Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines

Biomarker triterpenoids of Centella asiatica as potential antidepressant agents: Combining in vivo and in silico studies

Although there are various treatments available for depression, some patients may experience resistance to treatment or encounter adverse effects. Centella asiatica (C. asiatica) is an ancient medicinal herb used in Ayurvedic medicine for its rejuvenating, neuroprotective and psychoactive properties. This study aims to explore the antidepressant-like effects of the major constituents found in C. asiatica, i.e., asiatic acid, asiaticoside, madecassic acid, and madecassoside at three doses (1.25, 2.5, and 5 mg/kg, i.p), on the behavioural and cortisol level of unpredictable chronic stress (UCS) zebrafish model. Based on the findings from the behavioural study, the cortisol levels in the zebrafish body after treatment with the two most effective compounds were measured using enzyme-linked immunosorbent assay (ELISA). Furthermore, a molecular docking study was conducted to predict the inhibitory impact of the triterpenoid compounds on serotonin reuptake. The in vivo results indicate that madecassoside (1.25, 2.5, and 5 mg/kg), asiaticoside and asiatic acid (5 mg/kg) activated locomotor behaviour. Madecassoside at all tested doses and asiaticoside at 2.5 and 5 mg/kg significantly decreased cortisol levels compared to the stressed group, indicating the potential regulation effect of madecassoside and asiaticoside on the hypothalamic-pituitary-adrenal axis overactivity. This study highlights the potential benefits of madecassoside and asiaticoside in alleviating depressive symptoms through their positive effects on behaviour and the hypothalamic-pituitary-adrenal (HPA)- axis in a chronic unpredictable stress zebrafish model. Furthermore, the in silico study provided additional evidence to support these findings. These promising results suggest that C. asiatica may be a valuable and cost-effective therapeutic option for depression, and further research should be conducted to explore its potential benefits.

Structure-based virtual screening of anti-breast cancer compounds from Artemisia absinthium-insights through molecular docking, pharmacokinetics, and molecular dynamic simulations

Breast cancer is the world's second most frequent malignancy, with a significant mortality and morbidity rate. Nowadays, natural breast cancer medicine has piqued attention as disease-curing agent with low side effects. Herein, the leaf powder of Artemisia absinthium was extracted with ethanol, and GC-MS and LC-MS methods were employed to identify the phytocompounds. Using commercial software SeeSAR-9.2 and StarDrop, identified phytocompounds were docked with estrogen and progesterone breast cancer receptors as they promote breast cancer growth to find the binding affinity of the ligands, drugability, and toxicity. Hormone-mediated breast cancer accounts for about 80% of all cases of breast cancer. Cancer cells proliferate when estrogen and progesterone hormones are attached to these receptors. The molecular docking results demonstrated that 3',4',5,7-Tetrahydroxyisoflavanone (THIF) has stronger binding efficacy than standard drugs and other phytocompounds with -28.71 (3 hydrogen bonds) and -24.18 kcal/mol (6 hydrogen bonds) binding energies for estrogen and progesterone receptors, respectively. Pharmacokinetics and toxicity analysis were done to predict the drug-likeness of THIF which results in good drugability and less toxicity. The best fit THIF was subjected to a molecular dynamics simulation analysis by using Gromacs to analyze the conformational changes that occurred during protein-ligand interaction and found that, the structural changes were observed. The results from MD simulation and pharmacokinetic studies suggested that THIF can be expected that in vitro and in vivo research on this compound may lead to the development of a potent anti-breast cancer drug in the future.Communicated by Ramaswamy H. Sarma.

A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis

Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.

Antiemetic activity of abietic acid possibly through the 5HT3 and muscarinic receptors interaction pathways

The present study was designed to evaluate the antiemetic activity of abietic acid (AA) using in vivo and in silico studies. To assess the effect, doses of 50 mg/kg b.w. copper sulfate (CuSO4⋅5H2O) were given orally to 2-day-old chicks. The test compound (AA) was given orally at two doses of 20 and 40 mg/kg b.w. On the other hand, aprepitant (16 mg/kg), domperidone (6 mg/kg), diphenhydramine (10 mg/kg), hyoscine (21 mg/kg), and ondansetron (5 mg/kg) were administered orally as positive controls (PCs). The vehicle was used as a control group. Combination therapies with the referral drugs were also given to three separate groups of animals to see the synergistic and antagonizing activity of the test compound. Molecular docking and visualization of ligand-receptor interaction were performed using different computational tools against various emesis-inducing receptors (D2, D3, 5HT3, H1, and M1-M5). Furthermore, the pharmacokinetics and toxicity properties of the selected ligands were predicted by using the SwissADME and Protox-II online servers. Findings indicated that AA dose-dependently enhances the latency of emetic retching and reduces the number of retching compared to the vehicle group. Among the different treatments, animals treated with AA (40 mg/kg) exhibited the highest latency (98 ± 2.44 s) and reduced the number of retching (11.66 ± 2.52 times) compared to the control groups. Additionally, the molecular docking study indicated that AA exhibits the highest binding affinity (- 10.2 kcal/mol) toward the M4 receptors and an elevated binding affinity toward the receptors 5HT3 (- 8.1 kcal/mol), M1 (- 7.7 kcal/mol), M2 (- 8.7 kcal/mol), and H1 (- 8.5 kcal/mol) than the referral ligands. Taken together, our study suggests that AA has potent antiemetic effects by interacting with the 5TH3 and muscarinic receptor interaction pathways. However, additional extensive pre-clinical and clinical studies are required to evaluate the efficacy and toxicity of AA.

Integration of virtual screening of phytoecdysteroids as androgen receptor inhibitors by 3D-QSAR Model, CoMFA, molecular docking and ADMET analysis: An extensive and interactive machine learning

Ecdysteroids, a class of naturally isolated polyhydroxylated sterols, stands at a very good place in the pharmaceutical industry from their medicinal point of views like anti-inflammatory, neuroprotective, anti-microbial, anti-diabetic, antioxidant, and anti-tumor effects. Due to their excellent antioxidant and anti-microbial potential, ecdysteroids have extensive use in skin products, especially derma creams. To monitor the best anti-acne phytoecdysteroids, here made use of different computational approaches, by using the rapid, easy, cost-effective and high throughput method to screen and identify ecdysteroids as androgen receptor inhibitors. 3D-QSAR study was carried out on a dataset of ecdysteroids by using comparative molecular field analysis (CoMFA) to determine the factors responsible for the activity of compounds. Statistically a cross-validated (q2) 0.1457 and regression coefficient (r2) 0.9713 indicated the best model. Contour map results showed the influence of steric effect to enhance activity. A molecular docking analysis was done to further find out the binding sites and their anti-acne potential against three crystal structured macromolecules (PDB ID: 2REQ, 2BAC, 4EM0). Docking results were further evaluated by prime MM-GBSA analysis and findings confirmed the accuracy. Toxicity by ADMET assessment was carried out and M2 was found as lead druglike with best anti-acne activity against Propionium acnes GehA lipase bacteria after passing all filters. This research study is novel because it is representing first effort to explore ecdysteroids class for their high therapeutic output as androgen receptor inhibitor by using computational tools and expectedly led to novel scaffold for androgen receptor inhibitor. This is a novel and new approach to investigate the ecdysteroids for first time for their practical applications.

Optimization of an edible film formulation by incorporating carrageenan and red wine lees into fish gelatin film matrix

The study aimed to use response surface methodology (RSM) to create and understand a novel edible film made from fish gelatin (FG). This film includes wine lees (WL) and carrageenan (CAR). The concentrations of WL (0, 1, 2, and 3 %) and CAR (0, 1, and 3 %) were considered independent variables. The process variable combinations for the optimal response functions were 1.926 % WL and 3 % CAR, forming soft and rigid films with low tensile strength (TS) and high elongation at break (EAB%). Based on the evaluation of each response, FG film had the highest TS value, FG/CAR(3 %) film had the maximum EAB, and FG/WL (3 %)/CAR (3 %) film had the lowest vapor permeability (WVP) and the highest opacity (OP). The incorporation of WL considerably improved the functional properties of these films, enabling strong antioxidant activity and high phenolic content. Characterization of the films with analytical techniques: Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and X-ray diffraction (XRD) analysis demonstrated a considerable interaction between WL and FG, indicating a high level of compatibility between the two substances. Our data suggest that the formulation of edible films can be adjusted to fit the specific requirements of the design.

