ProTox: a web server for the in silico prediction of rodent oral toxicity

Synthesis and Spectroscopic Investigations of Schiff Base Ligand and Its Bimetallic Ag(I) Complex as DNA and BSA Binders

Generation of well-defined potential metallotherapeutics for cancer treatment, one of the most population-threatening diseases, is challenging and an active area of modern research in view of their unique properties and thus multiple possible pathways of action in cells. Specifically, Schiff base ligands were recognized as very promising building blocks for the construction of stable and active complexes of numerous geometries and topologies. Incorporation of Ag(I) ions allows for the formation of flat complexes with potential unoccupied coordination sites, thus giving rise to specific interactions between the metallotherapeutic and biomolecule of interest. Herein, we present the design, synthesis and characterization of new Schiff base ligand L and its Ag(I) bimetallic complex [Ag2L2]2+ with two planar moieties formed around the metal ions and connected through cyclohexane rings, confirmed by X-ray measurements. The compounds were described in context of their potential use as anticancer drugs through DNA and BSA binding pathways by several spectroscopic methods (CD, UV-Vis, fluorescence). We revealed that both, L and [Ag2L2]2+, interact with similar affinity with CT-DNA (Kb~106 M-1), while they differ in the type and strength of interactions with the model albumin-BSA. [Ag2L2]2+ binds BSA in both a dynamic and static manner with the Ksv = 8.8 × 104 M-1 in the Trp-134 and Trp-213 sites, whereas L interacts with BSA only dynamically (KSV = 2.4 × 104 M-1). This found further confirmation in the CD studies which revealed a reduction in α-helix content in the albumin of 16% in presence of [Ag2L2]2+.

In silico, in vitro, and ex vivo studies of the toxicological and pharmacological properties of the flavonoid 5,7-dihydroxy-3,8,4'-trimethoxy

Phytochemical studies of the species Pavonia glazioviana were performed. Quercetin, kaempferol, acacetin, and trimethoxylated flavonoid compounds (which present biological activity) were isolated. We aimed to evaluate the in silico, in vitro, and ex vivo toxicity of flavonoid 5,7-dihydroxy-3,8,4'-trimethoxy (Pg-1) obtained from P. glazioviana through chemical structure analyses, toxicity assessment, and predictive bioactive properties, using human samples in in vitro tests. In silico analysis suggested that Pg-1 presents a good absorption index for penetrating biological membranes (for oral bioavailability), while also suggesting potential antimutagenic, anticarcinogenic, antioxidant, antineoplastic, anti-inflammatory, anti-hemorrhagic, and apoptosis agonist bioactivities. Assessment of hemolytic and genotoxic effects revealed low hemolysis rates in red blood cells with no cellular toxicity in oral mucosa cells. The reduced cytotoxic activity suggested the safety of the concentrations used (500-1000 µg/mL), and demonstrated the varied interactions of Pg-1 with the analyzed cells. The data obtained in the present study suggested potential therapeutic application, and the non-toxic profile indicated viability for future studies.

Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase

Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), employs ten enzymes including imidazoleglycerol-phosphate dehydratase (IGPD) for de novo biosynthesis of histidine. The absence of histidine-biosynthesis in humans combined with its essentiality for Mtb makes the enzymes of this pathway major anti-TB drug targets. We explored the inhibitory potential of a small molecule β-(1,2,4-Triazole-3-yl)-DL-alanine (DLA) against Mtb IGPD. DLA exhibits an in vitro inhibitory efficacy in the lower micromolar range. Higher-resolution crystal structures of native and substrate-bound Mtb IGPD provided additional structural features of this important drug target. Crystal structure of IGPD-DLA complex at a resolution of 1.75 Å, confirmed that DLA locks down the function of the enzyme by binding in the active site pocket of the IGPD mimicking the substrate-binding mode to a high degree. In our biochemical study, DLA showed an efficient inhibition of Mtb IGPD. Furthermore, DLA also showed bactericidal activity against Mtb and Mycobacterium smegmatis and inhibited their growth in respective culture medium. Importantly, owing to the favorable ADME and physicochemical properties, it serves as an important lead molecule for further derivatizations.

nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine

An rare pandemic of viral pneumonia occurs in December 2019 in Wuhan, China, which is now recognized internationally as Corona Virus Disease 2019 (COVID-19), the etiological agent classified as Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). According to the World Health Organization (WHO), it has so far expanded to more than 213 countries/territories worldwide. Our study aims to find the viral peptides of SARS-COV-2 by peptide mass fingerprinting (PMF) in order to predict its novel structure and find an inhibitor for each viral peptide. For this reason, we calculated the mass of amino acid sequences translated from the SARS-CoV2 whole genome and identify the peptides that may be a target for inhibition. Molecular peptide docking with Moringa oleifera, phytochemicals (aqueous and ethanolic) leaf extracts of flavonoids (3.56 ± 0.03), (3.83 ± 0.02), anthraquinone (11.68 ± 0.04), (10.86 ± 0.06) and hydroxychloroquine present therapy of COVID-19 in Pakistan for comparative study. Results indicate that 15 peptides of SARS-CoV2 have been identified from PMF, which is then used as a selective inhibitor. The maximum energy obtained from AutoDock Vina for hydroxychloroquine is -5.1 kcal/mol, kaempferol (flavonoid) is -6.2 kcal/mol, and for anthraquinone -6 kcal/mol. Visualization of docking complex, important effects are observed regarding the binding of peptides to drug compounds. In conclusion, it is proposed that these compounds are effective antiviral agents against COVID-19 and can be used in clinical trials.Communicated by Ramaswamy H. Sarma.

Insights on a new sulfonamide chalcone with potential antineoplastic application

Chalcones (E)-1,3-diphenyl-2-propene-1-ones, a class of biosynthetic precursor molecules of flavonoids, have a wide variety of biological applications. Besides the natural products, many synthetic derivatives and analogs became an object of continued interest in academia and industry. In this work, a synthesis and an extensive structural study were performed on a sulfonamide chalcone 1-Benzenesulfonyl-3-(4-bromobenzylidene)-2-(2-chlorophenyl)-2,3-dihydro-1H-quinolin-4-one with potential antineoplastic application. In addition, in silico experiments have shown that the sulfonamide chalcone fits well in the ligand-binding site of EGFR with seven μ-alkyl binding energy interactions on the ligand-binding site. Finally, the kinetic stability and the pharmacophoric analysis for EGFR indicated the necessary spatial characteristics for potential activity of sulfonamide chalcone as an antagonist.

Analysis of the toxicological and pharmacokinetic profile of Kaempferol-3-O-β-D-(6"-E-p-coumaryl) glucopyranoside - Tiliroside: in silico, in vitro and ex vivo assay

Tiliroside is a glycosidic flavonoid present in many plants species including Helicteres velutina K. Schum (Malvaceae sensu lato), commonly known in Brazil as "pitó". This molecule has been shown to have many biological activities, however no study has been carried out to investigate the toxicity of this substance. The present work aimed to evaluate the possible cellular toxicity in silico, in vitro and ex-vivo of the kaempferol-3-O-β-D-(6"-E-p-coumaroyl) glucopyranoside (tiliroside), through chemical structure analysis, toxicity assessment and predictive bioactive properties, using human samples for in vitro and ex-vivo tests. The in silico analysis suggests that tiliroside exhibited great absorption index when penetrating biological membranes. In addition, it also displayed considerable potential for cellular protection against free radicals, and anticarcinogenic, antioxidant, antineoplastic, anti-inflammatory, anti-hemorrhagic and antithrombotic activities. The assessment of the hemolytic and genotoxic effects of tiliroside showed low hemolysis rates in red blood cells and absence of cellular toxicity in the oral mucosa cells. The data obtained indicate that this molecule could be a promising therapeutic approach as a possible new drug with biotechnological potential.

