vitro antimicrobial studies established them as better antifungal agent than that of antibacterial. SAR study along with AdmetSAR and SwissADME suggested that incorporation of alkanoyl and aromatic ester groups on octyl glucopyranoside core increase antimicrobial potentiality in very low concentration (10 μgmL^-1). Molecular docking revealed that novel 2,4-di-O-tosyl ester and 2,3,4,6-tetra-O-benzoyl ester may act as competitive inhibitors of lanosterol 14-alpha demethylase.

Advances in In-Silico based Predictive In-Vivo Profiling of Novel Potent β-Glucuronidase Inhibitors

BACKGROUND

Intestinal β-glucuronidase enzyme has a significant importance in colorectal carcinogenesis. Specific inhibition of the enzyme helps prevent immune reactivation of the glucuronide- carcinogens, thus protecting the intestine from ROS (Reactive Oxidative Species) mediatedcarcinogenesis.

OBJECTIVES

Advancement in In-silico based techniques has provided a broad range of studies to carry out the drug design and development process smoothly using SwissADME and BOILED-Egg tools.

METHODS

In our designed case study, we used SwissADME and BOILED-Egg predictive computational tools to estimate the physicochemical, human pharmacokinetics, drug-likeness, medicinal chemistry properties and membrane permeability characteristics of our recently In-vitro evaluated novel β-Glucuronidase inhibitors.

RESULTS

Out of the eleven screened potent inhibitors, compound (8) exhibited excellent bioavailability radar against the six molecular descriptors, good (ADME) Absorption, Distribution, Metabolism and Excretion along with P-glycoprotein, CYP450 isozymes and membranes permeability profile. On the basis of these factual observations, it is to be predicted that compound (8) can achieve in-vivo experimental clearance efficiently, Therefore, in the future, it can be a drug in the market to treat various disorders associated with the overexpression of β-Glucuronidase enzyme such as various types of cancer, particularly hormone-dependent cancer such as (breast, prostate, and colon cancer). Moreover, other compounds (1-7, & 9-11), have also shown good predictive pharmacokinetics, medicinal chemistry, BBB and HIA membranes permeability profiles with slight lead optimization to obtain improved results.

CONCLUSION

In consequence, in-silico based studies are considered to provide robustness for a rational drug design and development approach to avoid the possibility of failures of drug candidates in the later stages of drug development phases. The results of this study effectively reveal the possible attributes of potent β-Glucuronidase inhibitors, for further experimental evaluation.