Synergistic formulation approach for developing pea protein and guar gum enriched olive oil-in-water emulsion gels as solid fat substitutes: Formulation optimization, characterization, and molecular simulation

This study aimed to optimize the formulation of olive oil-in-water (O/W) emulsion gels by incorporating Pea Protein (PP) and Guar Gum (GG) as alternative options for solid fats. The optimum rheological (consistency index, apparent viscosity, recovery) and texture (firmness) properties of the emulsion gels were obtained using a mixture of 2 % PP, 1 % GG, 60 % Olive Oil (OO), and 37 % Water (W). The blend of PP2/GG1 showed the highest results for recovery and firmness, 111.27 % and 33.89 g, respectively. PP/GG blend emulsion gels exhibited higher absolute ζ-potential values, ranging between -72.3 and -77.4 mV. The polydispersity index (PDI) ranged from 0.185 to 0.535, with the most uniform distributions found in the PP/GG blend emulsion gels. Strong phase separation resistance indicated strong stability of PP-GG complex emulsion gels. Higher PP concentrations decreased emulsion oxidation. FTIR and XRD research showed that PP and GG interact strongly, indicating good compatibility. The free binding energy of the most stable configuration of the molecules was -6.8 kcal mol-1, indicating a high affinity. PP interacted with GG through 9 amino acid residues, with notable residues being Asp 224, Thr 235, Ala 332, Ile 334, and Arg 336, and their respective interaction distances ranged between 2.69 Å and 3.87 Å.

Aspirin as a potential drug repurposing candidate targeting estrogen receptor alpha in breast cancer: a molecular dynamics and in-vitro study

Estrogen receptor alpha (ERα) is expressed by 70% of breast cancers (BCs). Any deregulation in ERα signaling is crucial for the initiation and progression of BC. Because of development of resistance to anti-estrogenic compounds, repurposing existing drugs is an apt strategy to avoid a long drug-discovery process. Substantial epidemiologic evidence suggests that Aspirin use reduces the risk of different cancers including BC, while its role as an adjuvant or a possible antineoplastic agent in cancer treatment is being investigated. In this study, we attempted to explore possibilities of ERα inhibition by Aspirin which may act through competitive binding to the ligand binding domain (LBD) of ERα. A list of 48 ERα-LBD crystal structures bound with agonists, antagonists, and selective ER modulators (SERMs) was thoroughly analysed to determine interaction patterns specific to each ligand category. Exhaustive docking and 500 ns molecular dynamics (MD) studies were performed on three ERα - Aspirin complexes generated using agonist, antagonist, and SERM-bound crystal structures. Besides, three ERα crystal structures bound to agonist, antagonist, and SERM respectively were also subjected to MD simulations. Aspirin showed good affinity to LBD of ERα. Comparative analyses of binding patterns, conformational changes and molecular interaction profiles from the docking results and MD trajectories suggests that Aspirin was most stable in complex generated using SERM bound crystal structure of ERα and showed interactions with Gly-521, Ala-350, Leu-525 and Thr-347 like SERMs. In addition, in-vitro assays, qPCR, and immunofluorescent assay demonstrated the decline in the expression of ERα in MCF-7 upon treatment with Aspirin. These preliminary bioinformatical and in-vitro findings may form the basis to consider Aspirin as a potential candidate for targeting ERα, especially in tamoxifen-resistant cancers.Communicated by Ramaswamy H. Sarma.

Targeted Drug Designing for Treating Masticatory Myofascial Pain Dysfunction Syndrome: An In Silico Simulation Study

Background Masticatory Myofascial Pain Dysfunction Syndrome (MMPDS) is a musculoligamentous disorder that shares similarities with temporomandibular joint pain and odontogenic pain. It manifests as dull or aching pain in masticatory muscles, influenced by jaw movement. Computer-aided drug design (CADD) encompasses various theoretical and computational approaches used in modern drug discovery. Molecular docking is a prominent method in CADD that facilitates the understanding of drug-bimolecular interactions for rational drug design, mechanistic studies & the formation of stable complexes with increased specificity and potential efficacy. The docking technique provides valuable insights into binding energy, free energy, and complex stability predictions. Aim The aim of this study was to use the docking technique for myosin inhibitors. Materials and methods Four inhibitors of myosin were chosen from the literature. These compound structures were retrieved from the Zinc15 database. Myosin protein was chosen as the target and was optimized using the RCSB Protein Data Bank. After pharmacophore modeling, 20 novel compounds were found and the SwissDock was used to dock them with the target protein. We compared the binding energies of the newly discovered compounds to those of the previously published molecules with the target. Results The results indicated that among the 20 molecules ZINC035924607 and ZINC5110352 exhibited the highest binding energy and displayed superior properties compared to the other molecules. Conclusion The study concluded that ZINC035924607 and ZINC5110352 exhibited greater binding affinity than the reported inhibitors of myosin. Therefore, these two molecules can be used as a potential and promising lead for the treatment of MMPDS and could be employed in targeted drug therapy.

In vitro anticancer evaluation of Enceleamycin A and its underlying mechanism

It has become more crucial than ever to find novel anticancer compounds due to the rise in cancer mortality and resistance to the present chemotherapeutic drugs. Naphthoquinones are regarded as privileged structures for their ability to inhibit various cancers. The current study examined three novel furo-naphthoquinones (Enceleamycins A-C) previously isolated from Amycolatopsis sp. MCC 0218 for their anticancer potential. Enceleamycin A demonstrated considerable cytotoxicity for triple-negative breast cancer (TNBC) MDA-MB-231 cells with an IC50 value of 1.25 μg mL-1 (3.78 μM). It also showed the ability to inhibit MDA-MB-231 cell migration. Enceleamycin A raises intracellular ROS levels in TNBC cells, ultimately leading to apoptotic cell death, as demonstrated by Annexin V/PI staining. The molecular docking and simulation investigation revealed better binding affinity of Enceleamycin A with AKT2, which plays a vital role in breast cancer's invasiveness and chemo-resistance. Enceleamycin A inhibits the AKT2 enzyme in vitro with an IC50 value of 0.736 μg mL-1 (2.22 μM), further validating the docking study. The in silico physicochemical and pharmacokinetics characteristics of Enceleamycin A demonstrated its drug-likeness. Intriguingly, Enceleamycin A is non-hemolytic in nature. Taken together, Enceleamycin A could be a candidate molecule for treating TNBC cells by targeting the AKT2 signaling pathway.

Comprehensive in silico screening of flavonoids against SARS-CoV-2 main protease

In the current pandemic caused by the new coronavirus (SARS-CoV-2), computational drug discovery can play an essential role in finding potential therapeutic agents. Thanks to its anti-viral, antibacterial, and anti-inflammatory properties, sage (Salvia officinalis) is used in traditional medicine. In this study, drugs proposed against COVID-19, including Lopinavir, Remdesivir, Favipiravir, and main flavonoids of sage, were docked favorably against novel coronavirus main protease. Molecular docking findings indicate that Rutin, Luteolin-7-glucoside, Apigenin, and Hispidulin make strong interactions with better binding affinity than selected commercial drugs in the study. But Rutin is the only flavonoid that makes strong hydrogen bond interactions with catalytic dyad and crucial Mpro residues and has more binding affinity than protease inhibitor PF-07321332 as an oral antiviral (PAXLOVID™). Further analysis of Molecular Dynamics and MM-PBSA predicted that chosen ligands could form stable complexes with the main protease. Also, ADMET analysis shows that main flavonoids are expected to have appropriate pharmacokinetic and no toxic properties. The results of the in silico study suggest that Salvia officinalis as a rich source of potent anti-coronavirus flavonoids may play a significant role in counteracting the replication of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Attenuation of CFA-induced chronic inflammation by a bicyclic monoterpene fenchone targeting inducible nitric oxide, prostaglandins, C-reactive protein and urea

Fenchone (a bicyclic monoterpene) is present in the essential oils of plant species like Foeniculum vulgare and Peumus boldus and is used to treat GIT disorders. Research reports have indicated its strong anti-inflammatory, antioxidant, and anti-nociceptive properties. The present study was designed to investigate fenchone's anti-arthritic effects in a rat model of chronic joint inflammation (Complete Freud's Adjuvant-mediated inflammation [CFA]). Molecular docking analysis revealed a high binding interaction of fenchone with inducible nitric oxide synthase (iNOS), Interleukin-17, Prostaglandin E Receptor EP4, and Cycloxygenase-2 (COX-2), indicating its anti-inflammatory efficacy using computational tests. Fenchone treatment at 100 mg/kg, 200 mg/kg, and 400 mg/kg significantly enhanced the tail-flick latency when compared with the solvent-treated group. Correspondingly, the raised mRNA values of iNOS, IL-17, IL-1β, IL-6, TNF-α, and COX-2 in solvent-treated group were significantly reduced following treatment with fenchone. Moreover, fenchone significantly lowered spleen and thymus indices, Nitric oxide (NO) and PGE2 values as compared to solvent-treated group. Hence, the results of the present study indicated that fenchone has a potent anti-inflammatory effect by inhibiting pro-inflammatory markers and thus may have therapeutic potential for chronic joint inflammation as well as chronic inflammatory disorders.