Virtual screening FDA approved drugs against multiple targets of SARS-CoV-2

The outbreak of the novel coronavirus severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) respiratory disease, led to a global pandemic with high morbidity and mortality. Despite frenzied efforts in therapeutic development, there are currently no effective drugs for treatment, nor are there vaccines for its prevention. Drug repurposing, representing as an effective drug discovery strategy from existing drugs, is one of the most practical treatment options against the outbreak. In this study, we present a novel strategy for in silico molecular modeling screening for potential drugs that may interact with multiple main proteins of SARS-CoV-2. Targeting multiple viral proteins is a novel drug discovery concept in that it enables the potential drugs to act on different stages of the virus' life cycle, thereby potentially maximizing the drug potency. We screened 2631 US Food and Drug Administration (FDA)-approved small molecules against 4 key proteins of SARS-CoV-2 that are known as attractive targets for antiviral drug development. In total, we identified 29 drugs that could actively interact with 2 or more target proteins, with 5 drugs (avapritinib, bictegravir, ziprasidone, capmatinib, and pexidartinib) being common candidates for all 4 key host proteins and 3 of them possessing the desirable molecular properties. By overlaying docked positions of drug candidates onto individual host proteins, it has been further confirmed that the binding site conformations are conserved. The drugs identified in our screening provide potential guidance for experimental confirmation, such as in vitro molecular assays and in vivo animal testing, as well as incorporation into ongoing clinical studies.

Virtual Screening of Citrus Flavonoid Tangeretin: A Promising Pharmacological Tool for the Treatment and Prevention of Zika fever and COVID-19

It is of great importance for the pharmaceutical industry to find therapeutic substances extracted from natural sources, which are abundant, obtained with low costs and presenting the antiviral potential for the treatment of Zika virus (ZIKV) and COVID-19. Tangeretin (TAN) is a citrus polymethoxyflavone from Citrus reticulata peel oil with known antiviral activities, whose physico-chemical properties are not reported. The present study aimed to investigate by a theoretical screening of electronic, structural properties and pharmacodynamic and pharmacokinetic parameters that characterize TAN as a therapeutic drug in the treatment and prevention of zika fever and COVID-19. The molecule reached its minimum energy-forming state of [Formula: see text]795.85747[Formula: see text]kJ/mol and the HOMO and LUMO boundary orbitals reactivity descriptors suggest that the compound is stable and does not tend to be reactive in intermolecular interactions. The ligand connects to the NS1 ZIKV receptor with strong H-bond interactions, also connects with the NS5 ZIKV receptor in a competitive effect with the SAM inhibitor and acts in a supplementary effect with the N3 inhibitor and the BRT drug in the Mpro SARS-CoV-2 receptor. The properties of ADMET shows that the compound suffers few amounts of drug alterations because it inhibits the metabolic enzymes CYP2C9 and CYP3A4 and penetrates the central nervous system, without accumulation of drug residues in the blood or in the lumen in the gastrointestinal tract, without risk of toxicity to the patient. With the results obtained, it is possible to identify TAN as a promising pharmacological tool for the treatment and prevention of Zika fever and COVID-19.

A cross-industry collaboration to assess if acute oral toxicity (Q)SAR models are fit-for-purpose for GHS classification and labelling

This study assesses whether currently available acute oral toxicity (AOT) in silico models, provided by the widely employed Leadscope software, are fit-for-purpose for categorization and labelling of chemicals. As part of this study, a large data set of proprietary and marketed compounds from multiple companies (pharmaceutical, plant protection products, and other chemical industries) was assembled to assess the models' performance. The absolute percentage of correct or more conservative predictions, based on a comparison of experimental and predicted GHS categories, was approximately 95%, after excluding a small percentage of inconclusive (indeterminate or out of domain) predictions. Since the frequency distribution across the experimental categories is skewed towards low toxicity chemicals, a balanced assessment was also performed. Across all compounds which could be assigned to a well-defined experimental category, the average percentage of correct or more conservative predictions was around 80%. These results indicate the potential for reliable and broad application of these models across different industrial sectors. This manuscript describes the evaluation of these models, highlights the importance of an expert review, and provides guidance on the use of AOT models to fulfill testing requirements, GHS classification/labelling, and transportation needs.

Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: a computational approach

Background

Being one of the rapidly growing dementia type diseases in the world, Alzheimer’s disease (AD) has gained much attention from researchers in the recent decades. Many hypotheses have been developed that describe different reasons for the development of AD. Among them, the cholinergic hypothesis depicts that the degradation of an important neurotransmitter, acetylcholine by the enzyme acetylcholinesterase (AChE), is responsible for the development of AD. Although, many anti-AChE drugs are already available in the market, their performance sometimes yields unexpected results. For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources. In this study, 50 potential anti-AChE phytochemicals were analyzed using numerous tools of bioinformatics and in silico biology to find out the best possible anti-AChE agents among the selected 50 ligands through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.

Result

The predictions of this study suggested that among the selected 50 ligands, bellidifolin, naringenin, apigenin, and coptisine were the 4 best compounds with quite similar and sound performance in most of the experiments.

Conclusion

In this study, bellidifolin, naringenin, apigenin, and coptisine were found to be the most effective agents for treating the AD targeting AChE. However, more in vivo and in vitro analyses are required to finally confirm the outcomes of this research.

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

Introduction

In modern drug design, in silico methods are largely used to understand drug-receptor interactions and quantum chemical properties. In the present study, a computational de novo design approach was used to confirm mode of binding for antibacterial activity, elucidating quantum chemical properties and ADMET-drug-likeness of carbazole alkaloid (1) and three coumarins (2-4) isolated from roots of Clausena anisata.

Methods

Docking studies were performed with DNA-Gyrase (6F86) and LasR binding domain (2UV0) employing a flexible ligand docking approach using AutoDock Vina. SwissADME prediction and toxicological predictions were performed by ADMET. The optimized structures and molecular electrostatic potential surface of the isolated compounds were predicted by DFT analysis using B3LYP/6-31G basis levels.

Results and Discussion

The docking results revealed that compound 3 showed better docking scores against both DNA gyrase B and LasR binding domain compared with ciprofloxacin with potential as an inhibitor of bacterial DNA gyrase and quorum sensing LasR binding domain. The SwissADME prediction results showed that all the isolated compounds (1-4) satisfy Lipinski's rule of five with zero violations. Toxicological prediction results suggested that all compounds and ciprofloxacin are non-hepatotoxic, non-carcinogenic, non-irritant, immunogenic, and non-cytotoxic. The DFT analysis results revealed that compound 3 has large electronegativity (χeV), global softness (σ eV^-1), global electrophilicity (ωeV), and mutagenicity value closer to ciprofloxacin (with LD₅₀ value of 480 mg/kg) suggesting better bioactivity and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups.

Conclusion

Overall, compound 3 may serve as a lead molecule that could be developed into a potent E. coli DNA gyrase B inhibitor and efficient inhibitor for quorum sensing auto-inducer LasR binding domain of Pseudomonas aeruginosa.

Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods

Computational methods to predict molecular properties regarding safety and toxicology represent alternative approaches to expedite drug development, screen environmental chemicals, and thus significantly reduce associated time and costs. There is a strong need and interest in the development of computational methods that yield reliable predictions of toxicity, and many approaches, including the recently introduced deep neural networks, have been leveraged towards this goal. Herein, we report on the collection, curation, and integration of data from the public data sets that were the source of the ChemIDplus database for systemic acute toxicity. These efforts generated the largest publicly available such data set comprising > 80,000 compounds measured against a total of 59 acute systemic toxicity end points. This data was used for developing multiple single- and multitask models utilizing random forest, deep neural networks, convolutional, and graph convolutional neural network approaches. For the first time, we also reported the consensus models based on different multitask approaches. To the best of our knowledge, prediction models for 36 of the 59 end points have never been published before. Furthermore, our results demonstrated a significantly better performance of the consensus model obtained from three multitask learning approaches that particularly predicted the 29 smaller tasks (less than 300 compounds) better than other models developed in the study. The curated data set and the developed models have been made publicly available at https://github.com/ncats/ld50-multitask, https://predictor.ncats.io/, and https://cactus.nci.nih.gov/download/acute-toxicity-db (data set only) to support regulatory and research applications.

In silico study of garlic (Allium sativum L.)-derived compounds molecular interactions with α-glucosidase

Diabetes mellitus is a metabolic syndrome characterized by elevated blood glucose. The α-glucosidase enzyme is responsible for the hydrolysis of carbohydrates. This in silico study aimed to evaluate the inhibitory effects of the isolated compounds from Allium sativum L. on α-glucosidase. At first, sulfur and phenolic compounds of A. sativum L. were obtained from PubChem database, and α-glucosidase enzyme structure was obtained from Protein Data Bank. Toxicity class of compounds and the Lipinski parameter were predicted by Toxtree and Protox II and the Swiss ADME tools, respectively. Finally, the molecular interaction analysis between α-glucosidase and compounds from A. sativum L. was performed by AutoDock 4.2.6. Molecular interactions were investigated using Discovery Studio Visulizer and Ligplot 2.1 program. All of the selected sulfur and phenolic compounds from A. sativum L. followed the Lipinski's rules, had an acceptable binding energy, and lacked toxicity; therefore, they were appropriate candidates for α-glucosidase inhibition. Among these compounds, methionol and caffeic acid showed the lowest binding energy, and the highest inhibitory effect on α-glucosidase enzyme with - 3.9 and - 4.8 kcal/mol, respectively. These compounds also indicated the lower binding energy than the standard inhibitor (miglitol). Among the sulfur and phenolic compounds in A. sativum L., methionol and caffeic acid were predicted to be the powerful inhibitors, due to having more hydrogen binds and hydrophobic interactions with the active site of α-glucosidase.

Study of acute oral toxicity of the thiazole derivative N-(1-methyl-2-methyl-pyridine)-N-(p-bromophenylthiazol-2-yl)-hydrazine in a Syrian hamster

The thiazole derivative N-1-methyl-2-methyl-pyridine)-N-(p-bromophenylthiazol-2-yl)-hydrazine was used to evaluate the acute oral toxicity in Syrian hamsters. The concentration of the doses (300 mg/kg and 2000 mg/kg) were based on the "Class Acute Toxicity Method" displayed in the OECD-423 guide. In addition, renal and liver biochemical tests were performed, as well as histopathological analysis. Our results showed that the compound's lethal dose (LD50) was 1000 mg/kg and classified as category 4 according to the criteria adopted in the experiment's protocol. Biochemical analysis of the liver function's parameters showed that the LD50 values in all animals were higher than the reference values. However, the analyze of the kidney injury parameters showed an increase in the urea's dosage but a decrease in the albumin's dosage in all animals when compared to the reference values. Kidney biochemical analysis also showed that creatinine's level was only higher than the reference values in one animal. Massive damages in the liver were observed, such as hypertrophy and hyperplasia of the hepatocyte, coagulation necrosis, the presence of mononuclear cells in the sinusoidal capillaries, steatosis, cholestasis, and congestion of sinusoidal capillaries and central-lobular veins. The animals presented renal injuries related to congestion of glomerular and interstitial capillaries, nephrosis of contorted proximal and distal tubules and congestion in the medullary region. In conclusion, the thiazole derivative was well tolerated although it caused acute liver and kidney damages. Therefore, these results showed the need of further investigation of this compound in vivo to evaluate the potential therapeutic effects with chronic models.

Identification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches

Cyclooxygenase 2 (COX-2) is a well-established target for the design of anti-inflammatory intermediates. Celecoxib was selected as a template molecule to perform ligand-based virtual screening, i.e. to search for structures with similarity in shape and electrostatic potential, with a gradual increase in accuracy through the combined fitting of several steps using eight commercial databases. The molecules ZINC408709 and ZINC2090319 reproduced values within the limits established in an initial study of absorption and distribution in the body. No alert was fired for possible toxic groups when these molecules were subjected to toxicity prediction. Molecular docking results with these compounds showed a higher binding affinity in comparison to rofecoxib for the COX-2 target. Additionally, ZINC408709 and ZINC2090319 were predicted to be potentially biologically active. In in silico prediction of endocrine disruption potential, it was established that the molecule ZINC2090319 binds strongly to the target related to cardiovascular risk in a desirable way as a non-steroidal antagonist and ZINC408709 binds strongly to the target that is associated with the treatment of inflammatory pathologies and similar to celecoxib. Metabolites generated from these compounds are less likely to have side effects. Simulations were used to evaluate the interaction of compounds with COX-1 and COX-2 during 200 ns. Despite the differences, ZINC408709 molecule showed better stability for COX-2 during molecular dynamics simulation. In the calculations of free energy MM/PBSA, the molecule ZINC408709 ΔGbind value has a higher affinity to celecoxib and rofecoxib COX-2. This demonstrates that the selected substances can be considered as promising COX-2 inhibitors. Communicated by Ramaswamy H. Sarma.

A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase

Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were identified and subsequently adopted to create a pharmacophore model for virtual screening in the ZINC database. This search generated eight ADMET-compliant hits that were examined thoroughly to fit into the active site of CpIMPDH via molecular docking. Three compounds ZINC46542062, ZINC58646829, and ZINC89780094, with favorable docking scores of - 8.3 kcal/mol, - 8.2 kcal/mol, and - 7.5 kcal/mol, were selected. The potential inhibitory mechanism of these compounds was probed using molecular dynamics simulation and Molecular Mechanics Generalized Poisson Boltzmann Surface Area (MM/PBSA) analyses. Results revealed that one of the hits (ZINC46542062) exhibited a lower binding free energy of - 39.52 kcal/mol than P131, which had - 34.6 kcal/mol. Conformational perturbation induced by the binding of the identified hits to CpIMPDH was similar to P131, suggesting a similarity in inhibitory mechanisms. Also, in silico investigation of the properties of the hit compounds implied superior physicochemical properties with regards to their synthetic accessibility, lipophilicity, and number of hydrogen bond donors and acceptors in comparison with P131. ZINC46542062 was identified as a promising hit compound with the highest binding affinity to the target protein and favorable physicochemical and pharmacokinetic properties relative to P131. The identified compounds can serve as a basis for conducting further experimental investigations toward the development of anticryptosporidials, which can overcome the challenges of existing therapeutic options. Graphical abstract P131 and the identified compounds docked in the NAD⁺ binding site of Cryptosporidium parvum IMPDH.

Evaluation of certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis

SARS-CoV-2 is a new strain of coronavirus that appeared in China in December 2019, in recent years, great progress has been made in developing new antiviral drugs, and natural products, are important sources of potential and new antiviral drugs. The present study aimed to assess some biologically active compounds present in medicinal plants as potential COVID-19 inhibitors, using molecular docking methods. The Docking study was performed by Molecular Operating Environment software (MOE). About 20 Compounds were screened in this study; these compounds were selected based on classification of their chemical origin and their antiviral activity from literature. These compounds might be used to inhibit COVID-19 infection. The results demonstrate the effectiveness of this screening strategy, which can lead to rapid drug discovery in response to new infectious diseases. The results showed that many compounds isolated from medicinal plants such as; Gallic acid (- 17.45), Quercetin (- 15.81), Naringin (- 14.50), Capsaicin (- 13.90), and Psychotrine (- 13.5) are important sources for novel antiviral drugs targeting COVID-19.