Exploration of phenolic acid derivatives as inhibitors of SARS-CoV-2 main protease and receptor binding domain: potential candidates for anti-SARS-CoV-2 therapy

Severe acute respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the etiological virus of Coronavirus Disease 2019 (COVID-19) which has been a public health concern due to its high morbidity and high mortality. Hence, the search for drugs that incapacitate the virus via inhibition of vital proteins in its life cycle is ongoing due to the paucity of drugs in clinical use against the virus. Consequently, this study was aimed at evaluating the potentials of natural phenolics against the Main protease (Mpro) and the receptor binding domain (RBD) using molecular modeling techniques including molecular docking, molecular dynamics (MD) simulation, and density functional theory (DFT) calculations. To this end, thirty-five naturally occurring phenolics were identified and subjected to molecular docking simulation against the proteins. The results showed the compounds including rosmarinic acid, cynarine, and chlorogenic acid among many others possessed high binding affinities for both proteins as evident from their docking scores, with some possessing lower docking scores compared to the standard compound (Remdesivir). Further subjection of the hit compounds to drug-likeness, pharmacokinetics, and toxicity profiling revealed chlorogenic acid, rosmarinic acid, and chicoric acid as the compounds with desirable profiles and toxicity properties, while the study of their electronic properties via density functional theory calculations revealed rosmarinic acid as the most reactive and least stable among the sets of lead compounds that were identified in the study. Molecular dynamics simulation of the complexes formed after docking revealed the stability of the complexes. Ultimately, further experimental procedures are needed to validate the findings of this study.

Computer-aided identification of dengue virus NS2B/NS3 protease inhibitors: an integrated molecular modelling approach for screening of phytochemicals

Globally, dengue (DENV) fever has appeared as the most widespread vector-borne disease, affecting more than 100 million individuals annually. No approved anti-DENV therapy or preventive vaccine is available yet. DENV NS3 protein is associated with protease activity and is essential for viral replication process within the host cell. NS2B is linked with NS3 protein as a cofactor. Hence, NS3/NS2B is a potential druggable target for developing inhibitors against dengue virus. In the present study, a dataset of Beta vulgaris L.-based natural compounds was developed. Virtual ligand screening of 30 phytochemicals was carried out to find novel inhibitors against the NS2B/NS3 protein. Spatial affinity, drug-likeness, and binding behaviors of selected phytochemicals were analyzed. Post-simulation analysis, including Principal Component Analysis (PCA), MMGBSA, and Co-relation analysis, was also performed to provide deep insight for elucidating protein-ligand complexes. This computer-aided screening scrutinized four potent phytochemicals, including betavulgaroside II, vitexin xyloside, epicatechin, and isovitexin2-O-xyloside inhibitors exhibiting optimal binding with viral NS3/NS2B protein. Our study brings novel scaffolds against DENV NS2B/NS3 of serotype-2 to act as lead molecules for further biological optimization. In future, this study will prompt the exploration and development of adjuvant anti-DENV therapy based on natural compounds.Communicated by Ramaswamy H. Sarma.

Structural insights of novel mutational frames in Bromodomain Containing-2 gene (BRD2) in juvenile myoclonic epilepsy: bed, bench, and laptop profiles

PURPOSE

Juvenile myoclonic epilepsy (JME) is an adolescent onset type of idiopathic generalized epilepsies. Bromodomain containing protein-2 gene (BRD2), a transcriptional regulatory protein, has a susceptible role in the expression of JME. Considering the polymorphic variations observed in exon 3 of the BRD2 gene, we evaluated the molecular interactions with anti-seizure medication in individuals diagnosed with JME.

METHODS

The genomic DNA was extracted from 5 mL of peripheral venous blood of JME participants (n = 55) and healthy control subjects (n = 55). Detailed anti-seizure medication and outcomes were noted during the study period. Identified novel mutations at nucleotide and protein sequences, compared by multiple sequence alignment. Wild-type (WT) and mutated-type (MT) structures were investigated for molecular docking and interactions with anti-seizure drugs.

RESULTS

A common variant at c.1707G>A was found among 23 participants, while a single variant at c.1663ins C was found in one participant. The deletion positions were observed at c.1890delA, c.1892A>T, c.1895A>T, c.1896G>T, c.1897T>C, c.1898T>C, c.1899C>T, c.1900G>T, c.1901C>T and c.1902A>T exhibiting stop codon after p.111Pro>stop; these variants resulted in a truncated protein. In silico analysis was conducted to validate changes; docking analysis showed that novel variant has a significant role in the interactions with anti-seizure drugs.

SIGNIFICANCE

Besides clinical and genetic outcomes, ∼5.45% unique genetical variations were observed in the participants. Significant mimicked at the binding site position (92-111) of human BRD2 ranges ∼8.2%, ∼16.4%, and ∼10.6%. Further, research is needed to identify the importance of polymorphism alterations at the binding site and their molecular interactions with anti-seizure drugs, which might be confirmed in a diverse population with JME.

The combination of multi-approach studies to explore the potential therapeutic mechanisms of imidazole derivatives as an MCF-7 inhibitor in therapeutic strategies

Breast cancer covers a large area of research because of its prevalence and high frequency all over the world. This study is based on drug discovery against breast cancer from a series of imidazole derivatives. A 3D-QSAR and activity atlas model was developed by exploring the dataset computationally, using the machine learning process of Flare. The dataset of compounds was divided into active and inactive compounds according to their biological and structural similarity with the reference drug. The obtained PLS regression model provided an acceptable r ² = 0.81 and q² = 0.51. Protein-ligand interactions of active molecules were shown by molecular docking against six potential targets, namely, TTK, HER2, GR, NUDT5, MTHFS, and NQO2. Then, toxicity risk parameters were evaluated for hit compounds. Finally, after all these screening processes, compound C10 was recognized as the best-hit compound. This study identified a new inhibitor C10 against cancer and provided evidence-based knowledge to discover more analogs.

Application of an Integrative Drug Safety Model for Detection of Adverse Drug Events Associated With Inhibition of Glutathione Peroxidase 1 in Chronic Obstructive Pulmonary Disease

BACKGROUND

Chronic Obstructive Pulmonary Disease is characterised by declining lung function and a greater oxidative stress burden due to reduced activity of antioxidant enzymes such as Glutathione Peroxidase 1.

OBJECTIVES

The extent to which drugs may contribute to this compromised activity is largely unknown. An integrative drug safety model explores inhibition of Glutathione Peroxidase 1 by drugs and their association with chronic obstructive pulmonary disease adverse drug events.

METHODS

In silico molecular modelling approaches were utilised to predict the interactions that drugs have within the active site of Glutathione Peroxidase 1 in both human and bovine models. Similarities of chemical features between approved drugs and the known inhibitor tiopronin were also investigated. Subsequently the Food and Drug Administration Adverse Event System was searched to uncover adverse drug event signals associated with chronic obstructive pulmonary disease.

RESULTS

Statistical and molecular modelling analyses confirmed that the use of several registered drugs, including acetylsalicylic acid and atenolol may be associated with inhibition of Glutathione Peroxidase 1 and chronic obstructive pulmonary disease.

CONCLUSION

The integration of molecular modelling and pharmacoepidemological data has the potential to advance drug safety science. Ongoing review of medication use and further pharmacoepidemiological and biological analyses are warranted to ensure appropriate use is recommended.

Modulatory effects of phytol on the antiemetic property of domperidone, possibly through the D2 receptor interaction pathway: in vivo and in silico studies

The current study is designed to evaluate the antiemetic effect of the diterpenoid phytol (PHY) using in vivo and in silico studies. For this, emesis was induced in 4-day-old chicks by the oral administration of copper sulfate (CuSO4.5H2O) at 50 mg/kg. To see the possible antiemetic mechanism of PHY, we used a number of reference drugs such as domperidone (80 mg/kg), ondansetron (24 mg/kg) and hyoscine (100 mg/kg) as positive controls, while the vehicle served as a negative control group. PHY was administered orally at the doses of 50 and 75 mg/kg. Both PHY and reference drugs were given alone or in combined groups to evaluate their synergistic or antagonistic effects on the chicks. Molecular docking of PHY and reference drugs was carried out against 5HT3, D2, D3, H1, NK1, and mAChRs (M1-M5) receptors for estimating binding affinity to the receptors. Drug-receptor interactions and active sites of the receptors were observed with the aid of different computational tools. The drug-likeness and pharmacokinetics of all the drugs were predicted through the SwissADME online database. The results suggest that PHY reduces the mean number of retches and increases latency dose-dependently in the birds. In the combination groups, PHY75 showed better antiemetic effects with domperidone and ondansetron. In addition, PHY exhibited the highest binding affinity with the D2 receptor (6CM4) (- 7.3 kcal/mol). In conclusion, PHY showed an antiemetic activity in chicks, possibly through the D2 receptor interaction pathway.