Lower COVID-19 mortality in Italian forested areas suggests immunoprotection by Mediterranean plants

The COVID-19 pandemic has induced dramatic effects on the population of the industrialized north of Italy, whereas it has not heavily affected inhabitants of the southern regions. This might be explained in part by human exposure to high levels of fine particulate matter (PM) in the air of northern Italy, thus exacerbating the mortality. Since trees mitigate air pollution by intercepting PM onto plant surfaces and bolster the human immune system by emitting bioactive volatile organic compounds (VOCs), we hypothesize a protective role of evergreen forested areas in southern Italy. We compared the mortality rate  due to COVID-19, the death number, the positivity rate and the forest coverage per capita in various Italian regions. Hectares of forest per capita and prevalence of deciduous versus evergreen forestal species were also estimated. In silico docking studies of potentially protective compounds found in Laurus nobilis L., a typical Mediterranean plant, were performed to search for potential antivirals. We found that the pandemic's severity was generally lower in southern regions, especially those with more than 0.3 hectares of forest per capita. The lowest mortality rates were found in southern Italy, mainly in regions like Molise (0.007%) and Basilicata (0.005%) where the forest per capita ratio is higher than 0.5 Ha/person. Our findings suggest that evergreen Mediterranean forests and shrubland plants could have protected the southern population by emission of immuno-modulating VOCs and provision of dietary sources of bioactive compounds. Moreover, in silico studies revealed a potential anti-COVID-19 activity in laurusides, which are unexplored glycosides from bay laurel. Overall, our results highlight the importance of nature conservation and applications to the search for natural antivirals.

'In silico' toxicology methods in drug safety assessment

While experimental animal investigation has historically been the most conventional approach conducted to assess drug safety and is currently considered the main method for determining drug toxicity, these studies are constricted by cost, time, and ethical approvals. Over the last 20 years, there have been significant advances in computational sciences and computer data processing, while knowledge of alternative techniques and their application has developed into a valuable skill in toxicology. Thus, the application of in silico methods in drug safety assessment is constantly increasing. They are very complex and are grounded on accumulated knowledge from toxicology, bioinformatics, biochemistry, statistics, mathematics, as well as molecular biology. This review will summarize current state-of-the-art scientific data on the use of in silico methods in toxicity testing, taking into account their shortcomings, and highlighting the strategies that should deliver consistent results, while covering the applications of in silico methods in preclinical trials and drug impurities toxicity testing.

Mycotoxin Identification and In Silico Toxicity Assessment Prediction in Atlantic Salmon

The present study aimed to identify mycotoxins in edible tissues of Atlantic salmon (Salmo salar) using liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS). After using a non-targeted screening approach and a home-made spectral library, 233 mycotoxins were analyzed. Moreover, the occurrence of mycotoxins in fish filets was evaluated, and their potential toxicity was predicted by in silico methods. According to the obtained results, forty mycotoxins were identified in analyzed salmon samples, the predominant mycotoxins being enniatins (also rugulosin and 17 ophiobolins), commonly found in cereals and their by-products. Thus, mycotoxin carry-over can occur from feed to organs and edible tissues of cultivated fish. Moreover, the toxicity of detected mycotoxins was predicted by the in silico webserver ProTox-II, highlighting that special attention must be paid to some less reported mycotoxins due to their toxic predicted properties.

Computational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19

Since the SARS/MERS epidemic, scientists across the world have been racing to identify the novel-CoVs as it has been predicted that next epidemic can very well be a result from a new mutation of CoV, for which hundred mutations have already been discovered, and the same fear has come true with world facing a raging pandemic due to COVID-19, an infectious disease caused by a newly discovered coronavirus. COVID-19 or Severe acute respiratory syndrome coronavirus2 (SARS-CoV-2), is a single stranded RNA virus. COVID −19 is highly contagious and has resulted in current global pandemic with almost no country of the world unaffected by this virus. Owing to the lack of effective therapeutics or vaccines, the best measures to control human coronaviruses remain a strong public health surveillance system coupled with rapid diagnostic testing and quarantine/social; distancing/lockdowns as and when necessary. In the present study, we have used the insilico approach for the prediction of novel drug molecules from available antiviral drugs and also from natural compounds that can be best target against RNA-dependent RNA-polymerase (Pol/RdRp) protein of SARS-CoV-2 which can be suitable drugs for the treatment of COVID-19 virus. From the current study we observed that three antiviral and three phyto-chemicals have minimum binding energy with the target protein which were further evaluated in molecular dynamics studies and could specifically bind to RdRp protein of COVID-19. Based on results we suggest that these drugs may act as best or novel inhibitor that may be used for the treatment of SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Scutellaria baicalensis Flavones as Potent Drugs against Acute Respiratory Injury during SARS-CoV-2 Infection: Structural Biology Approaches

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in severe damage to the respiratory system. With no specific treatment to date, it is crucial to identify potent inhibitors of SARS-CoV-2 Chymotrypsin-like protease (3CLpro) that could also modulate the enzymes involved in the respiratory damage that accompanies SARS-CoV-2 infection. Here, flavones isolated from Scutellaria baicalensis (baicalein, baicalin, wogonin, norwogonin, and oroxylin A) were studied as possible compounds in the treatment of SARS-CoV-2 and SARS-CoV-2-induced acute lung injuries. We used structural bioinformatics and cheminformatics to (i) identify the critical molecular features of flavones for their binding activity at human and SARS-CoV-2 enzymes; (ii) predict their drug-likeness and lead-likeness features; (iii) calculate their pharmacokinetic profile, with an emphasis on toxicology; (iv) predict their pharmacodynamic profiles, with the identification of their human body targets involved in the respiratory system injuries; and (v) dock the ligands to SARS-CoV-2 3CLpro. All flavones presented appropriate drug-like and kinetics features, except for baicalin. Flavones could bind to SARS-CoV-2 3CLpro at a similar site, but interact slightly differently with the protease. Flavones’ pharmacodynamic profiles predict that (i) wogonin strongly binds at the cyclooxygenase2 and nitric oxide synthase; (ii) baicalein and norwogonin could modulate lysine-specific demethylase 4D-like and arachidonate 15-lipoxygenase; and (iii) baicalein, wogonin, norwogonin, and oroxylin A bind to SARS-CoV-2 3CLpro. Our results propose these flavones as possible potent drugs against respiratory damage that occurs during SARS-CoV-2 infections, with a strong recommendation for baicalein.

Traditional medicinal plants against replication, maturation and transmission targets of SARS-CoV-2: computational investigation

COVID-19 is an infectious pandemic caused by the SARS-CoV-2 virus. The critical components of SARS-CoV-2 are the spike protein (S-protein) and the main protease (M^pro). M^pro is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the host cells through the angiotensin-converting enzyme 2 (ACE2). Since ACE2 is required for the binding of SARS-CoV-2 on the host cells, ACE2 inhibitors and blockers have got wider attention, in addition to S-protein and M^pro modulators as potential therapeutics for COVID-19. So far, no specific drugs have shown promising therapeutic potential against COVID-19. The current study was undertaken to evaluate the therapeutic potential of traditional medicinal plants against COVID-19. The bioactives from the medicinal plants, along with standard drugs, were screened for their binding against S-protein, M^pro and ACE2 targets using molecular docking followed by molecular dynamics. Based on the higher binding affinity compared with standard drugs, bioactives were selected and further analyzed for their pharmacological properties such as drug-likeness, ADME/T-test, biological activities using in silico tools. The binding energies of several bioactives analyzed with target proteins were relatively comparable and even better than the standard drugs. Based on Lipinski factors and lower binding energies, seven bioactives were further analyzed for their pharmacological and biological characteristics. The selected bioactives were found to have lower toxicity with a higher GI absorption rate and potent anti-inflammatory and anti-viral activities against targets of COVID-19. Therefore, the bioactives from these medicinal plants can be further developed as phytopharmaceuticals for the effective treatment of COVID-19.