Chitosan Hydrogels Cross-Linked with Trimesic Acid for the Delivery of 5-Fluorouracil in Cancer Therapy

Chitosan exhibits unique properties making it a suitable material for drug delivery. Considering the rising popularity of hydrogels in this field, this work offers a comprehensive study of hydrogels constituted by chitosan and cross-linked with 1,3,5-benzene tricarboxylic acid (BTC; also known as trimesic acid). Hydrogels were prepared by cross-linking chitosan with BTC in different concentrations. The nature of the gels was studied through oscillatory amplitude strain and frequency sweep tests within the linear viscoelastic region (LVE) limit. The flow curves of the gels revealed shear thinning behavior. High G′ values imply strong cross-linking with improved stability. The rheological tests revealed that the strength of the hydrogel network increased with the cross-linking degree. Hardness, cohesiveness, adhesiveness, compressibility, and elasticity of the gels were determined using a texture analyzer. The scanning electron microscopy (SEM) data of the cross-linked hydrogels showed distinctive pores with a pore size increasing according to increasing concentrations (pore size range between 3–18 µm). Computational analysis was performed by docking simulations between chitosan and BTC. Drug release studies employing 5-fluorouracil (5-FU) yielded a more sustained release profile with 35 to 50% release among the formulations studied in a 3 h period. Overall, this work demonstrated that the presence of BTC as cross-linker leads to satisfactory mechanical properties of the chitosan hydrogel, suggesting potential applications in the sustained release of cancer therapeutics.

Tuning the aggregation behavior of human insulin in the presence of luteolin: An in vitro and in silico approach

Protein misfolding and related formation of amyloid fibrils are associated with several conformational diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), prion diseases, and Diabetes mellitus, Type 2 (DM-II). Several molecules including antibiotics, polyphenols, flavonoids, anthraquinones, and other small molecules are implicated to modulate amyloid assembly. The stabilization of the native forms of the polypeptides and prevention of their misfolding and aggregation are of clinical and biotechnological importance. Among the natural flavonoids, luteolin is of great importance because of its therapeutic role against neuroinflammation. Herein, we have explored the inhibitory effect of luteolin (LUT) on aggregation of a model protein, human insulin (HI). To understand the molecular mechanism of the inhibition of aggregation of HI by LUT, we employed molecular simulation, UV-Vis, fluorescence, and circular dichroism (CD) spectroscopies along with the dynamic light scattering (DLS). The analysis of the tuning of the HI aggregation process by luteolin revealed that interaction of HI with LUT resulted in the decrease in binding of the various fluorescent dyes, such as thioflavin T (ThT) and 8-anilinonaphthalene-1-sulfonic acid (ANS) to this protein. Retention of the native-like CD spectra and resistance to the aggregation in the presence of LUT has confirmed the aggregation inhibitory potential of LUT. The maximum inhibitory effect was found at the protein-to-drug ratio of 1:12, and no significant change was observed beyond this concentration.

In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants

Despite the rigorous global efforts to control SARS-CoV-2 transmission, it continues to pose a serious threat to humans with the frequent emergence of new variants. Thus, robust therapeutics to combat the virus are a desperate need. The SARS-CoV-2 spike (S) protein is an important target protein as it mediates the entry of the virus inside the host cells, which is initiated by the binding of the receptor-binding domain (RBD) to its cognate receptor, angiotensin-converting enzyme 2 (ACE-2). Herein, the inhibition potential of several naturally occurring coumarins was investigated against the spike proteins of SARS-CoV-2 variants using computational approaches. Molecular docking studies revealed 26 coumarins with better binding energies than the reference ligands, molnupiravir and ceftazidime, against the S-RBD of the omicron variant. The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. Physicochemical, QSAR, and pharmacokinetics analyses of the coumarins revealed wedelolactone as the best inhibitor of the spike protein with ideal Lipinski’s drug-likeness and optimal ADMET properties. Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. As an outcome, wedelolactone could be utilized to develop a potent drug candidate against COVID-19 by blocking the viral entry into the host cell.

Green synthesis of bovine serum albumin/oxidized gum Arabic nanocomposite as pH-responsive carrier for controlled release of piperine and the molecular docking study

A safe drug carrier was synthesized by albumin (BSA) and oxidized gum arabic (OGA). Piperine (PIP) was loaded into BSA/OGA nanobiocomposites by desolvation method. A set of experiments were designed by considering different contents of OGA (5, 7.5 and 10 mg) and PIP (1 and 2 mg). The presence of the band at 1600-1660 cm^-1 in FTIR spectra revealed the successful interaction between OGA and BSA. PIP2-BSA/OGA5 was selected as a suitable carrier due to its smaller size (<300 nm) and higher loading efficiency (1.5 ± 0.2 %). The encapsulation efficiency of PIP into BSA/OGA5 was 57.6 ± 2 %. The average size, polydispersity index and zeta potential of PIP2-BSA/OGA5 were 292 ± 4.4 nm, 0.185 ± 0.03 and - 24.4 ± 1.7 mV, respectively. SEM and TEM images proved the formation of spherical-shaped nanoparticles. The disappearance of endothermic peak belonging to free PIP in DSC thermogram of PIP2-BSA/OGA5 evidenced its encapsulation into carrier. PIP2-BSA/OGA5 exhibited the sustained drug release. The cell viability of MCF-7 cells after 48 h exposure to BSA/OGA5, PIP2-BSA/OGA5 and free PIP was reported 90 %, 40.1 % and 30.6 %, respectively. The molecular docking study reported that the binding affinity of PIP for BSA/OGA nanocomposite was -8.7 kcal/mol indicating the acceptable stability of the prepared drug carrier.

Identification of molecular mechanisms underlying the therapeutic effects of Celosia Cristata on immunoglobulin nephropathy

Immunoglobulin A (IgA) nephropathy also known as Berger's disease, is a silent monster and perhaps the most prevalent glomerulonephritis that often accounts for end-stage kidney failure, thereby signifying a growing public health problem worldwide. The limited amount of available data and a broad spectrum of dysregulated physiological processes of IgAN make it a challenging task and a disproportionate economic load on the community health sector. Celosia cristata is an Amaranthaceous plant with attractive colorful inflorescences that are used in various regions of earth for the treatment of numerous ailments. A list of studies evidences the therapeutic efficacy of C. cristata against complicated disorders, but the precise molecular mechanism is yet to be discovered. This study is attributed to the identification of bioactive compounds, pathways, and target genes for the better treatment of IgAN. In the current analysis, compound-target genes-pathway networks were explored which uncovered that isorhamnetin, stigmasterol, luteolin, amaranthin, and β-sitosterol may serve as a magic bullet against IgAN by influencing the targets genes involved in the disease pathogenesis. Later, the expression of hub genes was then further analyzed using a microarray dataset (GSE93798). Through expression analysis, it is worth noting that FOS, JUN, and EGFR were considerably upregulated, and at the same moment, AKT1 was considerably downregulated in IgAN patients. Lastly, docking analysis further strengthened the current findings by validating the effective activity of the active ingredients against putative target genes. In summary, we propose that five key compounds including, isorhamnetin, stigmasterol, luteolin, amaranthin, and β-sitosterol, aid in the regulation of JUN, FOS, AKT1, and EGFR, which may serve as a promising and enthralling therapeutic option for IgAN. The overall integration of network pharmacology with molecular docking unveiled the multi-target pharmacological mechanisms of C. cristata against IgAN. This study provides convincing evidence that C. cristata might partially alleviate the IgAN and ultimately lays a foundation for further experimental research on the anti-IgAN activity of C. cristata.

Structure-Based Virtual Screening and Functional Validation of Potential Hit Molecules Targeting the SARS-CoV-2 Main Protease

The recent global health emergency caused by the coronavirus disease 2019 (COVID-19) pandemic has taken a heavy toll, both in terms of lives and economies. Vaccines against the disease have been developed, but the efficiency of vaccination campaigns worldwide has been variable due to challenges regarding production, logistics, distribution and vaccine hesitancy. Furthermore, vaccines are less effective against new variants of the SARS-CoV-2 virus and vaccination-induced immunity fades over time. These challenges and the vaccines' ineffectiveness for the infected population necessitate improved treatment options, including the inhibition of the SARS-CoV-2 main protease (M^pro). Drug repurposing to achieve inhibition could provide an immediate solution for disease management. Here, we used structure-based virtual screening (SBVS) to identify natural products (from NP-lib) and FDA-approved drugs (from e-Drug3D-lib and Drugs-lib) which bind to the M^pro active site with high-affinity and therefore could be designated as potential inhibitors. We prioritized nine candidate inhibitors (e-Drug3D-lib: Ciclesonide, Losartan and Telmisartan; Drugs-lib: Flezelastine, Hesperidin and Niceverine; NP-lib: three natural products) and predicted their half maximum inhibitory concentration using DeepPurpose, a deep learning tool for drug-target interactions. Finally, we experimentally validated Losartan and two of the natural products as in vitro M^pro inhibitors, using a bioluminescence resonance energy transfer (BRET)-based M^pro sensor. Our study suggests that existing drugs and natural products could be explored for the treatment of COVID-19.

SARS-CoV-2 main protease (3CLpro) interaction with acyclovir antiviral drug/methyl-β-cyclodextrin complex: Physiochemical characterization and molecular docking

During the current outbreak of the novel coronavirus disease 2019 (COVID-19), researchers have examined several antiviral drugs with the potential to inhibit the proliferation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The antiviral drug acyclovir (AVR), which is used to treat COVID-19, in complex with methyl-β-cyclodextrin (Mβ-CD) was examined in the solution and solid phases. UV-visible and fluorescence spectroscopic analyses confirmed that the guest (AVR) was included inside the host (Mβ-CD) cavity. A solid inclusion complex of AVR was prepared by co-precipitation, physical mixing, kneading, and bath sonication methods at a 1:1 ratio of Mβ-CD:AVR. The prepared Mβ-CD:AVR inclusion complex was characterized using Fourier transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM) analysis. Phase solubility studies indicated the Mβ-CD:AVR inclusion complex exhibited a higher stability constant and linear enhancement in AVR solubility with increasing Mβ-CD concentrations. In silico analysis of the Mβ-CD/AVR inclusion complex confirmed that AVR drugs show potential as inhibitors of SARS-CoV-2 3C-like protease (3CL^pro) receptors. Results obtained using the PatchDock and FireDock servers indicated that the most favorable docking ligand was Mβ-CD:AVR, which interacted with SARS-CoV-2 (3CL^Pro) protease inhibitors with high geometric shape complementarity scores (2522 and 5872) and atomic contact energy (-313.77 and -214.70 kcal mol^-1). Our results suggest that the Mβ-CD/AVR inclusion complex inhibits the main protease of SARS-CoV-2, although further wet-lab experiments are needed to verify these findings.

Synthesis of Novel Benzimidazole-Based Thiazole Derivatives as Multipotent Inhibitors of α-Amylase and α-Glucosidase: In Vitro Evaluation along with Molecular Docking Study

In this study, hybrid analogs of benzimidazole containing a thiazole moiety (1-17) were afforded and then tested for their ability to inhibit α-amylase and α-glucosidase when compared to acarbose as a standard drug. The recently available analogs showed a wide variety of inhibitory potentials that ranged between 1.31 ± 0.05 and 38.60 ± 0.70 µM (against α-amylase) and between 2.71 ± 0.10 and 42.31 ± 0.70 µM (against α-glucosidase) under the positive control of acarbose (IC₅₀ = 10.30 ± 0.20 µM against α-amylase) (IC₅₀ = 9.80 ± 0.20 µM against α-glucosidase). A structure-activity relationship (SAR) study was carried out for all analogs based on substitution patterns around both rings B and C respectively. It was concluded from the SAR study that analogs bearing either substituent(s) of smaller size (-F and Cl) or substituent(s) capable of forming hydrogen bonding (-OH) with the catalytic residues of targeted enzymes enhanced the inhibitory potentials. Therefore, analogs 2 (bearing meta-fluoro substitution), 3 (having para-fluoro substitution) and 4 (with ortho-fluoro group) showed enhanced potency when evaluated against standard acarbose drug with IC₅₀ values of 4.10 ± 0.10, 1.30 ± 0.05 and 1.90 ± 0.10 (against α-amylase) and 5.60 ± 0.10, 2.70 ± 0.10 and 2.90 ± 0.10 µM (against α-glucosidase), correspondingly. On the other hand, analogs bearing substituent(s) of either a bulky nature (-Br) or that are incapable of forming hydrogen bonds (-CH₃) were found to lower the inhibitory potentials. In order to investigate the binding sites for synthetic analogs and how they interact with the active areas of both targeted enzymes, molecular docking studies were also conducted on the potent analogs. The results showed that these analogs adopted many important interactions with the active areas of enzymes. The precise structure of the newly synthesized compounds was confirmed using several spectroscopic techniques as NMR and HREI-MS.

Multi-Level High-Throughput Screening for Discovery of Ligands That Inhibit Insulin Aggregation

We have developed a multi-level virtual screening protocol to identify lead molecules from the FDA inactives database that can inhibit insulin aggregation. The method is based on the presence of structural and interaction specificity in non-native aggregation pathway protein-protein interactions. Some key challenges specific to the present problem, when compared with native protein association, include structural heterogeneity of the protein species involved, multiple association pathways, and relatively higher probability of conformational rearrangement of the association complex. In this multi-step method, the inactives database was first screened using the dominant pharmacophore features of previously identified molecules shown to significantly inhibit insulin aggregation nucleation by binding to its aggregation-prone conformers. We then performed ensemble docking of several low-energy ligand conformations on these aggregation-prone conformers followed by molecular dynamics simulations and binding affinity calculations on a subset of docked complexes to identify a final set of five potential lead molecules to inhibit insulin aggregation nucleation. Their effect on aggregation inhibition was extensively investigated by incubating insulin under aggregation-prone aqueous buffer conditions (low pH, high temperature). Aggregation kinetics were characterized using size exclusion chromatography and Thioflavin T fluorescence assay, and the secondary structure was determined using circular dichroism spectroscopy. Riboflavin provided the best aggregation inhibition, with 85% native monomer retention after 48 h incubation under aggregation-prone conditions, whereas the no-ligand formulation showed complete monomer loss after 36 h. Further, insulin incubated with two of the screened inactives (aspartame, riboflavin) had the characteristic α-helical dip in CD spectra, while the no-ligand formulation showed a change to β-sheet rich conformations.

Investigation of bioactive compounds from Bacillus sp. against protein homologs CDC42 of Colletotrichum gloeosporioides causing anthracnose disease in cassava by using molecular docking and dynamics studies

Manihot esculenta, commonly called cassava, is an economically valuable crop and important staple food, grown in tropical and subtropical regions of the world. Demand for cassava in the food and fuel industry is growing worldwide. However, anthracnose disease caused by Colletotrichum gloeosporioides severely affects cassava yield and production. The bioactive molecules from Bacillus are widely used to control fungal diseases in several plants. Therefore, in this study, bioactive compounds (erucamide, behenic acid, palmitic acid, phenylacetic acid, and β-sitosterol) from Bacillus megaterium were assessed against CDC42, a key protein for virulence, from C. gloeosporioides. Structure of the CDC42 protein was generated through the comparative homology modeling method. The binding site of the ligands and the stability of the complex were analyzed through docking and molecular dynamics simulation studies, respectively. Furthermore, a protein interaction network was envisaged through the STRING database, followed by enrichment analysis in the WebGestalt tool. From the enrichment analysis, it is apparent that bioactive from B. megaterium chiefly targets the MAP kinase pathway that is essential for filamentous growth and virulence. Further exploration through experimental studies could be advantageous for cassava improvement as well as to combat against C. gloeosporioides pathogen.

Development, Optimization, and In Vivo Validation of New Imidazopyridine Chemotypes as Dual TLR7/TLR9 Antagonists through Activity-Directed Sequential Incorporation of Relevant Structural Subunits

Undesirable activation of endosomal toll-like receptors TLR7 and TLR9 present in specific immune cells in response to host-derived ligands is implicated in several autoimmune diseases and other contexts of autoreactive inflammation, making them important therapeutic targets. We report a drug development strategy identifying a new chemotype for incorporating relevant structural subunits into the basic imidazopyridine core deemed necessary for potent TLR7 and TLR9 dual antagonism. We established minimal pharmacophoric features in the core followed by hit-to-lead optimization, guided by in vitro and in vivo biological assays and ADME. A ligand-receptor binding hypothesis was proposed, and selectivity studies against TLR8 were performed. Oral absorption and efficacy of lead candidate 42 were established through favorable in vitro pharmacokinetics and in vivo pharmacodynamic studies, with IC₅₀ values of 0.04 and 0.47 μM against TLR9 and TLR7, respectively. The study establishes imidazopyridine as a viable chemotype to therapeutically target TLR9 and TLR7 in relevant clinical contexts.

Binding energy analysis and molecular dynamic simulation studies of the designed orally active, non-toxic GABARAP modulators

Epilepsy is a severe neurological disorder that occurs when the communication between the neurons is disturbed. Gamma-amino butyric acid-associated protein (GABARAP) plays a key role in balancing Gamma-aminobutyric acid-A (GABA(A)) receptor functions of inhibiting the neurotransmission and controlling the seizure. In this study, we introduce the derivatives of the selected anti-epileptic drugs, namely Felbamate and Clobazam, by substituting different hydrophilic and hydrophobic groups at the specified positions. Molecular docking studies between the derivatives and GABARAP were carried out using PyRx software. The interacting residues were identified from LigPlot⁺. Drug-likeness, drug-related properties, and toxic endpoints of each derivative were analyzed using the SwissADME, Osiris property explorer, and ProTox-II servers. After analyzing the binding energy, drug-properties, and toxicity, the best five derivatives of Felbamate and Clobazam were selected. Molecular Dynamic simulation studies involving the target-ligand interaction were carried out for 100 nanoseconds using GROMACS 2018. The root mean square deviation, root mean square fluctuation, radius of gyration, Solvent accessible area, Energy plots and trajectories of the ten GABARAP complexes of the derivatives, and two GABARAP complexes of parent drugs were compared and critically analyzed. Among the five Felbamate derivatives, F7 formed the most stable complex with GABARAP. Among the five Clobazam derivatives, C27, C33 and C32 showed stable GABARAP interaction. In light of the above systematic computational analysis, we propose F7, C27, C33, and C32 as the potential anti-epileptic drug candidates for developing novel therapeutics. The substitution of hydrophobic groups at para position on benzene ring has promoted strong binding to GABARAP. Communicated by Ramaswamy H. Sarma.