Culinary spice bioactives as potential therapeutics against SARS-CoV-2: Computational investigation

Background

Coronavirus disease-2019 (COVID-19) is an infectious pandemic caused by SARS-CoV-2. SARS-CoV-2 main protease (M^pro) and spike protein are crucial for viral replication and transmission. Spike protein recognizes the human ACE2 receptor and transmits SARS-CoV-2 into the human body. Thus, M^pro, spike protein, and ACE2 receptor act as appropriate targets for the development of therapeutics against SARS-CoV-2. Spices are traditionally known to have anti-viral and immune-boosting activities. Therefore, we investigated the possible use of selected spice bioactives against the potential targets of SARS-CoV-2 using computational analysis.

Methods

Molecular docking analysis was performed to analyze the binding efficiency of spice bioactives against SARS-CoV-2 target proteins along with the standard drugs. Drug-likeness properties of selected spice bioactives were investigated using Lipinski's rule of five and the SWISSADME database. Pharmacological properties such as ADME/T, biological functions, and toxicity were analyzed using ADMETlab, PASS-prediction, and ProTox-II servers, respectively.

Results

Out of forty-six spice bioactives screened, six bioactives have shown relatively better binding energies than the standard drugs and have a higher binding affinity with at least more than two targets of SARS-CoV-2. The selected bioactives were analyzed for their binding similarities with the standard drug, remdesivir, towards the targets of SARS-CoV-2. Selected spice bioactives have shown potential drug-likeness properties, with higher GI absorption rate, lower toxicity with pleiotropic biological roles.

Conclusions

Spice bioactives have the potential to bind with the specific targets involved in SARS-CoV-2 infection and transmission. Therefore, spice-based nutraceuticals can be developed for the prevention and treatment of COVID-19.

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The SARS-CoV-2 M^pro, spike protein, and human ACE2 are critical targets for COVID-19.

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Spice bioactives from F. asafoetida and S. indicum potentially inhibit the SARS-CoV-2 targets.

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Selected bioactives have drug-likeness properties along with optimal pharmacological and biological activities.

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The development of spice-based nutraceuticals can be used for the prevention and treatment of COVID-19.

Pulsed Electric Fields (PEF) to Mitigate Emerging Mycotoxins in Juices and Smoothies

The development of innovative food processing technologies has increased to answer the growing demand to supply of fresh-like products. The aim of the present study is to investigate the effect of pulsed electric fields (PEF) technology on reducing the emerging mycotoxins (enniatins (ENs) and beauvericin (BEA)) contents in juice and smoothie samples. The products of degradation obtained after PEF treatment were identified and their toxicological endpoint toxicities predicted by Pro Tox-II web. Mycotoxin reduction ranged from 43 to 70% in juices and smoothies, but in water the expected effect was lower. The acidified pH increased BEA reduction in water. The degradation products that were produced were the result of the loss of aminoacidic fragments of the original molecules, such as HyLv, Val, Ile, or Phe. Pro Tox-II server assigned a toxicity class I for enniatin B (ENB) degradation products with a predicted LD50 of 3 mg/Kgbw. The other degradation products were classified in toxicity class III and IV.

Sucralose causes non-selective CD4 and CD8 lymphotoxicity via probable regulation of the MAPK8/APTX/EID1 genes: An in vitro/in silico study

One of the most widely used sweeteners in the world is sucralose. With sweetening power 600 times greater than sucrose, its use grows among those who seek to cut calories. Research shows that when heated, sucralose generates toxic products that attack the organism and interact with DNA. Our objective was to test this sweetener under unheated conditions and at average concentrations of consumption, evaluating parameters of cytotoxicity, genotoxicity, and immunotoxicity. For this purpose, we made use of lymphocyte cultures and the analysis of their CD3+ , CD4+ , and CD8+ subpopulations. In a complementary way, the mechanism of action is proposed here by computational methods. Our results showed that sucralose reduces non-selectively the total lymphocytes due to falls in the levels of the CD4+ , CD8+ , and CD4+ CD8+ subpopulations. We observed an increase in the level of DNA damage and a gradual incidence of structural changes in the lymphocyte chromosomal sets. It was possible to propose that sucralose modulates the gene expression, interfering especially with the MAPK8, APTX, and EID1 genes. This article presents the results of an evidence-based approach to the safety of human health in the use of sucralose. Finally, this study points out that sucralose has cytotoxic, genotoxic, and mutagenic effects in the concentrations and conditions tested in human lymphocyte cell culture.

The use of fructose as a sweetener. Is it a safe alternative for our immune system?

Fructose is a constituent of sucrose and other polymers referred to as inulin or fructans. We can find in cereals, vegetables, and honey. It has the property of being 1.5 times sweeter than sucrose. Our objective was to test this sweetener under and at average concentrations of consumption, evaluating parameters of cytotoxicity, genotoxicity, and immunotoxicity. For this purpose, we made use of lymphocyte cultures and the analysis of their CD4⁺ and CD8⁺ subpopulations. Computational methods propose the mechanism of action. Our data showed a reduction in all lymphocyte subfractions evaluated, resulting in a reduction in total lymphocytes, as well as an increase in the DNA damage of cells exposed to fructose. It was possible to propose that fructose modulates gene expression, mainly interfering with the MAPK8, APTX, TUBGCP3, and LST1 genes. Although fructose is used globally as a sweetener, its use should be cautious, as our study points out that it has cytotoxic and genotoxic effects. PRACTICAL APPLICATIONS: Fructose is one of the most sold and used sweeteners in the world. We show here that its use must be restricted and used carefully because it can alter the gene expression and also interfere with cellular and genetic metabolism and may even interfere with the immune response.

An in-silico evaluation of COVID-19 main protease with clinically approved drugs

A novel strain of coronavirus, namely, SARS-CoV-2 identified in Wuhan city of China in December 2019, continues to spread at a rapid rate worldwide. There are no specific therapies available and investigations regarding the treatment of this disease are still lacking. In order to identify a novel potent inhibitor, we performed blind docking studies on the main virus protease M^pro with eight approved drugs belonging to four pharmacological classes such as: anti-malarial, anti-bacterial, anti-infective and anti-histamine. Among the eight studied compounds, Lymecycline and Mizolastine appear as potential inhibitors of this protease. When docked against M^pro crystal structure, these two compounds revealed a minimum binding energy of −8.87 and −8.71 kcal/mol with 168 and 256 binding modes detected in the binding substrate pocket, respectively. Further, to study the interaction mechanism and conformational dynamics of protein-ligand complexes, Molecular dynamic simulation and MM/PBSA binding free calculations were performed. Our results showed that both Lymecycline and Mizolastine bind in the active site. And exhibited good binding affinities towards target protein. Moreover, the ADMET analysis also indicated drug-likeness properties. Thus it is suggested that the identified compounds can inhibit Chymotrypsin-like protease (3CL^pro) of SARS-CoV-2.