Combining empirical knowledge, in silico molecular docking and ADMET profiling to identify therapeutic phytochemicals from Brucea antidysentrica for acute myeloid leukemia

Acute myeloid leukemia (AML) is one of the deadly cancers. Chemotherapy is the first-line treatment and the only curative intervention is stem cell transplantation which are intolerable for aged and comorbid patients. Therefore, finding complementary treatment is still an active research area. For this, empirical knowledge driven search for therapeutic agents have been carried out by long and arduous wet lab processes. Nonetheless, currently there is an accumulated bioinformatics data about natural products that enabled the use of efficient and cost effective in silico methods to find drug candidates. In this work, therefore, we set out to computationally investigate the phytochemicals from Brucea antidysentrica to identify therapeutic phytochemicals for AML. We performed in silico molecular docking of compounds against AML receptors IDH2, MCL1, FLT3 and BCL2. Phytochemicals were docked to AML receptors at the same site where small molecule drugs were bound and their binding affinities were examined. In addition, random compounds from PubChem were docked with AML targets and their docking score was compared with that of phytochemicals using statistical analysis. Then, non-covalent interactions between phytochemicals and receptors were identified and visualized using discovery studio and Protein-Ligand Interaction Profiler web tool (PLIP). From the statistical analysis, most of the phytochemicals exhibited significantly lower (p-value ≤ 0.05) binding energies compared with random compounds. Using cutoff binding energy of less than or equal to one standard deviation from the mean of the phytochemicals’ binding energies for each receptor, 12 phytochemicals showed considerable binding affinity. Especially, hydnocarpin (-8.9 kcal/mol) and yadanzioside P (-9.4 kcal/mol) exhibited lower binding energy than approved drugs AMG176 (-8.6 kcal/mol) and gilteritinib (-9.1 kcal/mol) to receptors MCL1 and FLT3 respectively, indicating their potential to be lead molecules. In addition, most of the phytochemicals possessed acceptable drug-likeness and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Based on the binding affinities as exhibited by the molecular docking studies supported by the statistical analysis, 12 phytochemicals from Brucea antidysentrica (1,11-dimethoxycanthin-6-one, 1-methoxycanthin-6-one, 2-methoxycanthin-6-one, beta-carboline-1-propionic acid, bruceanol A, bruceanol D, bruceanol F, bruceantarin, bruceantin, canthin-6-one, hydnocarpin, and yadanzioside P) can be considered as candidate compounds to prevent and manage AML. However, the phytochemicals should be further studied using in vivo & in vitro experiments on AML models. Therefore, this study concludes that combination of empirical knowledge, in silico molecular docking and ADMET profiling is useful to find natural product-based drug candidates. This technique can be applied to other natural products with known empirical efficacy.

In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4

Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe, existing in the environment in complex mixtures potentially capable of initiating respiratory illnesses. Here, we use an in silico approach to evaluate the potential pro-inflammatory effects of various carcinogenic PAHs and VOCs through their binding affinity towards the human toll-like receptor 4 (TLR4). For receptors and ligands, RCSB Protein Data Bank and PubChem were used in obtaining their 3D structures, respectively. Autodock Vina was utilized to obtain the best docking poses and binding affinities of each PAH and VOC. Out of the 14 PAHs included in this study, indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values of −10, −9, and −8.9 kcal/mol, respectively. For the VOCs, out of the 10 compounds studied, benzene, 1,4-dichlorobenzene, and styrene had the highest binding affinity values of −3.6, −3.9, and −4.6 kcal/mol, respectively. Compounds with higher affinity than LPS (−4.1 kcal/com) could potentially induce inflammation, while compounds with lower affinity would be less likely to induce an inflammatory response. Meanwhile, molecular dynamics simulation and RMSF statistical analysis proved that the protein, TLR4, stably preserve its conformation despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.

Substantiation of propitious "Enzybiotic" from two novel bacteriophages isolated from a wastewater treatment plant in Qatar

Lysin of bacteriophages isolated from a particular ecosystem could be inducted as a bio-controlling tool against the inhabiting pathogenic bacterial strains. Our study aims at both experimental and computational characterization of the identical lysin gene product inherent in the genomes of two novel Myoviridae bacteriophages, Escherichia Phage C600M2 (GenBank accession number OK040807, Protein ID: UCJ01465) and Escherichia Phage CL1 (GenBank Genome accession number OK040806.1, Protein ID: UCJ01321) isolated from wastewater collected from the main water treatment plant in Qatar. The lysin protein, evinced to be a globular N-acetyl-muramidase with intrinsic “cd00737: endolysin_autolysin” domain, was further expressed and purified to be experimentally validated by turbidimetric assay for its utility as an anti-bacterial agent. Comprehensive computational analysis revealed that the scrutinized lysin protein shared 85–98% sequence identity with 61 bacteriophages, all native to wastewater allied environments. Despite varied Host Recognition Components encoded in their genomes, the similitude of lysins, suggests its apparent significance in host–pathogen interactions endemic to wastewater environment. The present study substantiates the identical lysin from Escherichia Phage C600M2 and Escherichia Phage CL1 as propitious “enzybiotic”, a hybrid term to describe enzymes analogous to anti-biotics to combat antibiotic-resistant bacteria by in silico analysis and subsequent experimental validation.

In Silico Screening of Synthetic and Natural Compounds to Inhibit the Binding Capacity of Heavy Metal Compounds against EGFR Protein of Lung Cancer

Inorganic pollutant, specifically heavy metals’ contamination, is a significant matter of concern and is one of the key contributors in various health disorders including cancer. However, the interaction of heavy metals (HMs) with lung cancer has rarely been explored yet. Therefore, the present study was intended with the aim to identify the interactions of HMs with the target protein “epidermal growth factor receptor (EGFR)” of lung cancer and explore potential drug candidates, which could inhibit the active site of EGFR against HM exposure. The molecular operating environment (MOE) tool was used to study the interactions of HMs with EGFR protein. The drug-drug interaction (DDI) network approach was used to identify the potential drug candidates, which were further confirmed and compared with the commercial medicines/control group. Various compounds of twenty-three HMs were docked with EGFR protein. Out of which tinidazole, thallium bromodimethyl, and silver acetate (Sn, Ti, and Ag compounds) showed strong interactions with EGFR based on lowest-scoring values (-20.42, -7.86, and -7.74 kcal/mol, respectively). Among 1280 collected drug candidates, three synthetic compounds viz., ZINC00602803, ZINC00602685, and ZINC06718468 and three natural compounds (berberine chloride, transresveratrol, and ellagic acid) depicted strong binding capacity with EGFR. Specifically, the scoring value of ZINC00602803 (-30.99 kcal/mol) was even lowest than standard lung cancer drugs (afatinib, erlotinib, and gefitinib). Our findings revealed that both natural and synthetic compounds having strong associations with EGFR protein could be potential candidates to inhibit the interaction between HMs and lung cancer protein and can also be used as an alternative for the prevention and treatment of lung cancer. However, in vitro and in vivo studies should be conducted to validate the aforementioned natural and synthetic compounds.

In silico targeting of red complex bacteria virulence factors of periodontitis with β-defensin 1

BACKGROUND

Periodontitis is a multi-factorial infection with red complex bacteria playing a crucial role in the pathogenesis. As bacteria are tending to develop resistance against conventional antibiotics, new treatment modalities need to be developed. Antimicrobial peptides (AMPs) are potential tools for drug development and are gaining widespread interest. β-defensin 1 is an important AMP and forms the first-line host defense mechanism. The present study analyzed the structure and molecular docking of β-defensin 1 with the virulence factors of red complex bacteria of periodontitis. The physico-chemical properties of β-defensin 1 were determined by various online tools such as ProtParam, ProteinPredict, ToxinPred, and BioPep web servers. The structure of β-defensin 1was predicted by the SWISS-MODEL web server and the structure was evaluated by different web tools. The structure of lipopolysaccharide of Porphyromonas gingivalis was drawn using Chem3D ultra 11.0 software. The structure of important protein virulence factors of red complex bacteria of periodontitis was determined by the SWISS-MODEL web server. The interaction study between β-defensin 1 and virulence factors was carried out by molecular docking using Auto dock version 4.0 software and pyDock WEB server.