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Lymecycline and Mizolastine fit into M^pro binding substrate pocket with a binding energies of −8.87 kcal/mol and −8.71 kcal/mol, respectively.

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ADMET analysis indicated drug-likeness properties of both Lymecycline and Mizolastine.

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Molecular dynamic simulation and MM/PBSA binding free calculations showed that both Lymecycline and Mizolastine bind in the active site. And exhibited good binding affinities towards target protein.

In silico authentication of amygdalin as a potent anticancer compound in the bitter kernels of family Rosaceae

Amygdalin a naturally occurring compound, predominantly in the bitter kernels of apricot, almond, apple and other members of Rosaceae family. Though, amygdalin is used as an alternative therapy to treat various types of cancer but its role in cancer pathways has rarely been explored yet. Therefore, present study was intended with the aim to investigate the alleged anti-cancerous effects of amygdalin specifically on PI3K-AKT-mTOR and Ras pathways of cancer in human body. Computational modelling and simulation techniques were used to assess the effect of amygdalin on PI3K-AKT-mTOR and Ras pathways using different level of dosage. It was observed that amygdalin had direct and substantial contribution to regulate PI3K-mTOR activities on threshold levels while the other caner pathways were effected indirectly. Consequently, amygdalin is a down-regulator of a cancer within a specified amount and contribute considerably to reduce various types of cancer in human. Furthermore, in-vitro and in-vivo analyses of amygdalin could be of helpful to authenticate its pharmacological effects.

Steviol, the active principle of the stevia sweetener, causes a reduction of the cells of the immunological system even consumed in low concentrations

AIM

Steviol is a natural diterpenoid glycoside isolated from Stevia rebaudiana Bertoni leaves and widely used as a non-caloric sweetener. In addition to their sweet taste, Steviol glycosides may also have some therapeutic benefits. There are few reports on the cytotoxicity of Steviol in human cells. Our objective was to test this sweetener under and at average concentrations of consumption, evaluating parameters of cytotoxicity, genotoxicity, and immunotoxicity.

METHODS

For this purpose, we made use of lymphocyte cultures and the analysis of their CD3⁺, CD4⁺, and CD8⁺ subpopulations. In a complementary way, the mechanism of action is proposed here by computational methods.

RESULTS AND CONCLUSION

Our results showed that Steviol reduces the number of lymphocytes due to falls of CD4⁺, CD8⁺, and CD4⁺CD8⁺ subpopulations. Besides, we observed an increase in the level of DNA damage and a gradual incidence of structural changes in the lymphocyte chromosomal sets. It was possible to propose that Steviol modulates gene expression, mainly interfering with the SESN1, NAP1L1, SOX4, and TREX1 genes. Although Steviol is used globally as a sweetener, its use should be cautious, as our study points out that Steviol has cytotoxic, genotoxic and mutagenic effects in the concentrations and conditions tested in the culture of human lymphocyte cells.

In-silico anti-inflammatory potential of guaiane dimers from Xylopia vielana targeting COX-2

Natural products of herbal origin are prodigious to display diverse pharmacological activities. In the present study, five guaiane-type sesquiterpene dimers, xylopidimers A - E (1-5), isolated from Xylopia vielana species were tested against COX-2 protein target (PDB: 1CX2), a potent target for anti-inflammatory agents. To better understand the pharmacological properties of all these compounds, in this work, a systemic in silico study was performed on xylopidimers A-E using molecular docking, ADMET analysis and MD simulations. During ADMET predictions the two compounds xylopidimer C, D displayed best results as compared to others. The compound xylopidimer C was further evaluated for its MD simulations and its molecular interactions with COX2 complex showed clear interactions with active gorge of the enzyme through hydrogen bonding as well as hydrophobic contacts. The xylopidimer C has shown the best binding potential with -10.57Kcal/mol energy with 17.92 nano molar of predicted inhibition constant better than Ibuprofen and Felbinac. These findings provide enough significant information for designing and developing novel targeted base anti-inflammatory drugs from guaiane dimers.

In silico toxicity evaluation of Salubrinal and its analogues

This paper reports on a comprehensive in silico toxicity assessment of Salubrinal and its analogues containing a cinnamic acid residue or quinoline ring using the online servers admetSAR, ADMETlab, ProTox, ADVERPred, Pred-hERG and Vienna LiverTox. Apart from rare exceptions, in all 55 studied structures, mild or practical absence of acute toxicity was predicted for rats (III or IV toxicity class). Cardiotoxic, hepatotoxic and immunotoxic effects were predicted for Salubrinal and its analogues. We constructed models of the main predicted anti-targets hERG, BSEP, MRP3, MRP4 and AhR using the principle of homologous modeling. Molecular docking studies were carried out with the obtained models. We carried out molecular docking for all targets using AutoDock Vina, implemented in the PyRx 0.8 software package. According to the results of molecular docking, the compounds analyzed are potential moderate or weak hERG blockers. Induction of cholestasis and, as a consequence, liver damage by these drugs, directly related to inhibition of BSEP, MRP3 and MRP4, most likely will not be observed. Interaction with AhR for the studied compounds is impossible for steric reasons and, as a consequence, toxic effects on the immune and other organ systems associated with the activation of the AhR signaling pathway are excluded.

In-silico elucidation of Moringa oleifera phytochemicals against diabetes mellitus

Moringa oleifera is also known as "Miracle tree", due to its multiple uses and adaptability. Because of nutritive and pharmacological values, it is widely cultivated across the world. M. oleifera leaves are rich source of minerals, vitamins and many health beneficial secondary metabolites, and possess significant anti-diabetic potential. Consequently, Insilco study could be noteworthy to expand effective anti-diabetic drugs from this plant. Present study was designed to find out the best bioactive compounds of M. oleifera as a potential therapeutic agent against diabetes mellitus through In-silico method. For this, structures of phytochemicals were extracted from PubChem and docked to mutated protein from PBD. Afterwards, datasets were prepared for ligand based pharmacophore and their pharmacophoric features were generated from LigandScout. Finally five phytochemicals viz. anthraquinone, 2-phenylchromenylium (Anthocyanins), hemlock tannin, sitogluside (glycoside) and A-phenolic steroid were selected, which exhibited effective binding within the active binding pocket of the targeted protein. Ligand based pharmacophore model showed the key features i.e. HBD, HBA, aromatic ring, hydrophobic, positively ionizable surface essential for receptor binding. Our findings suggest that screened phytochemicals present in M. oleifera can be used as potential therapeutic drug candidates to treat diabetes mellitus.

Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach

The cyclooxygenase-2 receptor is a therapeutic target for planning potential drugs with anti-inflammatory activity. The selective cyclooxygenase-2 (COX-2) inhibitor rofecoxib was selected as a pivot molecule to perform virtual ligand-based screening from six commercial databases. We performed the search for similarly shaped Rapid Overlay of Chemical Structures (ROCS) and electrostatic (EON) compounds. After, we used pharmacokinetic and toxicological parameters to determine the best potential compounds, obtained through the softwares QikProp and Derek, respectively. Then, the compounds proceeded to the molecular anchorage study, which showed promising results of binding affinity with the hCOX-2 receptor: LMQC72 (∆G = -11.0 kcal/mol), LMQC36 (∆G = -10.6 kcal/mol), and LMQC50 (∆G = -10.2 kcal/mol). LMQC72 and LMQC36 showed higher binding affinity compared to rofecoxib (∆G = -10.4 kcal/mol). Finally, molecular dynamics (MD) simulations were used to evaluate the interaction of the compounds with the target hCOX-2 during 150 ns. In all MD simulation trajectories, the ligands remained interacting with the protein until the end of the simulation. The compounds were also complexing with hCOX-2 favorably. The compounds obtained the following affinity energy values: rofecoxib: ΔGbind = -45.31 kcal/mol; LMQC72: ΔGbind = -38.58 kcal/mol; LMQC36: ΔGbind = -36.10 kcal/mol; and LMQC50: ΔGbind = -39.40 kcal/mol. The selected LMQC72, LMQC50, and LMQC36 structures showed satisfactory pharmacokinetic results related to absorption and distribution. The toxicological predictions of these compounds did not display alerts for possible toxic groups and lower risk of cardiotoxicity compared to rofecoxib. Therefore, future in vitro and in vivo studies are needed to confirm the anti-inflammatory potential of the compounds selected here with bioinformatics approaches based on rofecoxib ligand.

Toward a Computational Ecotoxicity Assay

Thousands of anthropogenic chemicals are released into the environment each year, posing potential hazards to human and environmental health. Toxic chemicals may cause a variety of adverse health effects, triggering immediate symptoms or delayed effects over longer periods of time. It is thus crucial to develop methods that can rapidly screen and predict the toxicity of chemicals to limit the potential harmful impacts of chemical pollutants. Computational methods are being increasingly used in toxicity predictions. Here, the method of molecular docking is assessed for screening potential toxicity of a variety of xenobiotic compounds, including pesticides, pharmaceuticals, pollutants, and toxins derived from the chemical industry. The method predicts the binding energy of pollutants to a set of carefully selected receptors under the assumption that toxicity in many cases is related to interference with biochemical pathways. The strength of the applied method lies in its rapid generation of interaction maps between potential toxins and the targeted enzymes, which could quickly yield molecular-level information and insight into potential perturbation pathways, aiding in the prioritization of chemicals for further tests. Two scoring functions are compared: Autodock Vina and the machine-learning scoring function RF-Score-VS. The results are promising, although hampered by the accuracy of the scoring functions. The strengths and weaknesses of the docking protocol are discussed, as well as future directions for improving the accuracy for the purpose of toxicity predictions.

Analysis of plant-derived phytochemicals as anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2

Cancer is caused by a variety of pathways, involving numerous types of enzymes. Among them three enzymes i.e. Cyclin-dependent kinase-2 (CDK-2), Human topoisomerase IIα, and Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) are three of the most common enzymes that are involved in the cancer development. Although many chemical drugs are already available in the market for cancer treatment, plant sources are known to contain a wide variety of agents that are proved to possess potential anticancer activity. In this experiment, total thirty phytochemicals were analyzed against the mentioned three enzymes using different tools of bioinformatics and in silico biology like molecular docking study, drug likeness property experiment, ADME/T test, PASS prediction, and P450 site of metabolism prediction as well as DFT calculation to determine the three best ligands among them that have the capability to inhibit the mentioned enzymes. From the experiment, Epigallocatechin gallate was found to be the best ligand to inhibit CDK-2, Daidzein showed the best inhibitory activities towards the Human topoisomerase IIα, and Quercetin was predicted to be the best agent against VEGFR-2. They were also predicted to be quite safe and effective agents to treat cancer. However, more in vivo and in vitro analyses are required to finally confirm their safety and efficacy in this regard.

Silica bonded N-(propylcarbamoyl)sulfamic acid (SBPCSA) as a highly efficient and recyclable solid catalyst for the synthesis of Benzylidene Acrylate derivatives: Docking and reverse docking integrated approach of network pharmacology

A green approach has been developed for the synthesis of a series of benzylidene acrylate 3(a-p) from differently substituted aromatic/heterocyclic aldehydes and ethyl cyanoacetate in excellent yields (90-98%), and employing silica bonded N-(Propylcarbamoyl)sulfamic acid as a recyclable catalyst under solvent-free condition. The molecular structure of compounds 3b, 3d and 3i were well supported by single-crystal X-ray crystallographic analysis. The present protocol bears wide substrate tolerance and is believed to be more practical, efficient, eco-friendly, and compatible as compared to existing methods. In-silico approaches were implemented to find the biochemical and physiological effects, toxicity, and biological profiles of the synthesized compounds to determine the expected biological nature and confirm a drug-like compound. A molecular docking study of the expected biologically active compound was performed to know the hypothetically binding mode with the receptor. Also, reverse docking is applied to recognize receptors from unknown protein targets for drug-like compounds to explain poly-pharmacology and binding postures with different receptors.

Momordica charantia and breast cancer: An in silico approach

Momordica charantia, known as “São Caetano Melon”, is a medicinal plant popularly used for its antitumor, anticarcinogenic, hypoglycemic, and other properties. Studies in mice have demonstrated its activity in vivo against breast, prostate, and ovarian cancers. In vitro studies have also indicated potential efficacy against cervical solid tumors, and breast cancer. In these studies, we sought to evaluate these putative activities. Our methods included use of in silico tools to assess predicted biological activities, pharmacodynamics, and toxicity. We also performed docking and pharmacophore modeling studies. We found phenolic compounds, flavonoids, alkaloids, and triterpenes. Four flavonoids possess predicted anticarcinogenic activity, and affinity for estrogen receptors. Quercetin was selected for the study because it is the most prevalent representative of its class.

High-throughput virtual screening approach involving pharmacophore mapping, ADME filtering, molecular docking and MM-GBSA to identify new dual target inhibitors of PfDHODH and PfCytbc1 complex to combat drug resistant malaria

Emerging cases of drug resistance against Artemisinin combination therapies which are the current and the last line of defense against malaria makes the situation very alarming. Due to the liability of single-target drugs to be more prone to drug resistance, the trend of development of dual or multi-target inhibitors is emerging. Recently, a malaria box molecule, MMV007571 which is a well known new permeability pathways inhibitor was investigated to be also multi-targeting Plasmodium falciparum dihydroorotate dehydrogenase and cytochrome bc1 complex. The aspiration behind this study was to use the information of its pharmacophoric features essential for binding as two of its new targets. In this regard, high throughput virtual screening involving pharmacophore mapping, ADME filtering, molecular docking, and MM-GBSA calculations were carried out. This approach has lead to the identification of two new hits namely DT00V1902 and DT00V1922 which binds with -37.85 and -24.65 kcal/mol of more stable ΔG Bind energy at two targets than the lead molecule, MMV007571. The screened compounds are indicated to be carry improvement in binding potential and pharmacokinetic characters as per in silico studies. The authors propose that DT00V1902 and DT00V1922 can be forwarded for experimental validation and clinical studies for antimalarial chemotherapy. Communicated by Ramaswamy H. Sarma.

Norditerpenoids with Selective Anti-Cholinesterase Activity from the Roots of Perovskia atriplicifolia Benth

Inhibition of cholinesterases remains one of a few available treatment strategies for neurodegenerative dementias such as Alzheimer’s disease and related conditions. The current study was inspired by previous data on anticholinesterase properties of diterpenoids from Perovskia atriplicifolia and other Lamiaceae species. The acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition by the three new natural compounds—(1R,15R)-1-acetoxycryptotanshinone (1), (1R)-1-acetoxytanshinone IIA (2), and (15R)-1-oxoaegyptinone A (3)—as well as, new for this genus, isograndifoliol (4) were assessed. Three of these compounds exhibited profound inhibition of butyrylcholinesterase (BChE) and much weaker inhibition of acetylcholinesterase (AChE). All compounds (1–4) selectively inhibited BChE (IC₅₀ = 2.4, 7.9, 50.8, and 0.9 µM, respectively), whereas only compounds 3 and 4 moderately inhibited AChE (IC₅₀ 329.8 µM and 342.9 µM). Molecular docking and in silico toxicology prediction studies were also performed on the active compounds. Natural oxygenated norditerpenoids from the traditional Central Asian medicinal plant P. atriplicifolia are selective BChE inhibitors. Their high potential makes them useful candidate molecules for further investigation as lead compounds in the development of a natural drug against dementia caused by neurodegenerative diseases.