RESULTS

Using online tools, β-defensin 1 was predicted to be stable and non-toxic. SWISS-MODEL web server predicted Ramachandran score as 94.12% and clash score 0.0 for β-defensin 1. Auto dock version 4.0 software and pyDock WEB server analyzed the interaction to have low binding energies and hydrogen bonds were formed between the peptide and virulence factors.

CONCLUSION

β-defensin 1 was found to have good binding interaction with the disease-causing factors of red complex bacteria of periodontitis and in turn could play a role in reducing the severity of infection. β-defensin 1 could be a potential candidate for drug development for periodontitis.

GC-MS Profiling, Vibriocidal, Antioxidant, Antibiofilm, and Anti-Quorum Sensing Properties of Carum carvi L. Essential Oil: In Vitro and In Silico Approaches

The main objectives of the present study were to investigate anti-Vibrio spp., antibiofilms, and anti-quorum-sensing (anti-QS) properties of caraway essential oil in relation to their phytochemical composition. The results obtained show the identification of twelve compounds, with carvone (58.2%) and limonene (38.5%) being the main ones. The obtained essential oil (EO) is particularly active against all Vibrio spp. species, with bacteriostatic action against all tested strains (MBC/MIC ratio ≥ 4) and with inhibition zones with high diameters of growth, ranging from 8.66 ± 0.58 mm for V. furnisii ATCC 35016 to 37.33 ± 0.58 mm for V. alginolyticus ATCC 17749. Caraway essential oil (Carvone/limonene chemotype) exhibits antioxidant activities by using four tests (DPPH = 15 ± 0.23 mg/mL; reducing power = 7.8 ± 0.01 mg/mL; β-carotene = 3.9 ± 0.025 mg/mL; chelating power = 6.8 ± 0.05 mg/mL). This oil is particularly able to prevent cell-to-cell communication by inhibiting swarming motility, production of elastase and protease in Pseudomonas aeruginosa PAO1, and violacein production in C. violaceum in a concentration-dependent manner. A molecular docking approach shows good interaction of the identified bioactive molecules in caraway EO, with known target enzymes involved in antioxidant, antibacterial, and anti-QS activities having high binding energy. Overall, the obtained results highlight the possible use of caraway essential oil against pathogenic Vibrio species and to attenuate the secretion of virulence-related factors controlled by QS systems in Gram-negative bacteria. Therefore, this oil can be used by food industries to prevent biofilm formation on abiotic surfaces by Vibrio strains.

In Silico Screening of Cinnamon (Cinnamomum burmannii) Bioactive Compounds as Acetylcholinesterase Inhibitors

Alzheimer’s is a progressive and neurodegenerative disease that mainly affects people aged 65 years and older. The pathophysiology of Alzheimer’s is possibly related to the depletion of the neurotransmitter acetylcholine (ACh) due to beta-amyloid plaques and neurofibrillary tangles. Secondary metabolites found in cinnamon bark (Cinnamomum burmannii) have the potential as anticholinesterases to treat Alzheimer’s symptoms. This study aimed to identify the potency of bioactive compounds from cinnamon bark as AChE inhibitors in silico through analysis of binding energy, inhibition constants, and types of interactions. The research was conducted by screening virtually 60 test ligands using the PyRx program and molecular docking using the Autodock Tools program. The results of the ligand-receptor interaction analysis showed that 12 of the 15 tested ligands had potential as AChE inhibitors. Epicatechin and medioresinol are the ligands with the best potential for AChE inhibition with affinity close to the natural ligand or donepezil. Epicatechin has a binding energy of −10.0 kcal/mol and inhibition constant of 0.0459 M, with four hydrogen bonds and seven hydrophobic bonds. Meanwhile, medioresinol has −9.9 kcal/mol binding energy and inhibition constant of 0.0543 M, with one hydrogen bond and thirteen hydrophobic bonds.

Therapeutical Potential of Imines; Synthesis, Single Crystal Structure, Computational, Molecular Modeling, and ADMET Evaluation

Imines are multipurpose pharmacophores, simply accessible compounds, and have a broad range of usage in several areas of chemistry especially in medicine. Two novel compound imines, (E)-4-methyl-2-((o-tolylimino)methyl)phenol (1) and (E)-2-(((4-methoxybenzyl)imino)methyl)-4-methylphenol (2), were synthesized with effective product via reported protocol in the literature. Single crystal X-ray diffraction (SCXRD) was employed for structural exposition, disclosing that both compounds are orthorhombic. To optimize the newly designed imines, a B3LYP functional with a basis set 6-31G(d,p) was mainly considered. DFT results were utilized to check correlation between the data recovered from SCXRD outcomes and also to measure the energy difference. Hirshfeld surface study was done to demonstrate the intermolecular contacts along the percentage of interaction in the overall crystalline compound. Molecular operating environment program was tested against AChE and BChE enzymes to perform a modeling study of the compounds. The docking score and binding affinity of the compounds revealed that 2 showed comparatively more inhibition than 1. In silico ADMET studies exposed the physiochemical nature of these novel compounds, and it also unveiled that both compounds behaved as drug-like candidates.

Molecular docking studies of natural immunomodulators indicate their interactions with the CD40L of CD40/CD40L pathway and CSF1R kinase domain of microglia

Natural products have proved beneficial in reducing neuroinflammation in neurological diseases. Their impacts have also been associated with the activities of microglia, responsible for brain-specific immunity. Recent studies have shown the involvement of the number of microglia-specific proteins in the regulation of brain-specific immunity. However, molecular targets of natural products and their mechanism of interaction with microglia-specific proteins are elusive. Since the genetic signature of microglia offers many potential targets for drug discovery, molecular docking followed by molecular dynamics (MD) simulations of cluster of differentiation 40 ligand (CD40L) and colony-stimulating factor 1 receptor (CSF1R) kinase domain protein with some known neuro-immunomodulators (Curcumin, Cannabidiol, Ginsenoside Rg1, Resveratrol, and Sulforaphane) has been evaluated. Curcumin and cannabidiol were observed likely to modulate CD40L and expression of cytokines and entry of inflammatory cells. Resveratrol and cannabidiol may affect the CSF1R kinase domain and activation of microglia. Our finding suggests that curcumin, cannabidiol, and resveratrol may serve specific drug ligands in regulating microglia-mediated brain immunity.

Synthesis, In Silico, and Biological Evaluation of a Borinic Tryptophan-Derivative That Induces Melatonin-like Amelioration of Cognitive Deficit in Male Rat

Preclinical and clinical evidence supports melatonin and its analogues as potential treatment for diseases involving cognitive deficit such as Alzheimer's disease. In this work, we evaluated by in silico studies a set of boron-containing melatonin analogues on MT1 and MT2 receptors. Then, we synthesized a compound (borolatonin) identified as potent agonist. After chemical characterization, its evaluation in a rat model with cognitive deficit showed that it induced ameliorative effects such as those induced by equimolar administration of melatonin in behavioral tests and in neuronal immunohistochemistry assays. Our results suggest the observed effects are by means of action on the melatonin system. Further studies are required to clarify the mechanism(s) of action, as the beneficial effects on disturbed memory by gonadectomy in male rats are attractive.

In silico Analysis of Allium sativum Bioactive Compounds against Effector Protein from Pseudomonas syringae pv. pisi

Allium sativum commonly known as Garlic is a familiar herb, highly studied for its valuable medicinal properties. The main objective involved in the current research is to analyze inhibitor and antibacterial action of bioactive compounds (ligands) present in the methanolic extract of Allium sativum bulbs against phytopathogen protein (receptor) through molecular docking. The effector protein AvrRps4 (4B6X) from phytopathogen Pseudomonas syringae pv. pisi, a protein responsible for Effector triggered immunity (ETI) activation and to subvert host responses in Pea plant was selected as protein target. The docking interactions between opted ligands and target protein, with ampicillin as control was done using PyRx software tool and analysed using Discovery studio 3.1 Visualiser. The outcomes obtained from in silico analysis suggested that the bioactive compound namely Diethyl 3-methyl-5-[(2,2,2-trifluoroacetyl)amino]thiophene-2,4-dicarboxylate bind effectively showing -5.7 binding energy value in comparison with antibiotic ampicillin which showed binding energy -5.8 value. This research study concluded that the bioactive compounds from methanolic extract of Allium sativum bulbs displayed a potential inhibitory activity against effector AvrRps4 protein exhibiting antibacterial properties and may be considered as possible substantial lead molecules in future prospects.