Molecular docking, simulation and MM-PBSA studies of nigella sativa compounds: a computational quest to identify potential natural antiviral for COVID-19 treatment

Nigella sativa or black seed is used as a medicinal plant around the globe. Oil and seeds have a long tradition of folklore use in various medicinal and food systems. The conventional therapeutic use of Nigella sativa, in different ways, has been reported in several studies to treat different diseases including influenza, headache, hypertension, diabetes, inflammation, eczema, fever, cough, asthma, bronchitis, and fever. Based on previously reported potential therapeutic uses of N. sativa compounds, and keeping in mind the dire need of time for the development of potent antiviral, a combined docking, ADMET properties calculation, molecular dynamics, and MM-PBSA approaches were applied in the current study to check the therapeutic potentials of N. sativa chief constituents against COVID-19. Among the studied compounds, we found that dithymoquinone (DTQ), with binding affinity of −8.6 kcal/mol compared to a positive control (chloroquine, −7.2 kcal/mol) , has the high potential of binding at SARS-CoV-2:ACE2 interface and thus could be predicted as a plausible inhibitor to disrupt viral-host interactions. Molecular dynamics simulation of 100 ns well complemented binding affinity of the compound and revealed strong stability of DTQ at the docked site. Additionally, MM-PBSA also affirms the docking results. Compound DTQ of the present study, if validated in wet lab experiments, could be used to treat COVID-19 and could serve as a lead in the future for development of more effective natural antivirals against COVID-19.

Communicated by Ramaswamy H. Sarma

Screening and druggability analysis of some plant metabolites against SARS-CoV-2: An integrative computational approach

The sudden outbreak of novel coronavirus has caused a global concern due to its infection rate and mortality. Despite extensive research, there are still no specific drugs or vaccines to combat SARS-CoV-2 infection. Hence, this study was designed to evaluate some plant-based active compounds for drug candidacy against SARS-CoV-2 by using virtual screening methods and various computational analyses. A total of 27 plant metabolites were screened against SARS-CoV-2 main protease proteins (MPP), Nsp9 RNA binding protein, spike receptor binding domain, spike ecto-domain and HR2 domain using a molecular docking approach. Four metabolites, i.e., asiatic acid, avicularin, guajaverin, and withaferin showed maximum binding affinity with all key proteins in terms of lowest global binding energy. The crucial binding sites and drug surface hotspots were unravelled for each viral protein. The top candidates were further employed for ADME (absorption, distribution, metabolism, and excretion) analysis to investigate their drug profiles. Results suggest that none of the compounds render any undesirable consequences that could reduce their drug likeness properties. The analysis of toxicity pattern revealed no significant tumorigenic, mutagenic, irritating, or reproductive effects by the compounds. However, withaferin was comparatively toxic among the top four candidates with considerable cytotoxicity and immunotoxicity. Most of the target class by top drug candidates belonged to enzyme groups (e.g. oxidoreductases hydrolases, phosphatases). Moreover, results of drug similarity prediction revealed two approved structural analogs of Asiatic acid i.e. Hydrocortisone (DB00741) (previously used for SARS-CoV-1 and MERS) and Dinoprost-tromethamine (DB01160) from DrugBank. In addition, two other biologically active compounds, Mupirocin (DB00410) and Simvastatin (DB00641) could be an option for the treatment of viral infections. The study may pave the way to develop effective medications and preventive measure against SARS-CoV-2. Due to the encouraging results, we highly recommend further in vivo trials for the experimental validation of our findings.

A Library of Thiazolidin-4-one Derivatives as Protein Tyrosine Phosphatase 1B (PTP1B) Inhibitors: An Attempt To Discover Novel Antidiabetic Agents

Protein tyrosine phosphatase 1B (PTP1B) is an important target for the treatment of diabetes. A series of thiazolidin-4-one derivatives 8-22 was designed, synthesized and investigated as PTP1B inhibitors. The new molecules inhibited PTP1B with IC₅₀ values in the micromolar range. 5-(Furan-2-ylmethylene)-2-(4-nitrophenylimino)thiazolidin-4-one (17) exhibited potency with a competitive type of enzyme inhibition. structure-activity relationship studies revealed various structural facets important for the potency of these analogues. The findings revealed a requirement for a nitro group-including hydrophobic heteroaryl ring for PTP1B inhibition. Molecular docking studies afforded good correlation with experimental results. H-bonding and π-π interactions were responsible for optimal binding and effective stabilization of virtual protein-ligand complexes. Furthermore, in-silico pharmacokinetic properties of test compounds predicted their drug-like characteristics for potential oral use as antidiabetic agents.Additionally, a binding site model demonstrating crucial pharmacophoric characteristics influencing potency and binding affinity of inhibitors has been proposed, which can be employed in the design of future potential PTP1B inhibitors.

Computational investigations on the dynamic binding effect of molecular tweezer CLR01 toward intrinsically disordered HIV-1 Nef

Intrinsically disordered proteins (IDPs) are highly flexible molecules that undergo disorder to order transition through their interaction with other molecules. IDPs play a vital role in several biological processes ranging from molecular recognition to several human diseases through the protein-protein interaction. The dynamic flexibility of IDPs and their implications in several human diseases enable these molecules to serve as novel therapeutic targets. However, the challenging task is to develop novel drugs against IDPs because of their lack of stable structures and the nature of high conformational flexibility. In this study, we have calculated the dynamic binding effect of the supramolecular tweezer CLR01 against the intrinsically disordered HIV-1 Nef by employing molecular docking and dynamics simulation approaches. From docking results, we predicted the strong binding affinity of the tweezer with the target residues of Nef. The docking results were further validated from the molecular dynamics simulation studies confirming the conformational stability of Nef upon tweezer binding. These findings provide useful insights into the development of potent inhibitors for targeting Nef protein functions.

Vanillin and vanillic acid modulate antioxidant defense system via amelioration of metabolic complications linked to Fe2+-induced brain tissues damage

The therapeutic effect of phenolics on neurodegenerative diseases has been attributed to their potent antioxidant properties. In the present study, the neuroprotective activities of vanillin and vanillic acid were investigated in Fe²⁺- induced oxidative toxicity in brain tissues by investigating their therapeutic effects on oxidative imbalance, cholinergic and nucleotide-hydrolyzing enzymes activities, dysregulated metabolic pathways. Their cytotoxicity was investigated in hippocampal neuronal cell lines (HT22). The reduced glutathione level, SOD and catalase activities were ameliorated in tissues treated with the phenolics, with concomitant depletion of malondialdehyde and nitric oxide levels. They inhibited acetylcholinesterase and butyrylcholinesterase activities, while concomitantly elevated ATPase activity. Treatment with vanillin led to restoration of oxidative-depleted metabolites and reactivation of the pentose phosphate and purine metabolism pathways, with concomitant activation of pathways for histidine and selenoamino metabolisms. While vanillic acid restored and reactivated oxidative-depleted metabolites and pathways but did not activate any additional pathway. Both phenolics portrayed good binding affinity for catalase, with vanillic acid having the higher binding energy of -7.0 kcal/mol. Both phenolics were not cytotoxic on HT22 cells, and their toxicity class were predicted to be 4. Only vanillin was predicted to be permeable across the blood brain barrier (BBB). These results insinuate that vanillin and vanillic acid confer a neuroprotective effect on oxidative brain damage, when vanillin being the most potent.