Effect on Osteoclast Differentiation and ER Stress Downregulation by Amygdalin and RANKL Binding Interaction

Bone diseases such as osteoporosis are the result of osteoclast over-activation. There are many therapeutic agents from natural compounds inhibiting the formation of osteoclast that have been reported and are continuously being interested. Amygdalin (AD) is isolated from seeds of Prunus armeniaca L. which has many pharmaceutical effects; however, the effect of AD on osteoclast formation and function remains unknown. Therefore, the underlying mechanism of AD on RANKL-induced osteoclast in RAW 264.7 cells was investigated. Molecular docking simulation revealed that AD can bind to the active sites of RANKL with negative binding affinities. Through TRAP activity, bone resorption, and migration, AD effectively inhibited osteoclast differentiation and function. Expression of transcription factors, such as NFATc1, c-fos, and osteospecific genes (including dcstamp, acp5, ATP6v0d2, and ctsk results) showed an osteoclast differentiated inhibitory effect by AD treatment. In addition, RANKL-induced activation of MAPK, ER stress, and ROS levels in RANKL-induced osteoclast was significantly inhibited while antioxidant enzymes were recovered in the presence of AD. These results suggest that AD may be a potential candidate derived from natural sources for the treatment of osteoclast bone-related diseases.

Assessment of Antioxidant, Immunomodulatory Activity of Oxidised Epigallocatechin-3-Gallate (Green Tea Polyphenol) and Its Action on the Main Protease of SARS-CoV-2—An In Vitro and In Silico Approach

Owing to the instability of Epigallocatechin Gallate (EGCG), it may undergo auto-oxidation and form oxidised products or dimers. In the present study, we aimed to evaluate the therapeutic effects, including antioxidation and immunomodulatory action, of the Oxidised Epigallocatechin Gallate (O-EGCG) as compared to native EGCG and the action of these compounds on main protease (Mpro) docking against SARS-CoV-2. HCT-116 (Human Colon Cancer) cell lines were used to estimate the total antioxidant capacity and lipid peroxidation levels and pro-inflammatory markers (human IL-6, IL-1β, TNF-α). Further, molecular docking analysis was performed by AutoDock and visualised in Discovery studio. Improved antioxidant capacity of O-EGCG was observed, and there was a significant decrease in the inflammatory markers (IL-1β, IL-6, and TNF-α) when O-EGCG was applied as compared to EGCG. The O-EGCG was shown to be strongly associated with the highest docking score and active site residues of IL-1, IL-6, and TNF- α, as well as the Mpro of SARS-CoV-2, according to in silico approach. The in vitro and in silico analyses indicate an improved therapeutic action of the oxidised form of EGCG. The effective inhibitory action of O-EGCG against SARS-CoV-2 suggests further exploration of the compound against COVID-19 and its efficacy. However, in vivo studies and understanding of the mechanism of action of O-EGCG may yield a better opinion on the use of O-EGCG and future human clinical trials.

4-Amino modified derivatives of cytidine towards interactions with the methyltransferase enzyme

By the importance of exploring novel compounds for inhibiting the cancerous enzymes activities, this work was performed to recognize advantages of employing 4-amino modified derivatives of cytidine for participating in more efficient interactions with the methyltransferase (MTN) cancerous enzyme target. To this aim, four groups of modified models of cytidine were investigated in addition the original models to recognize the structural features and the corresponding activities. The 4-amino site of cytidine was functionalized by different carbon-based groups in linear and cyclic modes through a bridging peptide linkage. The models were optimized to reach the minimized energy structures by performing quantum chemical calculations and their interactions with the target were analyzed by performing molecular docking simulations. The obtained results of 4-amino modified derivatives of cytidine showed advantages of employing structural modifications to find structures with better molecular orbital based features. Formations of interacting complexes indicated that the additional of carbon-based groups helped to improve possibility of interactions between the substances in both of chemical and physical modes. As a remarkable achievement of this work, the model of cytidine with a phenyl group showed the best advantage of participating in interactions with the MTN target among all twenty five models of the investigated cytidine compounds.

Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approach

The present research scintillates on the homology modelling of rat mitochondrial protein tyrosine phosphatase 1 (PTPMT1) and targeting its activity using flavonoids through a computational docking approach. PTPMT1 is a dual-specificity phosphatase responsible for protein phosphorylation and plays a vital role in the metabolism of cardiolipin biosynthesis, insulin regulation, etc. The inhibition of PTPMT1 has also shown enhanced insulin levels. The three-dimensional structure of the protein is not yet known. The homology modelling was performed using SWISS-MODEL and Geno3D webservers to compare the efficiencies. The PROCHECK for protein modelled using SWISS-MODEL showed 91.6% of amino acids in the most favoured region, 0.7% residues in the disallowed region that was found to be significant compared to the model built using Geno3D. 210 common flavonoids were docked in the modelled protein using the AutoDock 4.2.6 along with a control drug alexidine dihydrochloride. Our results show promising candidates that bind protein tyrosine phosphatase 1, including, prunin (- 8.66 kcal/mol); oroxindin (- 8.56 kcal/mol); luteolin 7-rutinoside (- 8.47 kcal/mol); 3(2H)-isoflavenes (- 8.36 kcal/mol); nicotiflorin (- 8.29 kcal/mol), ranked top in the docking experiments. We predicted the pharmacokinetic and Lipinski properties of the top ten compounds with the lowest binding energies. To further validate the stability of the modelled protein and docked complexes molecular dynamics simulations were performed using Desmond, Schrodinger for 150 ns in conjunction with MM-GBSA. Thus, flavonoids could act as potential inhibitors of PTPMT1, and further, in-vitro and in-vivo studies are essential to complete the drug development process.

Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer

A natural bioactive compound named calotropone has been reported as a drug candidate for several cancers, including pancreatic cancers. Herein, we used molecular docking approach to test the possible mechanisms of action of calotropone in inhibiting the growth of pancreatic cell cancer with gemcitabine as the positive control. By employing AutoDock Vina, we studied the molecular interaction between calotropone and pancreatic cancer-associated proteins, namely Glucosaminyl (N-Acetyl) Transferase 3, Glutamic-Oxaloacetic Transaminase 1, Tyrosine-protein kinase Met (c-Met), peroxisome proliferator-activated receptor γ, Budding Uninhibited by Benzimidazole 1, A Disintegrin and Metalloproteinase 10, Sex-determining region Y and Nuclear Factor kappa Beta (Nf-Kβ). Higher affinity energies of calotropone toward the aforementioned proteins (ranging from ‒7.3 to ‒9.3 kcal/mol) indicate that calotropone may work in the same manner as anticancer drug gemcitabine. Highest docking score was found at the interaction of calotropone and Nf-Kβ (‒9.3 kcal/mol).

In Silico and In Vitro Evaluation of the Antimicrobial Potential of Bacillus cereus Isolated from Apis dorsata Gut against Neisseria gonorrhoeae

Antimicrobial resistance is a major public health and development concern on a global scale. The increasing resistance of the pathogenic bacteria Neisseria gonorrhoeae to antibiotics necessitates efforts to identify potential alternative antibiotics from nature, including insects, which are already recognized as a source of natural antibiotics by the scientific community. This study aimed to determine the potential of components of gut-associated bacteria isolated from Apis dorsata, an Asian giant honeybee, as an antibacterial against N. gonorrhoeae by in vitro and in silico methods as an initial process in the stage of new drug discovery. The identified gut-associated bacteria of A. dorsata included Acinetobacter indicus and Bacillus cereus with 100% identity to referenced bacteria from GenBank. Cell-free culture supernatants (CFCS) of B. cereus had a very strong antibacterial activity against N. gonorrhoeae in an in vitro antibacterial testing. Meanwhile, molecular docking revealed that antimicrobial lipopeptides from B. cereus (surfactin, fengycin, and iturin A) had a comparable value of binding-free energy (BFE) with the target protein receptor for N. gonorrhoeae, namely penicillin-binding protein (PBP) 1 and PBP2 when compared with the ceftriaxone, cefixime, and doxycycline. The molecular dynamics simulation (MDS) study revealed that the surfactin remains stable at the active site of PBP2 despite the alteration of the H-bond and hydrophobic interactions. According to this finding, surfactin has the greatest antibacterial potential against PBP2 of N. gonorrhoeae.

Structural Diversity and Role of Phytochemicals against P38-α Mitogen-activated Protein Kinase and Epidermal Growth Factor Receptor Kinase Domain: A Privileged Computational Approach

Computational databases and tools in recent times have been proved to provide an essential aid for anticancer studies in the field of oncology. Molecular docking studies facilitate the structural diversity of plant-derived phytomolecules having anticancer properties against receptor proteins involved in cancer signaling pathways. The current study involves the investigation of phytocompounds-agasthisflavone, anacardic acid, zoapatanolide A, a purified product of the plant extract Amarogopinois546 were subjected to docking studies on p38-α MAPK and EGFR Kinase domain. The effectiveness of this study was evaluated by comparing the docking interactions of a standard drug, doxorubicin against the receptor molecules. The docking study is analyzed by compound estimated with lowest binding energy is considered to have the highest affinity towards the active site of the receptor proteins. The isolated plant compound Amarogopinois546 displayed the least binding score with a large number of hydrogen bonds and hydrophobic interactions towards the P38α MAP kinase receptor in comparison with the EGFR kinase domain. This preliminary result can strongly be supported for carrying out experimental evaluation in near future.